Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-05-18 r88218) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "349", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2025-05-21/deps.csv", task.str = "1274", release = "/scratch/th798/data.table-revdeps/2025-05-21/data.table_release_1.17.2.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-05-21/data.table_master_1.17.99.6f05e4aedd8dc298214f4a296e308bc2a35a2827.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/17408827/R-devel/1274" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/17408827/R-devel/1274/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "scCustomize" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/17408827/R-devel/1274/library" [2] "/projects/genomic-ml/R/R-devel/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-05-21 03:24:31 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/17408827/R-devel/1274/library' (as 'lib' is unspecified) Warning: dependency 'dittoSeq' is not available also installing the dependencies 'easy.utils', 'sccore', 'hdf5r.Extra', 'leidenAlg', 'RcppPlanc', 'hdf5r', 'rliger' trying URL 'http://cloud.r-project.org/src/contrib/easy.utils_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/sccore_1.0.6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/hdf5r.Extra_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leidenAlg_1.1.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/RcppPlanc_2.0.10.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/hdf5r_1.3.12.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rliger_2.2.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/scCustomize_3.0.1.tar.gz' * installing *source* package 'easy.utils' ... ** this is package 'easy.utils' version '0.1.0' ** package 'easy.utils' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (easy.utils) * installing *source* package 'sccore' ... ** this is package 'sccore' version '1.0.6' ** package 'sccore' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:205, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Dense:1, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigenForward.h:28, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:5: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:174: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:165: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:271: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/SparseCore:37, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Sparse:26, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigenForward.h:29: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase >': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c graph_embedding.cpp -o graph_embedding.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c matrix_utils.cpp -o matrix_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c propagate_labels.cpp -o propagate_labels.o In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:205, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Dense:1, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigenForward.h:28, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigen.h:25, from propagate_labels.cpp:6: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:174: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:165: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:271: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/SparseCore:37, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Sparse:26, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigenForward.h:29: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase >': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' propagate_labels.cpp:87:7: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' propagate_labels.cpp:87:7: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from 'class Eigen::CwiseNullaryOp, Eigen::Matrix >' propagate_labels.cpp:87:30: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 1, -1, false>, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1, -1, false>, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 1, -1, false>, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, 1, -1, false> >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, 1, -1, false> >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MapBase.h:37:34: required from 'class Eigen::MapBase, 1, -1, false>, 0>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MapBase.h:223:34: required from 'class Eigen::MapBase, 1, -1, false>, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Block.h:329:7: required from 'class Eigen::internal::BlockImpl_dense, 1, -1, false, true>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Block.h:154:7: required from 'class Eigen::BlockImpl, 1, -1, false, Eigen::Dense>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Block.h:103:81: required from 'class Eigen::Block, 1, -1, false>' propagate_labels.cpp:153:19: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from 'class Eigen::CwiseNullaryOp, const Eigen::Matrix >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:38:28: required from 'struct Eigen::internal::traits, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, Eigen::Dense>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, Eigen::Dense>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Matrix, const Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Matrix, const Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Matrix, const Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Matrix, const Eigen::Matrix, Eigen::Dense>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::Matrix >' propagate_labels.cpp:178:26: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Matrix, const Eigen::Matrix > >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Matrix, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/ArrayBase.h:39:34: required from 'class Eigen::ArrayBase, const Eigen::Matrix, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/ArrayWrapper.h:42:7: required from 'class Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >' propagate_labels.cpp:178:45: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/ArrayBase.h:39:34: required from 'class Eigen::ArrayBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:94:7: required from 'class Eigen::CwiseUnaryOpImpl, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >, Eigen::Dense>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:7: required from 'class Eigen::CwiseUnaryOp, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > >' propagate_labels.cpp:178:51: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/ArrayWrapper.h:140:7: required from 'class Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >' propagate_labels.cpp:178:60: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from 'class Eigen::CwiseNullaryOp, Eigen::Matrix >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/SelfCwiseBinaryOp.h:41:67: required from 'Derived& Eigen::DenseBase::operator/=(const Scalar&) [with Derived = Eigen::Block, 1, -1, false>; Scalar = double]' propagate_labels.cpp:173:52: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:94:7: required from 'class Eigen::CwiseUnaryOpImpl, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >, Eigen::Dense>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:7: required from 'class Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Dot.h:244:22: required from 'static Eigen::internal::lpNorm_selector::RealScalar Eigen::internal::lpNorm_selector::run(const Eigen::MatrixBase&) [with Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; RealScalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Dot.h:269:52: required from 'typename Eigen::NumTraits::Scalar>::Real Eigen::MatrixBase::lpNorm() const [with int p = -1; Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; typename Eigen::NumTraits::Scalar>::Real = double; typename Eigen::internal::traits::Scalar = double]' propagate_labels.cpp:178:86: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:277: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator, 1, -1, false> >': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:100:8: required from 'struct Eigen::internal::evaluator, 1, -1, false> >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:739:41: required from 'struct Eigen::internal::binary_evaluator, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:722:8: required from 'struct Eigen::internal::evaluator, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:774:20: required from 'void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block, 1, -1, false>; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Functor = add_assign_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:31: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block, 1, -1, false>; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Functor = Eigen::internal::add_assign_op; Weak = void]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Block, 1, -1, false>; Src = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Func = add_assign_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:27: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen::Block, 1, -1, false>; Src = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen::DenseShape]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:177:18: required from 'Derived& Eigen::MatrixBase::operator+=(const Eigen::MatrixBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Derived = Eigen::Block, 1, -1, false>]' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1071:54: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 1071 | PacketAlignment = unpacket_traits::alignment, | ^~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'Eigen::Index Eigen::internal::first_default_aligned(const Eigen::DenseBase&) [with Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; Eigen::Index = long int]': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Redux.h:243:63: required from 'static Eigen::internal::redux_impl::Scalar Eigen::internal::redux_impl::run(const Evaluator&, const Func&, const XprType&) [with XprType = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; Func = Eigen::internal::scalar_max_op; Evaluator = Eigen::internal::redux_evaluator, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > > >; Scalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Redux.h:418:56: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_max_op; Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; typename Eigen::internal::traits::Scalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Redux.h:448:25: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::maxCoeff() const [with int NaNPropagation = 0; Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; typename Eigen::internal::traits::Scalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:466:37: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::maxCoeff() const [with Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; typename Eigen::internal::traits::Scalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Dot.h:244:33: required from 'static Eigen::internal::lpNorm_selector::RealScalar Eigen::internal::lpNorm_selector::run(const Eigen::MatrixBase&) [with Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; RealScalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Dot.h:269:52: required from 'typename Eigen::NumTraits::Scalar>::Real Eigen::MatrixBase::lpNorm() const [with int p = -1; Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; typename Eigen::NumTraits::Scalar>::Real = double; typename Eigen::internal::traits::Scalar = double]' propagate_labels.cpp:178:86: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o sccore.so RcppExports.o graph_embedding.o matrix_utils.o propagate_labels.o -lpthread -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-sccore/00new/sccore/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for 'embeddingPlot' with signature '"Seurat"': no definition for class "Seurat" Note: wrong number of arguments to '*' ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sccore) * installing *source* package 'hdf5r' ... ** this is package 'hdf5r' version '1.3.12' ** package 'hdf5r' successfully unpacked and MD5 sums checked ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking for gawk... gawk checking for grep that handles long lines and -e... /usr/bin/grep checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for h5cc... /home/th798/.conda/envs/emacs1/bin/h5cc checking for HDF5 libraries... yes (version 1.10.2) checking for hdf5.h... yes checking for H5Fcreate in -lhdf5... yes checking for hdf5_hl.h... yes checking for H5LTpath_valid in -lhdf5_hl... yes checking for main in -lhdf5_hl... yes checking for matching HDF5 Fortran wrapper... /home/th798/.conda/envs/emacs1/bin/h5fc Found hdf5 with version: 1.10.2 checking for ggrep... /usr/bin/grep checking whether /usr/bin/grep accepts -o... yes checking for ggrep... (cached) /usr/bin/grep checking whether /usr/bin/grep accepts -o... yes Using variables: HDF5_LIBS= -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -lrt -lpthread -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm HDF5_CFLAGS= HDF5_CPPFLAGS=-I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' cp 1_10_2/*.c 1_10_2/*.h . /usr/bin/cp 1_10_2/Wrapper_auto_H5.c 1_10_2/Wrapper_auto_H5A.c 1_10_2/Wrapper_auto_H5D.c 1_10_2/Wrapper_auto_H5DS.c 1_10_2/Wrapper_auto_H5E.c 1_10_2/Wrapper_auto_H5F.c 1_10_2/Wrapper_auto_H5FDcore.c 1_10_2/Wrapper_auto_H5FDfamily.c 1_10_2/Wrapper_auto_H5FDlog.c 1_10_2/Wrapper_auto_H5FDsec2.c 1_10_2/Wrapper_auto_H5FDstdio.c 1_10_2/Wrapper_auto_H5G.c 1_10_2/Wrapper_auto_H5I.c 1_10_2/Wrapper_auto_H5IM.c 1_10_2/Wrapper_auto_H5L.c 1_10_2/Wrapper_auto_H5LT.c 1_10_2/Wrapper_auto_H5O.c 1_10_2/Wrapper_auto_H5P.c 1_10_2/Wrapper_auto_H5R.c 1_10_2/Wrapper_auto_H5S.c 1_10_2/Wrapper_auto_H5T.c 1_10_2/Wrapper_auto_H5TB.c 1_10_2/Wrapper_auto_H5Z.c 1_10_2/const_export.c 1_10_2/datatype_export.c 1_10_2/HelperStructs.h 1_10_2/Wrapper_auto_H5.h 1_10_2/Wrapper_auto_H5A.h 1_10_2/Wrapper_auto_H5D.h 1_10_2/Wrapper_auto_H5DS.h 1_10_2/Wrapper_auto_H5E.h 1_10_2/Wrapper_auto_H5F.h 1_10_2/Wrapper_auto_H5FDcore.h 1_10_2/Wrapper_auto_H5FDfamily.h 1_10_2/Wrapper_auto_H5FDlog.h 1_10_2/Wrapper_auto_H5FDsec2.h 1_10_2/Wrapper_auto_H5FDstdio.h 1_10_2/Wrapper_auto_H5G.h 1_10_2/Wrapper_auto_H5I.h 1_10_2/Wrapper_auto_H5IM.h 1_10_2/Wrapper_auto_H5L.h 1_10_2/Wrapper_auto_H5LT.h 1_10_2/Wrapper_auto_H5O.h 1_10_2/Wrapper_auto_H5P.h 1_10_2/Wrapper_auto_H5R.h 1_10_2/Wrapper_auto_H5S.h 1_10_2/Wrapper_auto_H5T.h 1_10_2/Wrapper_auto_H5TB.h 1_10_2/Wrapper_auto_H5Z.h 1_10_2/const_export.h 1_10_2/datatype_export.h 1_10_2/export_auto.h . if [ "" != "" ]; then patch -p2 < patch_; fi /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c const_export.c -o const_export.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c datatype_export.c -o datatype_export.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c convert.c -o convert.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hdf5r_init.c -o hdf5r_init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c H5Error.c -o H5Error.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c H5ls.c -o H5ls.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -D__USE_MINGW_ANSI_STDIO -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o hdf5r.so const_export.o datatype_export.o Wrapper_auto_H5A.o Wrapper_auto_H5.o Wrapper_auto_H5D.o Wrapper_auto_H5DS.o Wrapper_auto_H5E.o Wrapper_auto_H5F.o Wrapper_auto_H5G.o Wrapper_auto_H5I.o Wrapper_auto_H5IM.o Wrapper_auto_H5L.o Wrapper_auto_H5LT.o Wrapper_auto_H5O.o Wrapper_auto_H5P.o Wrapper_auto_H5R.o Wrapper_auto_H5S.o Wrapper_auto_H5TB.o Wrapper_auto_H5T.o Wrapper_auto_H5Z.o Wrapper_auto_H5FDcore.o Wrapper_auto_H5FDfamily.o Wrapper_auto_H5FDlog.o Wrapper_auto_H5FDsec2.o Wrapper_auto_H5FDstdio.o convert.o hdf5r_init.o H5Error.o H5ls.o Wrapper_manual_H5T.o -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -lrt -lpthread -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-hdf5r/00new/hdf5r/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hdf5r) * installing *source* package 'scCustomize' ... ** this is package 'scCustomize' version '3.0.1' ** package 'scCustomize' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scCustomize) * installing *source* package 'hdf5r.Extra' ... ** this is package 'hdf5r.Extra' version '0.1.0' ** package 'hdf5r.Extra' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hdf5r.Extra) * installing *source* package 'leidenAlg' ... ** this is package 'leidenAlg' version '1.1.5' ** package 'leidenAlg' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -I"./rigraph/include" -I"./leidenalg/include" -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:205, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Dense:1, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigenForward.h:28, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:5: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:174: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:165: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Core:271: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/SparseCore:37, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/Sparse:26, from /projects/genomic-ml/R/R-devel/library/RcppEigen/include/RcppEigenForward.h:29: /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase >': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -I"./rigraph/include" -I"./leidenalg/include" -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c leiden.cpp -o leiden.o make[1]: Entering directory '/tmp/th798/17408827/RtmpyWMGVL/R.INSTALLf184bb797866/leidenAlg/src/rigraph' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/betweenness.c -o core/centrality/betweenness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/centrality_other.c -o core/centrality/centrality_other.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/centralization.c -o core/centrality/centralization.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/closeness.c -o core/centrality/closeness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/coreness.c -o core/centrality/coreness.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_base_graph.cpp -o core/centrality/prpack/prpack_base_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_igraph_graph.cpp -o core/centrality/prpack/prpack_igraph_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o core/centrality/prpack/prpack_preprocessed_ge_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o core/centrality/prpack/prpack_preprocessed_gs_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o core/centrality/prpack/prpack_preprocessed_scc_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o core/centrality/prpack/prpack_preprocessed_schur_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_result.cpp -o core/centrality/prpack/prpack_result.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_solver.cpp -o core/centrality/prpack/prpack_solver.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_utils.cpp -o core/centrality/prpack/prpack_utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer/cliquer.c -o core/cliques/cliquer/cliquer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer/cliquer_graph.c -o core/cliques/cliquer/cliquer_graph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer/reorder.c -o core/cliques/cliquer/reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer_wrapper.c -o core/cliques/cliquer_wrapper.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliques.c -o core/cliques/cliques.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/glet.c -o core/cliques/glet.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/maximal_cliques.c -o core/cliques/maximal_cliques.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/community_misc.c -o core/community/community_misc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/edge_betweenness.c -o core/community/edge_betweenness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/fast_modularity.c -o core/community/fast_modularity.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/fluid.c -o core/community/fluid.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap.cc -o core/community/infomap/infomap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap_FlowGraph.cc -o core/community/infomap/infomap_FlowGraph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap_Greedy.cc -o core/community/infomap/infomap_Greedy.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap_Node.cc -o core/community/infomap/infomap_Node.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/label_propagation.c -o core/community/label_propagation.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/leading_eigenvector.c -o core/community/leading_eigenvector.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/leiden.c -o core/community/leiden.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/louvain.c -o core/community/louvain.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/modularity.c -o core/community/modularity.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/optimal_modularity.c -o core/community/optimal_modularity.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/NetDataTypes.cpp -o core/community/spinglass/NetDataTypes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/NetRoutines.cpp -o core/community/spinglass/NetRoutines.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/clustertool.cpp -o core/community/spinglass/clustertool.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/pottsmodel_2.cpp -o core/community/spinglass/pottsmodel_2.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap.cpp -o core/community/walktrap/walktrap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap_communities.cpp -o core/community/walktrap/walktrap_communities.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap_graph.cpp -o core/community/walktrap/walktrap_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap_heap.cpp -o core/community/walktrap/walktrap_heap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/connectivity/cohesive_blocks.c -o core/connectivity/cohesive_blocks.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/connectivity/components.c -o core/connectivity/components.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/connectivity/separators.c -o core/connectivity/separators.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/adjacency.c -o core/constructors/adjacency.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/atlas.c -o core/constructors/atlas.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/basic_constructors.c -o core/constructors/basic_constructors.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/de_bruijn.c -o core/constructors/de_bruijn.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/famous.c -o core/constructors/famous.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/full.c -o core/constructors/full.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/kautz.c -o core/constructors/kautz.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/lcf.c -o core/constructors/lcf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/linegraph.c -o core/constructors/linegraph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/prufer.c -o core/constructors/prufer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/regular.c -o core/constructors/regular.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/array.c -o core/core/array.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/buckets.c -o core/core/buckets.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/cutheap.c -o core/core/cutheap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/dqueue.c -o core/core/dqueue.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/error.c -o core/core/error.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/estack.c -o core/core/estack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/fixed_vectorlist.c -o core/core/fixed_vectorlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/grid.c -o core/core/grid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/heap.c -o core/core/heap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/indheap.c -o core/core/indheap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/interruption.c -o core/core/interruption.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/marked_queue.c -o core/core/marked_queue.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/matrix.c -o core/core/matrix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/memory.c -o core/core/memory.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/printing.c -o core/core/printing.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/progress.c -o core/core/progress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/psumtree.c -o core/core/psumtree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/set.c -o core/core/set.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/sparsemat.c -o core/core/sparsemat.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/spmatrix.c -o core/core/spmatrix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/stack.c -o core/core/stack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/statusbar.c -o core/core/statusbar.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/strvector.c -o core/core/strvector.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/trie.c -o core/core/trie.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/vector.c -o core/core/vector.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/vector_ptr.c -o core/core/vector_ptr.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/flow/flow.c -o core/flow/flow.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/flow/st-cuts.c -o core/flow/st-cuts.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/barabasi.c -o core/games/barabasi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/callaway_traits.c -o core/games/callaway_traits.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/citations.c -o core/games/citations.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/correlated.c -o core/games/correlated.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/degree_sequence.c -o core/games/degree_sequence.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_box_list.cpp -o core/games/degree_sequence_vl/gengraph_box_list.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_degree_sequence.cpp -o core/games/degree_sequence_vl/gengraph_degree_sequence.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_graph_molloy_hash.cpp -o core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.cpp -o core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_mr-connected.cpp -o core/games/degree_sequence_vl/gengraph_mr-connected.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_powerlaw.cpp -o core/games/degree_sequence_vl/gengraph_powerlaw.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_random.cpp -o core/games/degree_sequence_vl/gengraph_random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/dotproduct.c -o core/games/dotproduct.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/erdos_renyi.c -o core/games/erdos_renyi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/establishment.c -o core/games/establishment.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/forestfire.c -o core/games/forestfire.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/grg.c -o core/games/grg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/growing_random.c -o core/games/growing_random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/islands.c -o core/games/islands.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/k_regular.c -o core/games/k_regular.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/preference.c -o core/games/preference.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/recent_degree.c -o core/games/recent_degree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/sbm.c -o core/games/sbm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/static_fitness.c -o core/games/static_fitness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/tree.c -o core/games/tree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/watts_strogatz.c -o core/games/watts_strogatz.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/adjlist.c -o core/graph/adjlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/attributes.c -o core/graph/attributes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/basic_query.c -o core/graph/basic_query.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/cattributes.c -o core/graph/cattributes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/iterators.c -o core/graph/iterators.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/type_indexededgelist.c -o core/graph/type_indexededgelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/visitors.c -o core/graph/visitors.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/hrg/hrg.cc -o core/hrg/hrg.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/hrg/hrg_types.cc -o core/hrg/hrg_types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/glpk_support.c -o core/internal/glpk_support.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/hacks.c -o core/internal/hacks.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/lsap.c -o core/internal/lsap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/qsort.c -o core/internal/qsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/qsort_r.c -o core/internal/qsort_r.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/zeroin.c -o core/internal/zeroin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dimacs.c -o core/io/dimacs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dl-lexer.c -o core/io/dl-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dl-parser.c -o core/io/dl-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dl.c -o core/io/dl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dot.c -o core/io/dot.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/edgelist.c -o core/io/edgelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml-lexer.c -o core/io/gml-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml-parser.c -o core/io/gml-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml-tree.c -o core/io/gml-tree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml.c -o core/io/gml.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/graphdb.c -o core/io/graphdb.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/graphml.c -o core/io/graphml.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/leda.c -o core/io/leda.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/lgl-lexer.c -o core/io/lgl-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/lgl-parser.c -o core/io/lgl-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/lgl.c -o core/io/lgl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/ncol-lexer.c -o core/io/ncol-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/ncol-parser.c -o core/io/ncol-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/ncol.c -o core/io/ncol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/pajek-lexer.c -o core/io/pajek-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/pajek-parser.c -o core/io/pajek-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/pajek.c -o core/io/pajek.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss.cc -o core/isomorphism/bliss.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/defs.cc -o core/isomorphism/bliss/defs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/graph.cc -o core/isomorphism/bliss/graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/heap.cc -o core/isomorphism/bliss/heap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/orbit.cc -o core/isomorphism/bliss/orbit.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/partition.cc -o core/isomorphism/bliss/partition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/uintseqhash.cc -o core/isomorphism/bliss/uintseqhash.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/utils.cc -o core/isomorphism/bliss/utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/isoclasses.c -o core/isomorphism/isoclasses.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/isomorphism_misc.c -o core/isomorphism/isomorphism_misc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/lad.c -o core/isomorphism/lad.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/queries.c -o core/isomorphism/queries.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/vf2.c -o core/isomorphism/vf2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/circular.c -o core/layout/circular.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/davidson_harel.c -o core/layout/davidson_harel.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/DensityGrid.cpp -o core/layout/drl/DensityGrid.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/DensityGrid_3d.cpp -o core/layout/drl/DensityGrid_3d.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_graph.cpp -o core/layout/drl/drl_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_graph_3d.cpp -o core/layout/drl/drl_graph_3d.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_layout.cpp -o core/layout/drl/drl_layout.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_layout_3d.cpp -o core/layout/drl/drl_layout_3d.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_parse.cpp -o core/layout/drl/drl_parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/fruchterman_reingold.c -o core/layout/fruchterman_reingold.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/gem.c -o core/layout/gem.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/graphopt.c -o core/layout/graphopt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/kamada_kawai.c -o core/layout/kamada_kawai.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/large_graph.c -o core/layout/large_graph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/layout_bipartite.c -o core/layout/layout_bipartite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/layout_grid.c -o core/layout/layout_grid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/layout_random.c -o core/layout/layout_random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/mds.c -o core/layout/mds.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/merge_dla.c -o core/layout/merge_dla.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/merge_grid.c -o core/layout/merge_grid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/reingold_tilford.c -o core/layout/reingold_tilford.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/sugiyama.c -o core/layout/sugiyama.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/arpack.c -o core/linalg/arpack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/blas.c -o core/linalg/blas.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/eigen.c -o core/linalg/eigen.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/lapack.c -o core/linalg/lapack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/math/bfgs.c -o core/math/bfgs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/math/complex.c -o core/math/complex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/math/utils.c -o core/math/utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/bipartite.c -o core/misc/bipartite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/chordality.c -o core/misc/chordality.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/cocitation.c -o core/misc/cocitation.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/coloring.c -o core/misc/coloring.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/conversion.c -o core/misc/conversion.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/misc/degree_sequence.cpp -o core/misc/degree_sequence.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/embedding.c -o core/misc/embedding.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/feedback_arc_set.c -o core/misc/feedback_arc_set.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/graphicality.c -o core/misc/graphicality.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/matching.c -o core/misc/matching.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/microscopic_update.c -o core/misc/microscopic_update.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/mixing.c -o core/misc/mixing.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/motifs.c -o core/misc/motifs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/other.c -o core/misc/other.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/scan.c -o core/misc/scan.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/sir.c -o core/misc/sir.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/spanning_trees.c -o core/misc/spanning_trees.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/add_edge.c -o core/operators/add_edge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/complementer.c -o core/operators/complementer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/compose.c -o core/operators/compose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/connect_neighborhood.c -o core/operators/connect_neighborhood.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/contract.c -o core/operators/contract.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/difference.c -o core/operators/difference.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/disjoint_union.c -o core/operators/disjoint_union.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/intersection.c -o core/operators/intersection.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/misc_internal.c -o core/operators/misc_internal.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/permute.c -o core/operators/permute.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/rewire.c -o core/operators/rewire.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/rewire_edges.c -o core/operators/rewire_edges.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/simplify.c -o core/operators/simplify.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/subgraph.c -o core/operators/subgraph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/union.c -o core/operators/union.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/all_shortest_paths.c -o core/paths/all_shortest_paths.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/bellman_ford.c -o core/paths/bellman_ford.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/dijkstra.c -o core/paths/dijkstra.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/distances.c -o core/paths/distances.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/eulerian.c -o core/paths/eulerian.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/histogram.c -o core/paths/histogram.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/johnson.c -o core/paths/johnson.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/random_walk.c -o core/paths/random_walk.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/shortest_paths.c -o core/paths/shortest_paths.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/simple_paths.c -o core/paths/simple_paths.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/unweighted.c -o core/paths/unweighted.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/basic_properties.c -o core/properties/basic_properties.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/constraint.c -o core/properties/constraint.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/convergence_degree.c -o core/properties/convergence_degree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/dag.c -o core/properties/dag.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/degrees.c -o core/properties/degrees.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/girth.c -o core/properties/girth.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/loops.c -o core/properties/loops.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/multiplicity.c -o core/properties/multiplicity.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/neighborhood.c -o core/properties/neighborhood.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/spectral.c -o core/properties/spectral.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/trees.c -o core/properties/trees.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/triangles.c -o core/properties/triangles.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/random/random.c -o core/random/random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg.c -o core/scg/scg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_approximate_methods.c -o core/scg/scg_approximate_methods.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_exact_scg.c -o core/scg/scg_exact_scg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_kmeans.c -o core/scg/scg_kmeans.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_optimal_method.c -o core/scg/scg_optimal_method.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_utils.c -o core/scg/scg_utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/version.c -o core/version.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_add.c -o vendor/cs/cs_add.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_amd.c -o vendor/cs/cs_amd.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_chol.c -o vendor/cs/cs_chol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_cholsol.c -o vendor/cs/cs_cholsol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_compress.c -o vendor/cs/cs_compress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_counts.c -o vendor/cs/cs_counts.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_cumsum.c -o vendor/cs/cs_cumsum.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dfs.c -o vendor/cs/cs_dfs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dmperm.c -o vendor/cs/cs_dmperm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_droptol.c -o vendor/cs/cs_droptol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dropzeros.c -o vendor/cs/cs_dropzeros.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dupl.c -o vendor/cs/cs_dupl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_entry.c -o vendor/cs/cs_entry.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_ereach.c -o vendor/cs/cs_ereach.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_etree.c -o vendor/cs/cs_etree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_fkeep.c -o vendor/cs/cs_fkeep.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_gaxpy.c -o vendor/cs/cs_gaxpy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_happly.c -o vendor/cs/cs_happly.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_house.c -o vendor/cs/cs_house.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_ipvec.c -o vendor/cs/cs_ipvec.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_leaf.c -o vendor/cs/cs_leaf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_load.c -o vendor/cs/cs_load.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_lsolve.c -o vendor/cs/cs_lsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_ltsolve.c -o vendor/cs/cs_ltsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_lu.c -o vendor/cs/cs_lu.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_lusol.c -o vendor/cs/cs_lusol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_malloc.c -o vendor/cs/cs_malloc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_maxtrans.c -o vendor/cs/cs_maxtrans.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_multiply.c -o vendor/cs/cs_multiply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_norm.c -o vendor/cs/cs_norm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_permute.c -o vendor/cs/cs_permute.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_pinv.c -o vendor/cs/cs_pinv.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_post.c -o vendor/cs/cs_post.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_print.c -o vendor/cs/cs_print.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_pvec.c -o vendor/cs/cs_pvec.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_qr.c -o vendor/cs/cs_qr.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_qrsol.c -o vendor/cs/cs_qrsol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_randperm.c -o vendor/cs/cs_randperm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_reach.c -o vendor/cs/cs_reach.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_scatter.c -o vendor/cs/cs_scatter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_scc.c -o vendor/cs/cs_scc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_schol.c -o vendor/cs/cs_schol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_spsolve.c -o vendor/cs/cs_spsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_sqr.c -o vendor/cs/cs_sqr.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_symperm.c -o vendor/cs/cs_symperm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_tdfs.c -o vendor/cs/cs_tdfs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_transpose.c -o vendor/cs/cs_transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_updown.c -o vendor/cs/cs_updown.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_usolve.c -o vendor/cs/cs_usolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_util.c -o vendor/cs/cs_util.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_utsolve.c -o vendor/cs/cs_utsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/mini-gmp/mini-gmp.c -o vendor/mini-gmp/mini-gmp.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/gss.c -o vendor/plfit/gss.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/hzeta.c -o vendor/plfit/hzeta.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/kolmogorov.c -o vendor/plfit/kolmogorov.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/lbfgs.c -o vendor/plfit/lbfgs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/mt.c -o vendor/plfit/mt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/options.c -o vendor/plfit/options.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/platform.c -o vendor/plfit/platform.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/plfit.c -o vendor/plfit/plfit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/plfit_error.c -o vendor/plfit/plfit_error.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/rbinom.c -o vendor/plfit/rbinom.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/sampling.c -o vendor/plfit/sampling.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/second.f -o vendor/arpack/second.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Color.cpp -o vendor/simpleraytracer/Color.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Light.cpp -o vendor/simpleraytracer/Light.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Point.cpp -o vendor/simpleraytracer/Point.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/RIgraphRay.cpp -o vendor/simpleraytracer/RIgraphRay.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Ray.cpp -o vendor/simpleraytracer/Ray.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/RayTracer.cpp -o vendor/simpleraytracer/RayTracer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/RayVector.cpp -o vendor/simpleraytracer/RayVector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Shape.cpp -o vendor/simpleraytracer/Shape.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Sphere.cpp -o vendor/simpleraytracer/Sphere.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Triangle.cpp -o vendor/simpleraytracer/Triangle.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/unit_limiter.cpp -o vendor/simpleraytracer/unit_limiter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/R.c -o vendor/uuid/R.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/clear.c -o vendor/uuid/clear.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/compare.c -o vendor/uuid/compare.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/copy.c -o vendor/uuid/copy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/gen_uuid.c -o vendor/uuid/gen_uuid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/isnull.c -o vendor/uuid/isnull.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/pack.c -o vendor/uuid/pack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/parse.c -o vendor/uuid/parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/unpack.c -o vendor/uuid/unpack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/unparse.c -o vendor/uuid/unparse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c rinterface.c -o rinterface.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c rinterface_extra.c -o rinterface_extra.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c rrandom.c -o rrandom.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c lazyeval.c -o lazyeval.o ar rvs ../librigraph.a core/centrality/betweenness.o core/centrality/centrality_other.o core/centrality/centralization.o core/centrality/closeness.o core/centrality/coreness.o core/centrality/prpack/prpack_base_graph.o core/centrality/prpack/prpack_igraph_graph.o core/centrality/prpack/prpack_preprocessed_ge_graph.o core/centrality/prpack/prpack_preprocessed_gs_graph.o core/centrality/prpack/prpack_preprocessed_scc_graph.o core/centrality/prpack/prpack_preprocessed_schur_graph.o core/centrality/prpack/prpack_result.o core/centrality/prpack/prpack_solver.o core/centrality/prpack/prpack_utils.o core/cliques/cliquer/cliquer.o core/cliques/cliquer/cliquer_graph.o core/cliques/cliquer/reorder.o core/cliques/cliquer_wrapper.o core/cliques/cliques.o core/cliques/glet.o core/cliques/maximal_cliques.o core/community/community_misc.o core/community/edge_betweenness.o core/community/fast_modularity.o core/community/fluid.o core/community/infomap/infomap.o core/community/infomap/infomap_FlowGraph.o core/community/infomap/infomap_Greedy.o core/community/infomap/infomap_Node.o core/community/label_propagation.o core/community/leading_eigenvector.o core/community/leiden.o core/community/louvain.o core/community/modularity.o core/community/optimal_modularity.o core/community/spinglass/NetDataTypes.o core/community/spinglass/NetRoutines.o core/community/spinglass/clustertool.o core/community/spinglass/pottsmodel_2.o core/community/walktrap/walktrap.o core/community/walktrap/walktrap_communities.o core/community/walktrap/walktrap_graph.o core/community/walktrap/walktrap_heap.o core/connectivity/cohesive_blocks.o core/connectivity/components.o core/connectivity/separators.o core/constructors/adjacency.o core/constructors/atlas.o core/constructors/basic_constructors.o core/constructors/de_bruijn.o core/constructors/famous.o core/constructors/full.o core/constructors/kautz.o core/constructors/lcf.o core/constructors/linegraph.o core/constructors/prufer.o core/constructors/regular.o core/core/array.o core/core/buckets.o core/core/cutheap.o core/core/dqueue.o core/core/error.o core/core/estack.o core/core/fixed_vectorlist.o core/core/grid.o core/core/heap.o core/core/indheap.o core/core/interruption.o core/core/marked_queue.o core/core/matrix.o core/core/memory.o core/core/printing.o core/core/progress.o core/core/psumtree.o core/core/set.o core/core/sparsemat.o core/core/spmatrix.o core/core/stack.o core/core/statusbar.o core/core/strvector.o core/core/trie.o core/core/vector.o core/core/vector_ptr.o core/flow/flow.o core/flow/st-cuts.o core/games/barabasi.o core/games/callaway_traits.o core/games/citations.o core/games/correlated.o core/games/degree_sequence.o core/games/degree_sequence_vl/gengraph_box_list.o core/games/degree_sequence_vl/gengraph_degree_sequence.o core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o core/games/degree_sequence_vl/gengraph_mr-connected.o core/games/degree_sequence_vl/gengraph_powerlaw.o core/games/degree_sequence_vl/gengraph_random.o core/games/dotproduct.o core/games/erdos_renyi.o core/games/establishment.o core/games/forestfire.o core/games/grg.o core/games/growing_random.o core/games/islands.o core/games/k_regular.o core/games/preference.o core/games/recent_degree.o core/games/sbm.o core/games/static_fitness.o core/games/tree.o core/games/watts_strogatz.o core/graph/adjlist.o core/graph/attributes.o core/graph/basic_query.o core/graph/cattributes.o core/graph/iterators.o core/graph/type_indexededgelist.o core/graph/visitors.o core/hrg/hrg.o core/hrg/hrg_types.o core/internal/glpk_support.o core/internal/hacks.o core/internal/lsap.o core/internal/qsort.o core/internal/qsort_r.o core/internal/zeroin.o core/io/dimacs.o core/io/dl-lexer.o core/io/dl-parser.o core/io/dl.o core/io/dot.o core/io/edgelist.o core/io/gml-lexer.o core/io/gml-parser.o core/io/gml-tree.o core/io/gml.o core/io/graphdb.o core/io/graphml.o core/io/leda.o core/io/lgl-lexer.o core/io/lgl-parser.o core/io/lgl.o core/io/ncol-lexer.o core/io/ncol-parser.o core/io/ncol.o core/io/pajek-lexer.o core/io/pajek-parser.o core/io/pajek.o core/isomorphism/bliss.o core/isomorphism/bliss/defs.o core/isomorphism/bliss/graph.o core/isomorphism/bliss/heap.o core/isomorphism/bliss/orbit.o core/isomorphism/bliss/partition.o core/isomorphism/bliss/uintseqhash.o core/isomorphism/bliss/utils.o core/isomorphism/isoclasses.o core/isomorphism/isomorphism_misc.o core/isomorphism/lad.o core/isomorphism/queries.o core/isomorphism/vf2.o core/layout/circular.o core/layout/davidson_harel.o core/layout/drl/DensityGrid.o core/layout/drl/DensityGrid_3d.o core/layout/drl/drl_graph.o core/layout/drl/drl_graph_3d.o core/layout/drl/drl_layout.o core/layout/drl/drl_layout_3d.o core/layout/drl/drl_parse.o core/layout/fruchterman_reingold.o core/layout/gem.o core/layout/graphopt.o core/layout/kamada_kawai.o core/layout/large_graph.o core/layout/layout_bipartite.o core/layout/layout_grid.o core/layout/layout_random.o core/layout/mds.o core/layout/merge_dla.o core/layout/merge_grid.o core/layout/reingold_tilford.o core/layout/sugiyama.o core/linalg/arpack.o core/linalg/blas.o core/linalg/eigen.o core/linalg/lapack.o core/math/bfgs.o core/math/complex.o core/math/utils.o core/misc/bipartite.o core/misc/chordality.o core/misc/cocitation.o core/misc/coloring.o core/misc/conversion.o core/misc/degree_sequence.o core/misc/embedding.o core/misc/feedback_arc_set.o core/misc/graphicality.o core/misc/matching.o core/misc/microscopic_update.o core/misc/mixing.o core/misc/motifs.o core/misc/other.o core/misc/scan.o core/misc/sir.o core/misc/spanning_trees.o core/operators/add_edge.o core/operators/complementer.o core/operators/compose.o core/operators/connect_neighborhood.o core/operators/contract.o core/operators/difference.o core/operators/disjoint_union.o core/operators/intersection.o core/operators/misc_internal.o core/operators/permute.o core/operators/rewire.o core/operators/rewire_edges.o core/operators/simplify.o core/operators/subgraph.o core/operators/union.o core/paths/all_shortest_paths.o core/paths/bellman_ford.o core/paths/dijkstra.o core/paths/distances.o core/paths/eulerian.o core/paths/histogram.o core/paths/johnson.o core/paths/random_walk.o core/paths/shortest_paths.o core/paths/simple_paths.o core/paths/unweighted.o core/properties/basic_properties.o core/properties/constraint.o core/properties/convergence_degree.o core/properties/dag.o core/properties/degrees.o core/properties/girth.o core/properties/loops.o core/properties/multiplicity.o core/properties/neighborhood.o core/properties/spectral.o core/properties/trees.o core/properties/triangles.o core/random/random.o core/scg/scg.o core/scg/scg_approximate_methods.o core/scg/scg_exact_scg.o core/scg/scg_kmeans.o core/scg/scg_optimal_method.o core/scg/scg_utils.o core/version.o vendor/cs/cs_add.o vendor/cs/cs_amd.o vendor/cs/cs_chol.o vendor/cs/cs_cholsol.o vendor/cs/cs_compress.o vendor/cs/cs_counts.o vendor/cs/cs_cumsum.o vendor/cs/cs_dfs.o vendor/cs/cs_dmperm.o vendor/cs/cs_droptol.o vendor/cs/cs_dropzeros.o vendor/cs/cs_dupl.o vendor/cs/cs_entry.o vendor/cs/cs_ereach.o vendor/cs/cs_etree.o vendor/cs/cs_fkeep.o vendor/cs/cs_gaxpy.o vendor/cs/cs_happly.o vendor/cs/cs_house.o vendor/cs/cs_ipvec.o vendor/cs/cs_leaf.o vendor/cs/cs_load.o vendor/cs/cs_lsolve.o vendor/cs/cs_ltsolve.o vendor/cs/cs_lu.o vendor/cs/cs_lusol.o vendor/cs/cs_malloc.o vendor/cs/cs_maxtrans.o vendor/cs/cs_multiply.o vendor/cs/cs_norm.o vendor/cs/cs_permute.o vendor/cs/cs_pinv.o vendor/cs/cs_post.o vendor/cs/cs_print.o vendor/cs/cs_pvec.o vendor/cs/cs_qr.o vendor/cs/cs_qrsol.o vendor/cs/cs_randperm.o vendor/cs/cs_reach.o vendor/cs/cs_scatter.o vendor/cs/cs_scc.o vendor/cs/cs_schol.o vendor/cs/cs_spsolve.o vendor/cs/cs_sqr.o vendor/cs/cs_symperm.o vendor/cs/cs_tdfs.o vendor/cs/cs_transpose.o vendor/cs/cs_updown.o vendor/cs/cs_usolve.o vendor/cs/cs_util.o vendor/cs/cs_utsolve.o vendor/mini-gmp/mini-gmp.o vendor/plfit/gss.o vendor/plfit/hzeta.o vendor/plfit/kolmogorov.o vendor/plfit/lbfgs.o vendor/plfit/mt.o vendor/plfit/options.o vendor/plfit/platform.o vendor/plfit/plfit.o vendor/plfit/plfit_error.o vendor/plfit/rbinom.o vendor/plfit/sampling.o vendor/arpack/dgetv0.o vendor/arpack/dlaqrb.o vendor/arpack/dmout.o vendor/arpack/dnaitr.o vendor/arpack/dnapps.o vendor/arpack/dnaup2.o vendor/arpack/dnaupd.o vendor/arpack/dnconv.o vendor/arpack/dneigh.o vendor/arpack/dneupd.o vendor/arpack/dngets.o vendor/arpack/dsaitr.o vendor/arpack/dsapps.o vendor/arpack/dsaup2.o vendor/arpack/dsaupd.o vendor/arpack/dsconv.o vendor/arpack/dseigt.o vendor/arpack/dsesrt.o vendor/arpack/dseupd.o vendor/arpack/dsgets.o vendor/arpack/dsortc.o vendor/arpack/dsortr.o vendor/arpack/dstatn.o vendor/arpack/dstats.o vendor/arpack/dstqrb.o vendor/arpack/dvout.o vendor/arpack/ivout.o vendor/arpack/second.o vendor/arpack/wrap.o vendor/simpleraytracer/Color.o vendor/simpleraytracer/Light.o vendor/simpleraytracer/Point.o vendor/simpleraytracer/RIgraphRay.o vendor/simpleraytracer/Ray.o vendor/simpleraytracer/RayTracer.o vendor/simpleraytracer/RayVector.o vendor/simpleraytracer/Shape.o vendor/simpleraytracer/Sphere.o vendor/simpleraytracer/Triangle.o vendor/simpleraytracer/unit_limiter.o vendor/uuid/R.o vendor/uuid/clear.o vendor/uuid/compare.o vendor/uuid/copy.o vendor/uuid/gen_uuid.o vendor/uuid/isnull.o vendor/uuid/pack.o vendor/uuid/parse.o vendor/uuid/unpack.o vendor/uuid/unparse.o rinterface.o rinterface_extra.o rrandom.o lazyeval.o ar: creating ../librigraph.a a - core/centrality/betweenness.o a - core/centrality/centrality_other.o a - core/centrality/centralization.o a - core/centrality/closeness.o a - core/centrality/coreness.o a - core/centrality/prpack/prpack_base_graph.o a - core/centrality/prpack/prpack_igraph_graph.o a - core/centrality/prpack/prpack_preprocessed_ge_graph.o a - core/centrality/prpack/prpack_preprocessed_gs_graph.o a - core/centrality/prpack/prpack_preprocessed_scc_graph.o a - core/centrality/prpack/prpack_preprocessed_schur_graph.o a - core/centrality/prpack/prpack_result.o a - core/centrality/prpack/prpack_solver.o a - core/centrality/prpack/prpack_utils.o a - core/cliques/cliquer/cliquer.o a - core/cliques/cliquer/cliquer_graph.o a - core/cliques/cliquer/reorder.o a - core/cliques/cliquer_wrapper.o a - core/cliques/cliques.o a - core/cliques/glet.o a - core/cliques/maximal_cliques.o a - core/community/community_misc.o a - core/community/edge_betweenness.o a - core/community/fast_modularity.o a - core/community/fluid.o a - core/community/infomap/infomap.o a - core/community/infomap/infomap_FlowGraph.o a - core/community/infomap/infomap_Greedy.o a - core/community/infomap/infomap_Node.o a - core/community/label_propagation.o a - core/community/leading_eigenvector.o a - core/community/leiden.o a - core/community/louvain.o a - core/community/modularity.o a - core/community/optimal_modularity.o a - core/community/spinglass/NetDataTypes.o a - core/community/spinglass/NetRoutines.o a - core/community/spinglass/clustertool.o a - core/community/spinglass/pottsmodel_2.o a - core/community/walktrap/walktrap.o a - core/community/walktrap/walktrap_communities.o a - core/community/walktrap/walktrap_graph.o a - core/community/walktrap/walktrap_heap.o a - core/connectivity/cohesive_blocks.o a - core/connectivity/components.o a - core/connectivity/separators.o a - core/constructors/adjacency.o a - core/constructors/atlas.o a - core/constructors/basic_constructors.o a - core/constructors/de_bruijn.o a - core/constructors/famous.o a - core/constructors/full.o a - core/constructors/kautz.o a - core/constructors/lcf.o a - core/constructors/linegraph.o a - core/constructors/prufer.o a - core/constructors/regular.o a - core/core/array.o a - core/core/buckets.o a - core/core/cutheap.o a - core/core/dqueue.o a - core/core/error.o a - core/core/estack.o a - core/core/fixed_vectorlist.o a - core/core/grid.o a - core/core/heap.o a - core/core/indheap.o a - core/core/interruption.o a - core/core/marked_queue.o a - core/core/matrix.o a - core/core/memory.o a - core/core/printing.o a - core/core/progress.o a - core/core/psumtree.o a - core/core/set.o a - core/core/sparsemat.o a - core/core/spmatrix.o a - core/core/stack.o a - core/core/statusbar.o a - core/core/strvector.o a - core/core/trie.o a - core/core/vector.o a - core/core/vector_ptr.o a - core/flow/flow.o a - core/flow/st-cuts.o a - core/games/barabasi.o a - core/games/callaway_traits.o a - core/games/citations.o a - core/games/correlated.o a - core/games/degree_sequence.o a - core/games/degree_sequence_vl/gengraph_box_list.o a - core/games/degree_sequence_vl/gengraph_degree_sequence.o a - core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o a - core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o a - core/games/degree_sequence_vl/gengraph_mr-connected.o a - core/games/degree_sequence_vl/gengraph_powerlaw.o a - core/games/degree_sequence_vl/gengraph_random.o a - core/games/dotproduct.o a - core/games/erdos_renyi.o a - core/games/establishment.o a - core/games/forestfire.o a - core/games/grg.o a - core/games/growing_random.o a - core/games/islands.o a - core/games/k_regular.o a - core/games/preference.o a - core/games/recent_degree.o a - core/games/sbm.o a - core/games/static_fitness.o a - core/games/tree.o a - core/games/watts_strogatz.o a - core/graph/adjlist.o a - core/graph/attributes.o a - core/graph/basic_query.o a - core/graph/cattributes.o a - core/graph/iterators.o a - core/graph/type_indexededgelist.o a - core/graph/visitors.o a - core/hrg/hrg.o a - core/hrg/hrg_types.o a - core/internal/glpk_support.o a - core/internal/hacks.o a - core/internal/lsap.o a - core/internal/qsort.o a - core/internal/qsort_r.o a - core/internal/zeroin.o a - core/io/dimacs.o a - core/io/dl-lexer.o a - core/io/dl-parser.o a - core/io/dl.o a - core/io/dot.o a - core/io/edgelist.o a - core/io/gml-lexer.o a - core/io/gml-parser.o a - core/io/gml-tree.o a - core/io/gml.o a - core/io/graphdb.o a - core/io/graphml.o a - core/io/leda.o a - core/io/lgl-lexer.o a - core/io/lgl-parser.o a - core/io/lgl.o a - core/io/ncol-lexer.o a - core/io/ncol-parser.o a - core/io/ncol.o a - core/io/pajek-lexer.o a - core/io/pajek-parser.o a - core/io/pajek.o a - core/isomorphism/bliss.o a - core/isomorphism/bliss/defs.o a - core/isomorphism/bliss/graph.o a - core/isomorphism/bliss/heap.o a - core/isomorphism/bliss/orbit.o a - core/isomorphism/bliss/partition.o a - core/isomorphism/bliss/uintseqhash.o a - core/isomorphism/bliss/utils.o a - core/isomorphism/isoclasses.o a - core/isomorphism/isomorphism_misc.o a - core/isomorphism/lad.o a - core/isomorphism/queries.o a - core/isomorphism/vf2.o a - core/layout/circular.o a - core/layout/davidson_harel.o a - core/layout/drl/DensityGrid.o a - core/layout/drl/DensityGrid_3d.o a - core/layout/drl/drl_graph.o a - core/layout/drl/drl_graph_3d.o a - core/layout/drl/drl_layout.o a - core/layout/drl/drl_layout_3d.o a - core/layout/drl/drl_parse.o a - core/layout/fruchterman_reingold.o a - core/layout/gem.o a - core/layout/graphopt.o a - core/layout/kamada_kawai.o a - core/layout/large_graph.o a - core/layout/layout_bipartite.o a - core/layout/layout_grid.o a - core/layout/layout_random.o a - core/layout/mds.o a - core/layout/merge_dla.o a - core/layout/merge_grid.o a - core/layout/reingold_tilford.o a - core/layout/sugiyama.o a - core/linalg/arpack.o a - core/linalg/blas.o a - core/linalg/eigen.o a - core/linalg/lapack.o a - core/math/bfgs.o a - core/math/complex.o a - core/math/utils.o a - core/misc/bipartite.o a - core/misc/chordality.o a - core/misc/cocitation.o a - core/misc/coloring.o a - core/misc/conversion.o a - core/misc/degree_sequence.o a - core/misc/embedding.o a - core/misc/feedback_arc_set.o a - core/misc/graphicality.o a - core/misc/matching.o a - core/misc/microscopic_update.o a - core/misc/mixing.o a - core/misc/motifs.o a - core/misc/other.o a - core/misc/scan.o a - core/misc/sir.o a - core/misc/spanning_trees.o a - core/operators/add_edge.o a - core/operators/complementer.o a - core/operators/compose.o a - core/operators/connect_neighborhood.o a - core/operators/contract.o a - core/operators/difference.o a - core/operators/disjoint_union.o a - core/operators/intersection.o a - core/operators/misc_internal.o a - core/operators/permute.o a - core/operators/rewire.o a - core/operators/rewire_edges.o a - core/operators/simplify.o a - core/operators/subgraph.o a - core/operators/union.o a - core/paths/all_shortest_paths.o a - core/paths/bellman_ford.o a - core/paths/dijkstra.o a - core/paths/distances.o a - core/paths/eulerian.o a - core/paths/histogram.o a - core/paths/johnson.o a - core/paths/random_walk.o a - core/paths/shortest_paths.o a - core/paths/simple_paths.o a - core/paths/unweighted.o a - core/properties/basic_properties.o a - core/properties/constraint.o a - core/properties/convergence_degree.o a - core/properties/dag.o a - core/properties/degrees.o a - core/properties/girth.o a - core/properties/loops.o a - core/properties/multiplicity.o a - core/properties/neighborhood.o a - core/properties/spectral.o a - core/properties/trees.o a - core/properties/triangles.o a - core/random/random.o a - core/scg/scg.o a - core/scg/scg_approximate_methods.o a - core/scg/scg_exact_scg.o a - core/scg/scg_kmeans.o a - core/scg/scg_optimal_method.o a - core/scg/scg_utils.o a - core/version.o a - vendor/cs/cs_add.o a - vendor/cs/cs_amd.o a - vendor/cs/cs_chol.o a - vendor/cs/cs_cholsol.o a - vendor/cs/cs_compress.o a - vendor/cs/cs_counts.o a - vendor/cs/cs_cumsum.o a - vendor/cs/cs_dfs.o a - vendor/cs/cs_dmperm.o a - vendor/cs/cs_droptol.o a - vendor/cs/cs_dropzeros.o a - vendor/cs/cs_dupl.o a - vendor/cs/cs_entry.o a - vendor/cs/cs_ereach.o a - vendor/cs/cs_etree.o a - vendor/cs/cs_fkeep.o a - vendor/cs/cs_gaxpy.o a - vendor/cs/cs_happly.o a - vendor/cs/cs_house.o a - vendor/cs/cs_ipvec.o a - vendor/cs/cs_leaf.o a - vendor/cs/cs_load.o a - vendor/cs/cs_lsolve.o a - vendor/cs/cs_ltsolve.o a - vendor/cs/cs_lu.o a - vendor/cs/cs_lusol.o a - vendor/cs/cs_malloc.o a - vendor/cs/cs_maxtrans.o a - vendor/cs/cs_multiply.o a - vendor/cs/cs_norm.o a - vendor/cs/cs_permute.o a - vendor/cs/cs_pinv.o a - vendor/cs/cs_post.o a - vendor/cs/cs_print.o a - vendor/cs/cs_pvec.o a - vendor/cs/cs_qr.o a - vendor/cs/cs_qrsol.o a - vendor/cs/cs_randperm.o a - vendor/cs/cs_reach.o a - vendor/cs/cs_scatter.o a - vendor/cs/cs_scc.o a - vendor/cs/cs_schol.o a - vendor/cs/cs_spsolve.o a - vendor/cs/cs_sqr.o a - vendor/cs/cs_symperm.o a - vendor/cs/cs_tdfs.o a - vendor/cs/cs_transpose.o a - vendor/cs/cs_updown.o a - vendor/cs/cs_usolve.o a - vendor/cs/cs_util.o a - vendor/cs/cs_utsolve.o a - vendor/mini-gmp/mini-gmp.o a - vendor/plfit/gss.o a - vendor/plfit/hzeta.o a - vendor/plfit/kolmogorov.o a - vendor/plfit/lbfgs.o a - vendor/plfit/mt.o a - vendor/plfit/options.o a - vendor/plfit/platform.o a - vendor/plfit/plfit.o a - vendor/plfit/plfit_error.o a - vendor/plfit/rbinom.o a - vendor/plfit/sampling.o a - vendor/arpack/dgetv0.o a - vendor/arpack/dlaqrb.o a - vendor/arpack/dmout.o a - vendor/arpack/dnaitr.o a - vendor/arpack/dnapps.o a - vendor/arpack/dnaup2.o a - vendor/arpack/dnaupd.o a - vendor/arpack/dnconv.o a - vendor/arpack/dneigh.o a - vendor/arpack/dneupd.o a - vendor/arpack/dngets.o a - vendor/arpack/dsaitr.o a - vendor/arpack/dsapps.o a - vendor/arpack/dsaup2.o a - vendor/arpack/dsaupd.o a - vendor/arpack/dsconv.o a - vendor/arpack/dseigt.o a - vendor/arpack/dsesrt.o a - vendor/arpack/dseupd.o a - vendor/arpack/dsgets.o a - vendor/arpack/dsortc.o a - vendor/arpack/dsortr.o a - vendor/arpack/dstatn.o a - vendor/arpack/dstats.o a - vendor/arpack/dstqrb.o a - vendor/arpack/dvout.o a - vendor/arpack/ivout.o a - vendor/arpack/second.o a - vendor/arpack/wrap.o a - vendor/simpleraytracer/Color.o a - vendor/simpleraytracer/Light.o a - vendor/simpleraytracer/Point.o a - vendor/simpleraytracer/RIgraphRay.o a - vendor/simpleraytracer/Ray.o a - vendor/simpleraytracer/RayTracer.o a - vendor/simpleraytracer/RayVector.o a - vendor/simpleraytracer/Shape.o a - vendor/simpleraytracer/Sphere.o a - vendor/simpleraytracer/Triangle.o a - vendor/simpleraytracer/unit_limiter.o a - vendor/uuid/R.o a - vendor/uuid/clear.o a - vendor/uuid/compare.o a - vendor/uuid/copy.o a - vendor/uuid/gen_uuid.o a - vendor/uuid/isnull.o a - vendor/uuid/pack.o a - vendor/uuid/parse.o a - vendor/uuid/unpack.o a - vendor/uuid/unparse.o a - rinterface.o a - rinterface_extra.o a - rrandom.o a - lazyeval.o make[1]: Leaving directory '/tmp/th798/17408827/RtmpyWMGVL/R.INSTALLf184bb797866/leidenAlg/src/rigraph' make[1]: Entering directory '/tmp/th798/17408827/RtmpyWMGVL/R.INSTALLf184bb797866/leidenAlg/src/leidenalg' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c CPMVertexPartition.cpp -o CPMVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c LinearResolutionParameterVertexPartition.cpp -o LinearResolutionParameterVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RBConfigurationVertexPartition.cpp -o RBConfigurationVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c SurpriseVertexPartition.cpp -o SurpriseVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ModularityVertexPartition.cpp -o ModularityVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RBERVertexPartition.cpp -o RBERVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c GraphHelper.cpp -o GraphHelper.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c MutableVertexPartition.cpp -o MutableVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ResolutionParameterVertexPartition.cpp -o ResolutionParameterVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Optimiser.cpp -o Optimiser.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c SignificanceVertexPartition.cpp -o SignificanceVertexPartition.o ar rvs ../libleidenalg.a CPMVertexPartition.o LinearResolutionParameterVertexPartition.o RBConfigurationVertexPartition.o SurpriseVertexPartition.o ModularityVertexPartition.o RBERVertexPartition.o GraphHelper.o MutableVertexPartition.o ResolutionParameterVertexPartition.o Optimiser.o SignificanceVertexPartition.o ar: creating ../libleidenalg.a a - CPMVertexPartition.o a - LinearResolutionParameterVertexPartition.o a - RBConfigurationVertexPartition.o a - SurpriseVertexPartition.o a - ModularityVertexPartition.o a - RBERVertexPartition.o a - GraphHelper.o a - MutableVertexPartition.o a - ResolutionParameterVertexPartition.o a - Optimiser.o a - SignificanceVertexPartition.o make[1]: Leaving directory '/tmp/th798/17408827/RtmpyWMGVL/R.INSTALLf184bb797866/leidenAlg/src/leidenalg' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o leidenAlg.so RcppExports.o leiden.o -L. -lpthread -lleidenalg -lrigraph -lm -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-leidenAlg/00new/leidenAlg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leidenAlg) * installing *source* package 'RcppPlanc' ... ** this is package 'RcppPlanc' version '2.0.10' ** package 'RcppPlanc' successfully unpacked and MD5 sums checked ** using staged installation -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /packages/gcc/12.2.0-nnbserq/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /packages/gcc/12.2.0-nnbserq/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done This is libplanc 1.0.2 containing component nmflib 1.0.1 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") CMake Debug Log at cmake/FindR.cmake:38 (find_program): find_program called with the following settings: VAR: R_EXECUTABLE NAMES: "R" Documentation: Path to a program. Framework Only Search Frameworks: 0 Search Frameworks Last: 0 Search Frameworks First: 0 AppBundle Only Search AppBundle: 0 Search AppBundle Last: 0 Search AppBundle First: 0 CMAKE_FIND_USE_CMAKE_PATH: 1 CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH: 0 CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH: 0 CMAKE_FIND_USE_CMAKE_SYSTEM_PATH: 0 find_program considered the following locations: The item was found at /home/th798/R/R-devel/bin/R Call Stack (most recent call first): CMakeLists.txt:73 (find_package) CMake Debug Log at cmake/FindR.cmake:64 (find_program): find_program called with the following settings: VAR: RSCRIPT_EXECUTABLE NAMES: "Rscript" Documentation: Rscript executable. Framework Only Search Frameworks: 0 Search Frameworks Last: 0 Search Frameworks First: 0 AppBundle Only Search AppBundle: 0 Search AppBundle Last: 0 Search AppBundle First: 0 CMAKE_FIND_USE_CMAKE_PATH: 1 CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH: 1 CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH: 1 CMAKE_FIND_USE_CMAKE_SYSTEM_PATH: 1 find_program considered the following locations: /packages/gcc/12.2.0-nnbserq/bin/Rscript /packages/gcc/12.2.0-nnbserq/sbin/Rscript /packages/gcc/12.2.0-nnbserq/Rscript /packages/zstd/1.5.2-cs5ansz/bin/Rscript /packages/zstd/1.5.2-cs5ansz/sbin/Rscript /packages/zstd/1.5.2-cs5ansz/Rscript /packages/zlib/1.2.13-po6bkge/bin/Rscript /packages/zlib/1.2.13-po6bkge/sbin/Rscript /packages/zlib/1.2.13-po6bkge/Rscript /packages/mpc/1.2.1-nnfoiwh/bin/Rscript /packages/mpc/1.2.1-nnfoiwh/sbin/Rscript /packages/mpc/1.2.1-nnfoiwh/Rscript /packages/mpfr/4.1.0-yfsqqka/bin/Rscript /packages/mpfr/4.1.0-yfsqqka/sbin/Rscript /packages/mpfr/4.1.0-yfsqqka/Rscript /packages/gmp/6.2.1-7ydtie6/bin/Rscript /packages/gmp/6.2.1-7ydtie6/sbin/Rscript /packages/gmp/6.2.1-7ydtie6/Rscript /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/bin/Rscript /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/sbin/Rscript /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/Rscript /packages/gcc-8.3.1/proj/7.1.0/bin/Rscript /packages/gcc-8.3.1/proj/7.1.0/sbin/Rscript /packages/gcc-8.3.1/proj/7.1.0/Rscript /packages/gdal/3.3.1/bin/Rscript /packages/gdal/3.3.1/sbin/Rscript /packages/gdal/3.3.1/Rscript The item was found at /home/th798/R/R-devel/bin/Rscript Call Stack (most recent call first): CMakeLists.txt:73 (find_package) -- Found R: /home/th798/R/R-devel/bin/R (found version "R Under development (unstable) (2025-05-18 r88218) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/. ") CMake Debug Log at CMakeLists.txt:73 (find_package): find_package considered the following paths for R.cmake /projects/genomic-ml/.conda/envs/emacs1/share/cmake-3.22/Modules/FindR.cmake The file was found at /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/cmake/FindR.cmake -- Could NOT find MKL (missing: MKL_DIR) -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /projects/genomic-ml/.conda/envs/emacs1/lib/libopenblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /projects/genomic-ml/.conda/envs/emacs1/lib/libopenblas.so;-lpthread;-lm;-ldl -- Could NOT find OpenBLAS (missing: OpenBLAS_DIR) -- Looking for openblas/cblas.h -- Looking for openblas/cblas.h - not found -- Found HDF5: /home/th798/.conda/envs/emacs1/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/packages/zlib/1.2.13-po6bkge/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.2") -- Performing Test HDF5_LINKS CMake Warning at /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles/CMakeTmp/CMakeLists.txt:17 (add_executable): Cannot generate a safe runtime search path for target cmTC_6c62b because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /packages/zlib/1.2.13-po6bkge/lib may be hidden by files in: /home/th798/.conda/envs/emacs1/lib Some of these libraries may not be found correctly. -- Performing Test HDF5_LINKS - Success -- Found R_Rcpp: /projects/genomic-ml/R/R-devel/library/Rcpp -- Found R_RcppArmadillo: /projects/genomic-ml/R/R-devel/library/RcppArmadillo -- Found R_RcppProgress: /projects/genomic-ml/R/R-devel/library/RcppProgress -- Performing Test UNSAFE_MATH -- Performing Test UNSAFE_MATH - Success -- Performing Test FINITE_MATH -- Performing Test FINITE_MATH - Success -- Performing Test TRAPPING_MATH -- Performing Test TRAPPING_MATH - Success -- Performing Test ERRNO_MATH -- Performing Test ERRNO_MATH - Success -- Performing Test UNSIGNED_ZERO -- Performing Test UNSIGNED_ZERO - Success -- Performing Test RECIPROCAL_MATH -- Performing Test RECIPROCAL_MATH - Success -- Performing Test ARCH_AVX -- Performing Test ARCH_AVX - Success -- Performing Test HAS_POPCNT -- Performing Test HAS_POPCNT - Success -- Looking for cblas.h -- Looking for cblas.h - not found -- Looking for flexiblas/cblas.h -- Looking for flexiblas/cblas.h - not found -- A cache variable, namely HWLOC_DIR, has been set to specify the install directory of HWLOC -- Checking for one of the modules 'hwloc' -- Looking for HWLOC - not found using PkgConfig. Perhaps you should add the directory containing hwloc.pc to the PKG_CONFIG_PATH environment variable. -- Looking for HWLOC - PkgConfig not used -- Looking for hwloc -- hwloc.h not found -- Looking for hwloc -- lib hwloc not found -- Could NOT find HWLOC (missing: HWLOC_LIBRARIES HWLOC_WORKS) -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- NNLS_SOURCE_DIR = /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls -- NMF_SOURCE_DIR = /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nmf -- NMFLIB_COMMON = /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done CMake Warning at nmf/CMakeLists.txt:12 (add_library): Cannot generate a safe runtime search path for target nmflib because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /packages/zlib/1.2.13-po6bkge/lib may be hidden by files in: /projects/genomic-ml/.conda/envs/emacs1/lib /home/th798/.conda/envs/emacs1/lib Some of these libraries may not be found correctly. -- Generating done CMake Warning: Manually-specified variables were not used by the project: R_SHLIB_EXT -- Build files have been written to: /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -S/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc -B/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build --check-build-system CMakeFiles/Makefile.cmake 0 /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_progress_start /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles/utils.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 5%] Building CXX object CMakeFiles/utils.dir/common/utils.cpp.o /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -MD -MT CMakeFiles/utils.dir/common/utils.cpp.o -MF CMakeFiles/utils.dir/common/utils.cpp.o.d -o CMakeFiles/utils.dir/common/utils.cpp.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common/utils.cpp make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 5%] Built target utils make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles/hwloc.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 11%] Creating directories for 'hwloc' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/tmp /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-mkdir [ 17%] Performing download step (download, verify and extract) for 'hwloc' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -P /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/download-hwloc.cmake -- Downloading... dst='/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.11.2.tar.gz' timeout='none' inactivity timeout='none' -- Using src='https://download.open-mpi.org/release/hwloc/v2.11/hwloc-2.11.2.tar.gz' -- [download 0% complete] -- [download 1% complete] -- [download 2% complete] -- [download 3% complete] -- [download 4% complete] -- [download 5% complete] -- [download 6% complete] -- [download 7% complete] -- [download 8% complete] -- [download 9% complete] -- [download 10% complete] -- [download 11% complete] -- [download 12% complete] -- [download 13% complete] -- [download 14% complete] -- [download 15% complete] -- [download 16% complete] -- [download 17% complete] -- [download 18% complete] -- [download 19% complete] -- [download 20% complete] -- [download 21% complete] -- [download 22% complete] -- [download 23% complete] -- [download 24% complete] -- [download 25% complete] -- [download 26% complete] -- [download 27% complete] -- [download 28% complete] -- [download 29% complete] -- [download 30% complete] -- [download 31% complete] -- [download 32% complete] -- [download 53% complete] -- [download 58% complete] -- [download 75% complete] -- [download 81% complete] -- [download 86% complete] -- [download 100% complete] -- verifying file... file='/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.11.2.tar.gz' -- Downloading... done cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -P /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/verify-hwloc.cmake cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -P /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/extract-hwloc.cmake -- extracting... src='/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.11.2.tar.gz' dst='/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-download [ 23%] No update step for 'hwloc' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E echo_append /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-update [ 29%] Performing patch step for 'hwloc' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cat /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/../../tools/patches/00_remove_stdio.patch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/../../tools/patches/01_remove_sprintf.patch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/../../tools/patches/02_adjust_windows_types.patch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/../../tools/patches/03_remove_abort.patch | /usr/bin/patch -p1 -l patching file hwloc/components.c patching file hwloc/distances.c patching file hwloc/memattrs.c patching file hwloc/pci-common.c patching file hwloc/topology-aix.c patching file hwloc/topology-bgq.c patching file hwloc/topology-cuda.c patching file hwloc/topology-darwin.c patching file hwloc/topology-levelzero.c patching file hwloc/topology-linux.c patching file hwloc/topology-nvml.c patching file hwloc/topology-opencl.c patching file hwloc/topology-pci.c patching file hwloc/topology-rsmi.c patching file hwloc/topology-solaris.c patching file hwloc/topology-synthetic.c patching file hwloc/topology-windows.c patching file hwloc/topology-x86.c patching file hwloc/topology-xml-libxml.c patching file hwloc/topology-xml-nolibxml.c patching file hwloc/topology-xml.c patching file hwloc/topology.c patching file hwloc/cpukinds.c patching file hwloc/topology-freebsd.c patching file hwloc/topology-linux.c patching file hwloc/topology-rsmi.c patching file hwloc/topology-windows.c patching file hwloc/topology-xml.c patching file include/hwloc/cuda.h patching file include/hwloc/cudart.h patching file include/hwloc/levelzero.h patching file include/hwloc/nvml.h patching file include/hwloc/opencl.h patching file include/hwloc/openfabrics-verbs.h patching file include/hwloc/rsmi.h patching file hwloc/topology-windows.c patching file hwloc/distances.c patching file hwloc/topology-linux.c cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-patch [ 35%] Performing configure step for 'hwloc' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E env LD= "CFLAGS=-DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " sh ../hwloc/configure --with-pic --prefix=/out/ --disable-picky --enable-shared=no --enable-static=yes --disable-cairo --disable-libxml2 --disable-io --disable-plugin-dlopen --disable-plugin-ltdl --enable-embedded-mode && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate ../hwloc/aclocal.m4 && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate ../hwloc/Makefile.in && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate ../hwloc/configure && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate config.status ### ### Configuring hwloc distribution tarball ### Startup tests ### checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '682419' is supported by ustar format... yes checking whether GID '3301' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports nested variables... (cached) yes checking whether make supports the include directive... yes (GNU style) checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc understands -c and -o together... yes checking dependency style of /packages/gcc/12.2.0-nnbserq/bin/gcc... /usr/bin/cp ../hwloc/./config//depcomp conftest.dir gcc3 checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for ar... ar checking the archiver (ar) interface... ar checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /packages/gcc/12.2.0-nnbserq/bin/gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from /packages/gcc/12.2.0-nnbserq/bin/gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -fno-rtti -fno-exceptions... no checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to produce PIC... -fPIC -DPIC checking if /packages/gcc/12.2.0-nnbserq/bin/gcc PIC flag -fPIC -DPIC works... yes checking if /packages/gcc/12.2.0-nnbserq/bin/gcc static flag -static works... no checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -c -o file.o... yes checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -c -o file.o... (cached) yes checking whether the /packages/gcc/12.2.0-nnbserq/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking whether the compiler supports GNU C++... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/g++ accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/g++ option to enable C++11 features... none needed checking dependency style of /packages/gcc/12.2.0-nnbserq/bin/g++... /usr/bin/cp ../hwloc/./config//depcomp conftest.dir gcc3 checking how to run the C++ preprocessor... /packages/gcc/12.2.0-nnbserq/bin/g++ -E checking for ld used by /packages/gcc/12.2.0-nnbserq/bin/g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the /packages/gcc/12.2.0-nnbserq/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for /packages/gcc/12.2.0-nnbserq/bin/g++ option to produce PIC... -fPIC -DPIC checking if /packages/gcc/12.2.0-nnbserq/bin/g++ PIC flag -fPIC -DPIC works... yes checking if /packages/gcc/12.2.0-nnbserq/bin/g++ static flag -static works... no checking if /packages/gcc/12.2.0-nnbserq/bin/g++ supports -c -o file.o... yes checking if /packages/gcc/12.2.0-nnbserq/bin/g++ supports -c -o file.o... (cached) yes checking whether the /packages/gcc/12.2.0-nnbserq/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the compiler supports GNU C... (cached) yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... (cached) yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... (cached) none needed checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc understands -c and -o together... (cached) yes checking dependency style of /packages/gcc/12.2.0-nnbserq/bin/gcc... (cached) gcc3 checking for /packages/gcc/12.2.0-nnbserq/bin/gcc options needed to detect all undeclared functions... none needed checking for pkg-config... /home/th798/.conda/envs/emacs1/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking how to run the C preprocessor... /packages/gcc/12.2.0-nnbserq/bin/gcc -E checking for X... libraries , headers ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build configure: hwloc srcdir: /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc configure: Detected VPATH build checking for hwloc version... 2.11.2 checking if want hwloc maintainer support... disabled (embedded mode) checking for hwloc directory prefix... (none) checking for hwloc symbol prefix... hwloc_ checking for the C compiler vendor... gnu checking size of void *... 8 checking which OS support to include... Linux checking which CPU support to include... x86_64 checking size of unsigned long... 8 checking size of unsigned int... 4 checking for __attribute__... yes checking for __attribute__(aligned)... yes checking for __attribute__(always_inline)... yes checking for __attribute__(cold)... yes checking for __attribute__(const)... yes checking for __attribute__(deprecated)... yes checking for __attribute__(constructor)... yes checking for __attribute__(format)... yes checking for __attribute__(hot)... yes checking for __attribute__(malloc)... yes checking for __attribute__(may_alias)... yes checking for __attribute__(no_instrument_function)... yes checking for __attribute__(nonnull)... yes checking for __attribute__(noreturn)... yes checking for __attribute__(packed)... yes checking for __attribute__(pure)... yes checking for __attribute__(sentinel)... yes checking for __attribute__(unused)... yes checking for __attribute__(warn_unused_result)... yes checking for __attribute__(weak_alias)... yes checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -fvisibility=hidden... yes checking whether to enable symbol visibility... yes (via -fvisibility=hidden) configure: WARNING: "-fvisibility=hidden" has been added to the hwloc CFLAGS checking whether the C compiler rejects function calls with too many arguments... yes checking whether the C compiler rejects function calls with too few arguments... yes checking for unistd.h... (cached) yes checking for dirent.h... yes checking for strings.h... (cached) yes checking for ctype.h... yes checking for strcasecmp... yes checking whether strcasecmp is declared... yes checking whether function strcasecmp has a complete prototype... yes checking for strncasecmp... yes checking whether strncasecmp is declared... yes checking whether function strncasecmp has a complete prototype... yes checking for strftime... yes checking for setlocale... yes checking for stdint.h... (cached) yes checking for sys/mman.h... yes **** Linux-specific checks checking whether sched_getcpu is declared... yes checking whether sched_setaffinity is declared... yes checking whether function sched_setaffinity has a complete prototype... yes checking for old prototype of sched_setaffinity... no checking for working CPU_SET... yes checking for working CPU_SET_S... yes checking for working syscall with 6 parameters... yes checking for libudev.h... no **** end of Linux-specific checks checking whether pthread_setaffinity_np is declared... yes checking whether pthread_getaffinity_np is declared... yes checking whether fabsf is declared... yes checking for fabsf in -lm... yes checking whether modff is declared... yes checking for modff in -lm... yes checking whether _SC_NPROCESSORS_ONLN is declared... yes checking whether _SC_NPROCESSORS_CONF is declared... yes checking whether _SC_NPROC_ONLN is declared... no checking whether _SC_NPROC_CONF is declared... no checking whether _SC_PAGESIZE is declared... yes checking whether _SC_PAGE_SIZE is declared... yes checking whether _SC_LARGE_PAGESIZE is declared... no checking for mach/mach_init.h... no checking for mach_init.h... no checking for mach/mach_host.h... no checking whether strtoull is declared... yes checking for ssize_t... yes checking whether snprintf is declared... yes checking whether _strdup is declared... no checking whether _putenv is declared... no checking whether snprintf is correct... yes checking whether getprogname is declared... no checking whether getexecname is declared... no checking for program_invocation_name... yes checking for __progname... yes checking for pthread_t... yes checking for ffs... yes checking whether ffs is declared... yes checking whether function ffs has a complete prototype... yes checking for ffsl... yes checking whether ffsl is declared... yes checking whether function ffsl has a complete prototype... yes checking for fls... no checking for flsl... no checking for clz... no checking for clzl... no checking for openat... yes checking for malloc.h... yes checking for getpagesize... yes checking for memalign... yes checking for posix_memalign... yes checking for sys/utsname.h... yes checking for uname... yes checking for pthread_mutex_lock... yes **** x86 CPUID configuration checking for x86 cpuid... yes **** end of x86 CPUID configuration **** component and plugin-specific configuration checking if plugin support is enabled... no checking components to build statically... noos xml synthetic xml_nolibxml linux x86 checking components to build as plugins... **** end of component and plugin configuration checking for diff... /usr/bin/diff ### ### Performing final hwloc configuration ### checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating hwloc/Makefile config.status: creating include/private/autogen/config.h config.status: creating include/hwloc/autogen/config.h config.status: executing depfiles commands config.status: executing libtool commands ----------------------------------------------------------------------------- Hwloc optional build support status (more details can be found above): Probe / display I/O devices: no Graphical output: no (disabled in embedded mode) XML input / output: basic Plugin support: no ----------------------------------------------------------------------------- cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-configure [ 41%] Performing build step for 'hwloc' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && make make[3]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' /bin/sh ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating hwloc/Makefile config.status: creating include/private/autogen/config.h config.status: include/private/autogen/config.h is unchanged config.status: creating include/hwloc/autogen/config.h config.status: include/hwloc/autogen/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands Making all in include make[4]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' Making all in hwloc make[4]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' CC topology.lo CC traversal.lo CC distances.lo CC memattrs.lo CC cpukinds.lo CC components.lo CC bind.lo CC bitmap.lo CC pci-common.lo CC diff.lo CC shmem.lo CC misc.lo CC base64.lo CC topology-noos.lo CC topology-synthetic.lo CC topology-xml.lo CC topology-xml-nolibxml.lo CC topology-linux.lo CC topology-hardwired.lo CC topology-x86.lo CCLD libhwloc_embedded.la make[4]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[4]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[3]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-build [ 47%] Performing install step for 'hwloc' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && make install make[3]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' Making install in include make[4]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[5]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[4]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' Making install in hwloc make[4]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make install-exec-hook make[6]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[6]: Nothing to be done for 'install-exec-hook'. make[6]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[4]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[4]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[5]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[4]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[3]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-install [ 52%] Completed 'hwloc' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles/hwloc-complete /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-done /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E remove_directory /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc/utils/lstopo make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 52%] Built target hwloc make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles/hw_detect.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 58%] Building C object CMakeFiles/hw_detect.dir/common/hw_detect.c.o /packages/gcc/12.2.0-nnbserq/bin/gcc -DUSING_R -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/hwloc-prefix/src/hwloc/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -std=gnu99 -MD -MT CMakeFiles/hw_detect.dir/common/hw_detect.c.o -MF CMakeFiles/hw_detect.dir/common/hw_detect.c.o.d -o CMakeFiles/hw_detect.dir/common/hw_detect.c.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common/hw_detect.c make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 58%] Built target hw_detect make -f CMakeFiles/detect_blas.dir/build.make CMakeFiles/detect_blas.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles/detect_blas.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' make -f CMakeFiles/detect_blas.dir/build.make CMakeFiles/detect_blas.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 64%] Building C object CMakeFiles/detect_blas.dir/common/detect_blas.c.o /packages/gcc/12.2.0-nnbserq/bin/gcc -DUSING_R -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -std=gnu99 -MD -MT CMakeFiles/detect_blas.dir/common/detect_blas.c.o -MF CMakeFiles/detect_blas.dir/common/detect_blas.c.o.d -o CMakeFiles/detect_blas.dir/common/detect_blas.c.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common/detect_blas.c make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 64%] Built target detect_blas make -f nmf/CMakeFiles/nmflib.dir/build.make nmf/CMakeFiles/nmflib.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nmf /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf/CMakeFiles/nmflib.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' make -f nmf/CMakeFiles/nmflib.dir/build.make nmf/CMakeFiles/nmflib.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [ 70%] Building CXX object nmf/CMakeFiles/nmflib.dir/nmf_lib.cpp.o cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/nmf_lib.cpp.o -MF CMakeFiles/nmflib.dir/nmf_lib.cpp.o.d -o CMakeFiles/nmflib.dir/nmf_lib.cpp.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nmf/nmf_lib.cpp [ 76%] Building CXX object nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o -MF CMakeFiles/nmflib.dir/bppnmf.cpp.o.d -o CMakeFiles/nmflib.dir/bppnmf.cpp.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nmf/bppnmf.cpp [ 82%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o -MF CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o.d -o CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls/nnls_lib.cpp [ 88%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o -MF CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o.d -o CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common/parseutils.cpp [ 94%] Building CXX object nmf/CMakeFiles/nmflib.dir/__/common/data.cpp.o cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-devel/include -I/projects/genomic-ml/R/R-devel/library/Rcpp/include -I/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-devel/library/RcppProgress/include -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/__/common/data.cpp.o -MF CMakeFiles/nmflib.dir/__/common/data.cpp.o.d -o CMakeFiles/nmflib.dir/__/common/data.cpp.o -c /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/planc/common/data.cpp [100%] Linking CXX shared library libnmflib.so cd /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/nmf && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_link_script CMakeFiles/nmflib.dir/link.txt --verbose=1 /packages/gcc/12.2.0-nnbserq/bin/g++ -fPIC -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fopenmp -Wl,-rpath,/packages/gcc/12.2.0-nnbserq/lib -L/packages/gcc/12.2.0-nnbserq/lib -Wl,-rpath,/packages/zstd/1.5.2-cs5ansz/lib -L/packages/zstd/1.5.2-cs5ansz/lib -Wl,-rpath,/packages/zlib/1.2.13-po6bkge/lib -L/packages/zlib/1.2.13-po6bkge/lib -Wl,-rpath,/packages/mpc/1.2.1-nnfoiwh/lib -L/packages/mpc/1.2.1-nnfoiwh/lib -Wl,-rpath,/packages/mpfr/4.1.0-yfsqqka/lib -L/packages/mpfr/4.1.0-yfsqqka/lib -Wl,-rpath,/packages/gmp/6.2.1-7ydtie6/lib -L/packages/gmp/6.2.1-7ydtie6/lib -shared -Wl,-soname,libnmflib.so -o libnmflib.so CMakeFiles/nmflib.dir/nmf_lib.cpp.o CMakeFiles/nmflib.dir/bppnmf.cpp.o CMakeFiles/nmflib.dir/__/nnls/nnls_lib.cpp.o CMakeFiles/nmflib.dir/__/common/parseutils.cpp.o CMakeFiles/nmflib.dir/__/common/data.cpp.o ../CMakeFiles/utils.dir/common/utils.cpp.o ../CMakeFiles/hw_detect.dir/common/hw_detect.c.o ../CMakeFiles/detect_blas.dir/common/detect_blas.c.o -Wl,-rpath,/projects/genomic-ml/.conda/envs/emacs1/lib:/home/th798/.conda/envs/emacs1/lib: /projects/genomic-ml/.conda/envs/emacs1/lib/libopenblas.so /projects/genomic-ml/.conda/envs/emacs1/lib/libopenblas.so -lpthread -lm -ldl ../hwloc-prefix/src/hwloc-build/hwloc/.libs/libhwloc_embedded.a /home/th798/.conda/envs/emacs1/lib/libhdf5.so /usr/lib64/librt.so /usr/lib64/libpthread.so /packages/zlib/1.2.13-po6bkge/lib/libz.so /usr/lib64/libdl.so -lm make[2]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' [100%] Built target nmflib make[1]: Leaving directory '/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_progress_start /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/CMakeFiles 0 -- Install configuration: "RelWithDebInfo" -- Installing: /tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/../libnmflib.so -- Set runtime path of "/tmp/th798/17408827/RtmpD3rtn2/R.INSTALLf64a554f77f90/RcppPlanc/src/build/../libnmflib.so" to "" ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++17 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rcppplanc_nmf.cpp -o rcppplanc_nmf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rcppplanc_nnls.cpp -o rcppplanc_nnls.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o RcppPlanc.so RcppExports.o rcppplanc_nmf.o rcppplanc_nnls.o -L./ -lnmflib -fopenmp -Wl,-rpath,$ORIGIN/../libs,--enable-new-dtags installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-RcppPlanc/00new/RcppPlanc/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RcppPlanc) * installing *source* package 'rliger' ... ** this is package 'rliger' version '2.2.0' ** package 'rliger' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ModularityOptimizer.cpp -o ModularityOptimizer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RModularityOptimizer.cpp -o RModularityOptimizer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c centoidAlign.cpp -o centoidAlign.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c data_processing.cpp -o data_processing.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c feature_mat.cpp -o feature_mat.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c objErr.cpp -o objErr.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quantile_norm.cpp -o quantile_norm.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snn.cpp -o snn.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DARMA_DONT_USE_OPENMP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wilcoxon.cpp -o wilcoxon.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rliger.so ModularityOptimizer.o RModularityOptimizer.o RcppExports.o centoidAlign.o data_processing.o feature_mat.o objErr.o quantile_norm.o snn.o wilcoxon.o -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-rliger/00new/rliger/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for 'rawData<-' with signature 'x="liger",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'normData<-' with signature 'x="liger",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'scaleData<-' with signature 'x="liger",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'scaleData<-' with signature 'x="liger",dataset="ANY",check="ANY",value="H5Group"': no definition for class "H5Group" in method for 'scaleUnsharedData<-' with signature 'x="liger",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'scaleUnsharedData<-' with signature 'x="liger",dataset="ANY",check="ANY",value="H5Group"': no definition for class "H5Group" in method for 'rawData<-' with signature 'x="ligerDataset",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'normData<-' with signature 'x="ligerDataset",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'scaleData<-' with signature 'x="ligerDataset",dataset="ANY",check="ANY",value="H5D"': no definition for class "H5D" in method for 'scaleData<-' with signature 'x="ligerDataset",dataset="ANY",check="ANY",value="H5Group"': no definition for class "H5Group" in method for 'scaleUnsharedData<-' with signature 'x="ligerDataset",dataset="missing",check="ANY",value="H5D"': no definition for class "H5D" in method for 'scaleUnsharedData<-' with signature 'x="ligerDataset",dataset="missing",check="ANY",value="H5Group"': no definition for class "H5Group" ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rliger) The downloaded source packages are in '/tmp/th798/17408827/Rtmp9B6X8L/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 541.617 47.995 633.680 > print(Sys.time()) [1] "2025-05-21 03:35:05 MST" > downloaded_packages <- file.path( + tempdir(), + "downloaded_packages") > dl.glob <- file.path( + downloaded_packages, + paste0(rev.dep,"_*.tar.gz")) > rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob)) > colnames(rev.dep.dl.row) <- c("pkg","path") > rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE) > pkg.Rcheck <- paste0(rev.dep, ".Rcheck") > > proj.dir <- "~/genomic-ml/data.table-revdeps" > source(file.path(proj.dir, "myStatus.R")) > Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]])) > dir.create(Rvers, showWarnings=FALSE) > Rcheck.list <- list() > for(dt.version.short in c("release", "master")){ + dt.tar.gz <- cargs[[dt.version.short]] + dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz) + print(Sys.time()) + install.packages(dt.tar.gz, repos=NULL) + print(Sys.time()) + check.cmd <- get_check_cmd(rev.dep.release.tar.gz) + system(check.cmd) + print(Sys.time()) + dest.Rcheck <- file.path( + Rvers, + paste0(dt.version, ".Rcheck")) + unlink(dest.Rcheck, recursive=TRUE) + file.rename(pkg.Rcheck, dest.Rcheck) + Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log") + } [1] "2025-05-21 03:35:05 MST" Installing package into '/tmp/th798/17408827/R-devel/1274/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.2' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2025-05-21 03:35:32 MST" * using log directory '/tmp/th798/17408827/R-devel/1274/scCustomize.Rcheck' * using R Under development (unstable) (2025-05-18 r88218) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * checking for file 'scCustomize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scCustomize' version '3.0.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'dittoSeq' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'scCustomize' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-05-21 03:42:09 MST" [1] "2025-05-21 03:42:09 MST" Installing package into '/tmp/th798/17408827/R-devel/1274/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.99' ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/17408827/R-devel/1274/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2025-05-21 03:42:40 MST" * using log directory '/tmp/th798/17408827/R-devel/1274/scCustomize.Rcheck' * using R Under development (unstable) (2025-05-18 r88218) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * checking for file 'scCustomize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scCustomize' version '3.0.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'dittoSeq' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'scCustomize' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-05-21 03:49:18 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$checking), + sig.diff.row$release, + rev.dep.release.tar.gz, + release.tag) + print(bisect.cmd) + bisect.out <- system(bisect.cmd, intern=TRUE) + cat(bisect.out,sep="\n") + if(is.null(attr(bisect.out,"status"))){ + first.bad.sha <- nc::capture_all_str( + bisect.out, + sha="[0-9a-f]+", + " is the first new commit")$sha + parent.cmd <- paste( + "cd ~/R/data.table && git log --pretty=%P -n 1", + first.bad.sha) + parent.sha <- system(parent.cmd, intern=TRUE) + sig.diff.dt[diff.i, first.bad.commit := first.bad.sha] + parent.msg <- paste0("parent=", parent.sha) + this.comment <- if(parent.sha==old.sha){ + paste(parent.msg, "same as git bisect old") + }else if(first.bad.sha==master.sha){ + paste("same as git bisect new=master,", parent.msg) + }else{ + parent.msg + } + sig.diff.dt[diff.i, comments := this.comment] + } + } + ## add CRAN column. + sig.diff.dt[, CRAN := { + flavor <- get_flavor(Rvers) + details <- data.table(flavor=unique(flavor))[, { + base <- "https://www.r-project.org/nosvn/R.check/" + u <- paste0(base, flavor, "/", rev.dep, "-00check.txt") + check.txt <- tempfile() + tryCatch({ + download.file(u, check.txt, quiet=TRUE) + }, error=function(e){ + NULL + }) + check.lines <- if(file.exists(check.txt)){ + readLines(check.txt,encoding="UTF-8") + }else{ + "" + } + repl.lines <- gsub("[\u2018\u2019]", "'", check.lines) + ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C. + myStatus(line.vec=repl.lines) + }, by=flavor] + select.dt <- data.table(flavor, checking) + details[select.dt, msg, on=.(flavor, checking)] + }] + dir.create(file.path(job.dir, Rvers)) + diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv") + data.table::fwrite(sig.diff.dt, diffs.csv) + print(sig.diff.dt) + } > WARNING: ignoring environment value of R_HOME R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "349", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2025-05-21/deps.csv", task.str = "1274", release = "/scratch/th798/data.table-revdeps/2025-05-21/data.table_release_1.17.2.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-05-21/data.table_master_1.17.99.6f05e4aedd8dc298214f4a296e308bc2a35a2827.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/17408827/R-release/1274" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/17408827/R-release/1274/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "scCustomize" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/17408827/R-release/1274/library" [2] "/projects/genomic-ml/R/R-release/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-05-21 03:49:25 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/17408827/R-release/1274/library' (as 'lib' is unspecified) also installing the dependencies 'easy.utils', 'sccore', 'hdf5r.Extra', 'leidenAlg', 'RcppPlanc', 'rliger' trying URL 'http://cloud.r-project.org/src/contrib/easy.utils_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/sccore_1.0.6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/hdf5r.Extra_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leidenAlg_1.1.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/RcppPlanc_2.0.10.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rliger_2.2.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/scCustomize_3.0.1.tar.gz' * installing *source* package 'easy.utils' ... ** this is package 'easy.utils' version '0.1.0' ** package 'easy.utils' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (easy.utils) * installing *source* package 'sccore' ... ** this is package 'sccore' version '1.0.6' ** package 'sccore' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:205, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Dense:1, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigenForward.h:28, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:5: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:174: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:165: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:271: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/SparseCore:37, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Sparse:26, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigenForward.h:29: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase >': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c graph_embedding.cpp -o graph_embedding.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c matrix_utils.cpp -o matrix_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c propagate_labels.cpp -o propagate_labels.o In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:205, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Dense:1, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigenForward.h:28, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigen.h:25, from propagate_labels.cpp:6: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:174: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:165: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:271: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/SparseCore:37, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Sparse:26, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigenForward.h:29: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase >': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' propagate_labels.cpp:87:7: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' propagate_labels.cpp:87:7: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from 'class Eigen::CwiseNullaryOp, Eigen::Matrix >' propagate_labels.cpp:87:30: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 1, -1, false>, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1, -1, false>, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 1, -1, false>, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, 1, -1, false> >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, 1, -1, false> >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MapBase.h:37:34: required from 'class Eigen::MapBase, 1, -1, false>, 0>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MapBase.h:223:34: required from 'class Eigen::MapBase, 1, -1, false>, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Block.h:329:7: required from 'class Eigen::internal::BlockImpl_dense, 1, -1, false, true>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Block.h:154:7: required from 'class Eigen::BlockImpl, 1, -1, false, Eigen::Dense>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Block.h:103:81: required from 'class Eigen::Block, 1, -1, false>' propagate_labels.cpp:153:19: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from 'class Eigen::CwiseNullaryOp, const Eigen::Matrix >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:38:28: required from 'struct Eigen::internal::traits, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, Eigen::Dense>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, Eigen::Dense>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Matrix, const Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Matrix, const Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::Matrix, const Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148:7: required from 'class Eigen::CwiseBinaryOpImpl, const Eigen::Matrix, const Eigen::Matrix, Eigen::Dense>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:7: required from 'class Eigen::CwiseBinaryOp, const Eigen::Matrix, const Eigen::Matrix >' propagate_labels.cpp:178:26: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::Matrix, const Eigen::Matrix > >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::Matrix, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/ArrayBase.h:39:34: required from 'class Eigen::ArrayBase, const Eigen::Matrix, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/ArrayWrapper.h:42:7: required from 'class Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >' propagate_labels.cpp:178:45: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/ArrayBase.h:39:34: required from 'class Eigen::ArrayBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:94:7: required from 'class Eigen::CwiseUnaryOpImpl, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > >, Eigen::Dense>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:7: required from 'class Eigen::CwiseUnaryOp, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > >' propagate_labels.cpp:178:51: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/ArrayWrapper.h:140:7: required from 'class Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >' propagate_labels.cpp:178:60: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, Eigen::Matrix >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, Eigen::Matrix > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseNullaryOp.h:60:7: required from 'class Eigen::CwiseNullaryOp, Eigen::Matrix >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/SelfCwiseBinaryOp.h:41:67: required from 'Derived& Eigen::DenseBase::operator/=(const Scalar&) [with Derived = Eigen::Block, 1, -1, false>; Scalar = double]' propagate_labels.cpp:173:52: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:94:7: required from 'class Eigen::CwiseUnaryOpImpl, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >, Eigen::Dense>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseUnaryOp.h:55:7: required from 'class Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Dot.h:244:22: required from 'static Eigen::internal::lpNorm_selector::RealScalar Eigen::internal::lpNorm_selector::run(const Eigen::MatrixBase&) [with Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; RealScalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Dot.h:269:52: required from 'typename Eigen::NumTraits::Scalar>::Real Eigen::MatrixBase::lpNorm() const [with int p = -1; Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; typename Eigen::NumTraits::Scalar>::Real = double; typename Eigen::internal::traits::Scalar = double]' propagate_labels.cpp:178:86: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:277: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: In instantiation of 'struct Eigen::internal::evaluator, 1, -1, false> >': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:100:8: required from 'struct Eigen::internal::evaluator, 1, -1, false> >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:739:41: required from 'struct Eigen::internal::binary_evaluator, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >, Eigen::internal::IndexBased, Eigen::internal::IndexBased, double, double>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:722:8: required from 'struct Eigen::internal::evaluator, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:774:20: required from 'void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block, 1, -1, false>; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Functor = add_assign_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:954:31: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block, 1, -1, false>; SrcXprType = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Functor = Eigen::internal::add_assign_op; Weak = void]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:890:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Block, 1, -1, false>; Src = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Func = add_assign_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:858:27: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen::Block, 1, -1, false>; Src = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Func = add_assign_op; typename enable_if<(! evaluator_assume_aliasing::value), void*>::type = void*; typename evaluator_traits::Shape = Eigen::DenseShape]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:177:18: required from 'Derived& Eigen::MatrixBase::operator+=(const Eigen::MatrixBase&) [with OtherDerived = Eigen::CwiseBinaryOp, const Eigen::Block, 1, -1, false>, const Eigen::CwiseNullaryOp, const Eigen::Matrix > >; Derived = Eigen::Block, 1, -1, false>]' propagate_labels.cpp:153:62: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:1071:54: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 1071 | PacketAlignment = unpacket_traits::alignment, | ^~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'Eigen::Index Eigen::internal::first_default_aligned(const Eigen::DenseBase&) [with Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; Eigen::Index = long int]': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Redux.h:243:63: required from 'static Eigen::internal::redux_impl::Scalar Eigen::internal::redux_impl::run(const Evaluator&, const Func&, const XprType&) [with XprType = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; Func = Eigen::internal::scalar_max_op; Evaluator = Eigen::internal::redux_evaluator, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > > >; Scalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Redux.h:418:56: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_max_op; Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; typename Eigen::internal::traits::Scalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Redux.h:448:25: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::maxCoeff() const [with int NaNPropagation = 0; Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; typename Eigen::internal::traits::Scalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:466:37: required from 'typename Eigen::internal::traits::Scalar Eigen::DenseBase::maxCoeff() const [with Derived = Eigen::CwiseUnaryOp, const Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > > >; typename Eigen::internal::traits::Scalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Dot.h:244:33: required from 'static Eigen::internal::lpNorm_selector::RealScalar Eigen::internal::lpNorm_selector::run(const Eigen::MatrixBase&) [with Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; RealScalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Dot.h:269:52: required from 'typename Eigen::NumTraits::Scalar>::Real Eigen::MatrixBase::lpNorm() const [with int p = -1; Derived = Eigen::MatrixWrapper, const Eigen::ArrayWrapper, const Eigen::Matrix, const Eigen::Matrix > > > >; typename Eigen::NumTraits::Scalar>::Real = double; typename Eigen::internal::traits::Scalar = double]' propagate_labels.cpp:178:86: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 654 | return internal::first_aligned::alignment),Derived>(m); | ^~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o sccore.so RcppExports.o graph_embedding.o matrix_utils.o propagate_labels.o -lpthread -L/home/th798/R/R-release/lib -lRlapack -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath installing to /tmp/th798/17408827/R-release/1274/library/00LOCK-sccore/00new/sccore/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading in method for 'embeddingPlot' with signature '"Seurat"': no definition for class "Seurat" Note: wrong number of arguments to '*' ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sccore) * installing *source* package 'scCustomize' ... ** this is package 'scCustomize' version '3.0.1' ** package 'scCustomize' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scCustomize) * installing *source* package 'hdf5r.Extra' ... ** this is package 'hdf5r.Extra' version '0.1.0' ** package 'hdf5r.Extra' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hdf5r.Extra) * installing *source* package 'leidenAlg' ... ** this is package 'leidenAlg' version '1.1.5' ** package 'leidenAlg' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -I"./rigraph/include" -I"./leidenalg/include" -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:205, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Dense:1, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigenForward.h:28, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigen.h:25, from RcppExports.cpp:5: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:46:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 46 | typedef eigen_packet_wrapper<__m128i, 0> Packet4i; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:47:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 47 | typedef eigen_packet_wrapper<__m128i, 1> Packet16b; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:49:39: warning: ignoring attributes on template argument '__m128' [-Wignored-attributes] 49 | template<> struct is_arithmetic<__m128> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:50:40: warning: ignoring attributes on template argument '__m128i' [-Wignored-attributes] 50 | template<> struct is_arithmetic<__m128i> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:51:40: warning: ignoring attributes on template argument '__m128d' [-Wignored-attributes] 51 | template<> struct is_arithmetic<__m128d> { enum { value = true }; }; | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:222:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 222 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:228:43: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 228 | template<> struct unpacket_traits { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1124:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 1124 | ptranspose(PacketBlock& kernel) { | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:1129:34: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 1129 | ptranspose(PacketBlock& kernel) { | ^ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:174: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet4f' {aka '__m128'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:173:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 173 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet2cf,Packet4f) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:16:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 16 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/Default/ConjHelper.h:29:60: warning: ignoring attributes on template argument 'Eigen::internal::Packet2d' {aka '__m128d'} [-Wignored-attributes] 29 | struct conj_helper { \ | ^ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/arch/SSE/Complex.h:298:1: note: in expansion of macro 'EIGEN_MAKE_CONJ_HELPER_CPLX_REAL' 298 | EIGEN_MAKE_CONJ_HELPER_CPLX_REAL(Packet1cd,Packet2d) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:165: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:24:46: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(4) float>::half' {aka '__m128'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Core:271: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:27:3: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h: In instantiation of 'struct Eigen::internal::find_best_packet': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:22:57: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:266:49: required from 'struct Eigen::internal::traits >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:98:47: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:44: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 190 | bool Stop = Size==Dynamic || (Size%unpacket_traits::size)==0 || is_same::half>::value> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:190:83: warning: ignoring attributes on template argument 'Eigen::internal::unpacket_traits<__vector(2) double>::half' {aka '__m128d'} [-Wignored-attributes] /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/util/XprHelper.h:208:88: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 208 | typedef typename find_best_packet_helper::type>::type type; | ^~~~ /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h: In instantiation of 'class Eigen::DenseCoeffsBase, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:302:7: required from 'class Eigen::DenseCoeffsBase, 1>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:555:7: required from 'class Eigen::DenseCoeffsBase, 3>' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34: required from 'class Eigen::DenseBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34: required from 'class Eigen::MatrixBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:98:7: required from 'class Eigen::PlainObjectBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/Matrix.h:178:7: required from 'class Eigen::Matrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:46:50: required from 'class Eigen::QuaternionBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/Quaternion.h:273:7: required from 'class Eigen::Quaternion' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Geometry/arch/Geometry_SIMD.h:102:3: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:56:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 56 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ In file included from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/SparseCore:37, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/Sparse:26, from /projects/genomic-ml/R/R-release/library/RcppEigen/include/RcppEigenForward.h:29: /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h: In instantiation of 'class Eigen::SparseMatrixBase >': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:36:7: required from 'class Eigen::SparseCompressedBase >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:96:7: required from 'class Eigen::SparseMatrix' /projects/genomic-ml/R/R-release/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h:61:25: required from here /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrixBase.h:47:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__m128d'} [-Wignored-attributes] 47 | >::type PacketReturnType; | ^~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"../inst/include" -I"./rigraph/include" -I"./leidenalg/include" -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c leiden.cpp -o leiden.o make[1]: Entering directory '/tmp/th798/17408827/RtmpVczuMa/R.INSTALL112c6f5e5ceebf/leidenAlg/src/rigraph' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/betweenness.c -o core/centrality/betweenness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/centrality_other.c -o core/centrality/centrality_other.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/centralization.c -o core/centrality/centralization.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/closeness.c -o core/centrality/closeness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/centrality/coreness.c -o core/centrality/coreness.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_base_graph.cpp -o core/centrality/prpack/prpack_base_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_igraph_graph.cpp -o core/centrality/prpack/prpack_igraph_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o core/centrality/prpack/prpack_preprocessed_ge_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o core/centrality/prpack/prpack_preprocessed_gs_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o core/centrality/prpack/prpack_preprocessed_scc_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o core/centrality/prpack/prpack_preprocessed_schur_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_result.cpp -o core/centrality/prpack/prpack_result.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_solver.cpp -o core/centrality/prpack/prpack_solver.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/centrality/prpack/prpack_utils.cpp -o core/centrality/prpack/prpack_utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer/cliquer.c -o core/cliques/cliquer/cliquer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer/cliquer_graph.c -o core/cliques/cliquer/cliquer_graph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer/reorder.c -o core/cliques/cliquer/reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliquer_wrapper.c -o core/cliques/cliquer_wrapper.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/cliques.c -o core/cliques/cliques.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/glet.c -o core/cliques/glet.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/cliques/maximal_cliques.c -o core/cliques/maximal_cliques.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/community_misc.c -o core/community/community_misc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/edge_betweenness.c -o core/community/edge_betweenness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/fast_modularity.c -o core/community/fast_modularity.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/fluid.c -o core/community/fluid.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap.cc -o core/community/infomap/infomap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap_FlowGraph.cc -o core/community/infomap/infomap_FlowGraph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap_Greedy.cc -o core/community/infomap/infomap_Greedy.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/infomap/infomap_Node.cc -o core/community/infomap/infomap_Node.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/label_propagation.c -o core/community/label_propagation.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/leading_eigenvector.c -o core/community/leading_eigenvector.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/leiden.c -o core/community/leiden.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/louvain.c -o core/community/louvain.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/modularity.c -o core/community/modularity.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/community/optimal_modularity.c -o core/community/optimal_modularity.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/NetDataTypes.cpp -o core/community/spinglass/NetDataTypes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/NetRoutines.cpp -o core/community/spinglass/NetRoutines.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/clustertool.cpp -o core/community/spinglass/clustertool.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/spinglass/pottsmodel_2.cpp -o core/community/spinglass/pottsmodel_2.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap.cpp -o core/community/walktrap/walktrap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap_communities.cpp -o core/community/walktrap/walktrap_communities.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap_graph.cpp -o core/community/walktrap/walktrap_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/community/walktrap/walktrap_heap.cpp -o core/community/walktrap/walktrap_heap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/connectivity/cohesive_blocks.c -o core/connectivity/cohesive_blocks.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/connectivity/components.c -o core/connectivity/components.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/connectivity/separators.c -o core/connectivity/separators.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/adjacency.c -o core/constructors/adjacency.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/atlas.c -o core/constructors/atlas.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/basic_constructors.c -o core/constructors/basic_constructors.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/de_bruijn.c -o core/constructors/de_bruijn.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/famous.c -o core/constructors/famous.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/full.c -o core/constructors/full.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/kautz.c -o core/constructors/kautz.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/lcf.c -o core/constructors/lcf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/linegraph.c -o core/constructors/linegraph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/prufer.c -o core/constructors/prufer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/constructors/regular.c -o core/constructors/regular.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/array.c -o core/core/array.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/buckets.c -o core/core/buckets.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/cutheap.c -o core/core/cutheap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/dqueue.c -o core/core/dqueue.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/error.c -o core/core/error.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/estack.c -o core/core/estack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/fixed_vectorlist.c -o core/core/fixed_vectorlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/grid.c -o core/core/grid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/heap.c -o core/core/heap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/indheap.c -o core/core/indheap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/interruption.c -o core/core/interruption.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/marked_queue.c -o core/core/marked_queue.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/matrix.c -o core/core/matrix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/memory.c -o core/core/memory.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/printing.c -o core/core/printing.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/progress.c -o core/core/progress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/psumtree.c -o core/core/psumtree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/set.c -o core/core/set.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/sparsemat.c -o core/core/sparsemat.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/spmatrix.c -o core/core/spmatrix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/stack.c -o core/core/stack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/statusbar.c -o core/core/statusbar.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/strvector.c -o core/core/strvector.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/trie.c -o core/core/trie.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/vector.c -o core/core/vector.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/core/vector_ptr.c -o core/core/vector_ptr.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/flow/flow.c -o core/flow/flow.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/flow/st-cuts.c -o core/flow/st-cuts.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/barabasi.c -o core/games/barabasi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/callaway_traits.c -o core/games/callaway_traits.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/citations.c -o core/games/citations.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/correlated.c -o core/games/correlated.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/degree_sequence.c -o core/games/degree_sequence.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_box_list.cpp -o core/games/degree_sequence_vl/gengraph_box_list.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_degree_sequence.cpp -o core/games/degree_sequence_vl/gengraph_degree_sequence.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_graph_molloy_hash.cpp -o core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.cpp -o core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_mr-connected.cpp -o core/games/degree_sequence_vl/gengraph_mr-connected.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_powerlaw.cpp -o core/games/degree_sequence_vl/gengraph_powerlaw.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/games/degree_sequence_vl/gengraph_random.cpp -o core/games/degree_sequence_vl/gengraph_random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/dotproduct.c -o core/games/dotproduct.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/erdos_renyi.c -o core/games/erdos_renyi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/establishment.c -o core/games/establishment.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/forestfire.c -o core/games/forestfire.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/grg.c -o core/games/grg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/growing_random.c -o core/games/growing_random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/islands.c -o core/games/islands.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/k_regular.c -o core/games/k_regular.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/preference.c -o core/games/preference.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/recent_degree.c -o core/games/recent_degree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/sbm.c -o core/games/sbm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/static_fitness.c -o core/games/static_fitness.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/tree.c -o core/games/tree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/games/watts_strogatz.c -o core/games/watts_strogatz.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/adjlist.c -o core/graph/adjlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/attributes.c -o core/graph/attributes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/basic_query.c -o core/graph/basic_query.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/cattributes.c -o core/graph/cattributes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/iterators.c -o core/graph/iterators.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/type_indexededgelist.c -o core/graph/type_indexededgelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/graph/visitors.c -o core/graph/visitors.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/hrg/hrg.cc -o core/hrg/hrg.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/hrg/hrg_types.cc -o core/hrg/hrg_types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/glpk_support.c -o core/internal/glpk_support.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/hacks.c -o core/internal/hacks.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/lsap.c -o core/internal/lsap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/qsort.c -o core/internal/qsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/qsort_r.c -o core/internal/qsort_r.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/internal/zeroin.c -o core/internal/zeroin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dimacs.c -o core/io/dimacs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dl-lexer.c -o core/io/dl-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dl-parser.c -o core/io/dl-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dl.c -o core/io/dl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/dot.c -o core/io/dot.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/edgelist.c -o core/io/edgelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml-lexer.c -o core/io/gml-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml-parser.c -o core/io/gml-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml-tree.c -o core/io/gml-tree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/gml.c -o core/io/gml.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/graphdb.c -o core/io/graphdb.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/graphml.c -o core/io/graphml.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/leda.c -o core/io/leda.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/lgl-lexer.c -o core/io/lgl-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/lgl-parser.c -o core/io/lgl-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/lgl.c -o core/io/lgl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/ncol-lexer.c -o core/io/ncol-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/ncol-parser.c -o core/io/ncol-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/ncol.c -o core/io/ncol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/pajek-lexer.c -o core/io/pajek-lexer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/pajek-parser.c -o core/io/pajek-parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/io/pajek.c -o core/io/pajek.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss.cc -o core/isomorphism/bliss.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/defs.cc -o core/isomorphism/bliss/defs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/graph.cc -o core/isomorphism/bliss/graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/heap.cc -o core/isomorphism/bliss/heap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/orbit.cc -o core/isomorphism/bliss/orbit.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/partition.cc -o core/isomorphism/bliss/partition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/uintseqhash.cc -o core/isomorphism/bliss/uintseqhash.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/isomorphism/bliss/utils.cc -o core/isomorphism/bliss/utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/isoclasses.c -o core/isomorphism/isoclasses.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/isomorphism_misc.c -o core/isomorphism/isomorphism_misc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/lad.c -o core/isomorphism/lad.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/queries.c -o core/isomorphism/queries.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/isomorphism/vf2.c -o core/isomorphism/vf2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/circular.c -o core/layout/circular.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/davidson_harel.c -o core/layout/davidson_harel.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/DensityGrid.cpp -o core/layout/drl/DensityGrid.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/DensityGrid_3d.cpp -o core/layout/drl/DensityGrid_3d.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_graph.cpp -o core/layout/drl/drl_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_graph_3d.cpp -o core/layout/drl/drl_graph_3d.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_layout.cpp -o core/layout/drl/drl_layout.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_layout_3d.cpp -o core/layout/drl/drl_layout_3d.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/layout/drl/drl_parse.cpp -o core/layout/drl/drl_parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/fruchterman_reingold.c -o core/layout/fruchterman_reingold.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/gem.c -o core/layout/gem.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/graphopt.c -o core/layout/graphopt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/kamada_kawai.c -o core/layout/kamada_kawai.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/large_graph.c -o core/layout/large_graph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/layout_bipartite.c -o core/layout/layout_bipartite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/layout_grid.c -o core/layout/layout_grid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/layout_random.c -o core/layout/layout_random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/mds.c -o core/layout/mds.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/merge_dla.c -o core/layout/merge_dla.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/merge_grid.c -o core/layout/merge_grid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/reingold_tilford.c -o core/layout/reingold_tilford.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/layout/sugiyama.c -o core/layout/sugiyama.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/arpack.c -o core/linalg/arpack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/blas.c -o core/linalg/blas.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/eigen.c -o core/linalg/eigen.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/linalg/lapack.c -o core/linalg/lapack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/math/bfgs.c -o core/math/bfgs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/math/complex.c -o core/math/complex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/math/utils.c -o core/math/utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/bipartite.c -o core/misc/bipartite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/chordality.c -o core/misc/chordality.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/cocitation.c -o core/misc/cocitation.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/coloring.c -o core/misc/coloring.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/conversion.c -o core/misc/conversion.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c core/misc/degree_sequence.cpp -o core/misc/degree_sequence.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/embedding.c -o core/misc/embedding.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/feedback_arc_set.c -o core/misc/feedback_arc_set.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/graphicality.c -o core/misc/graphicality.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/matching.c -o core/misc/matching.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/microscopic_update.c -o core/misc/microscopic_update.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/mixing.c -o core/misc/mixing.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/motifs.c -o core/misc/motifs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/other.c -o core/misc/other.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/scan.c -o core/misc/scan.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/sir.c -o core/misc/sir.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/misc/spanning_trees.c -o core/misc/spanning_trees.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/add_edge.c -o core/operators/add_edge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/complementer.c -o core/operators/complementer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/compose.c -o core/operators/compose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/connect_neighborhood.c -o core/operators/connect_neighborhood.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/contract.c -o core/operators/contract.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/difference.c -o core/operators/difference.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/disjoint_union.c -o core/operators/disjoint_union.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/intersection.c -o core/operators/intersection.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/misc_internal.c -o core/operators/misc_internal.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/permute.c -o core/operators/permute.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/rewire.c -o core/operators/rewire.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/rewire_edges.c -o core/operators/rewire_edges.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/simplify.c -o core/operators/simplify.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/subgraph.c -o core/operators/subgraph.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/operators/union.c -o core/operators/union.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/all_shortest_paths.c -o core/paths/all_shortest_paths.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/bellman_ford.c -o core/paths/bellman_ford.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/dijkstra.c -o core/paths/dijkstra.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/distances.c -o core/paths/distances.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/eulerian.c -o core/paths/eulerian.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/histogram.c -o core/paths/histogram.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/johnson.c -o core/paths/johnson.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/random_walk.c -o core/paths/random_walk.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/shortest_paths.c -o core/paths/shortest_paths.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/simple_paths.c -o core/paths/simple_paths.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/paths/unweighted.c -o core/paths/unweighted.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/basic_properties.c -o core/properties/basic_properties.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/constraint.c -o core/properties/constraint.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/convergence_degree.c -o core/properties/convergence_degree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/dag.c -o core/properties/dag.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/degrees.c -o core/properties/degrees.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/girth.c -o core/properties/girth.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/loops.c -o core/properties/loops.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/multiplicity.c -o core/properties/multiplicity.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/neighborhood.c -o core/properties/neighborhood.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/spectral.c -o core/properties/spectral.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/trees.c -o core/properties/trees.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/properties/triangles.c -o core/properties/triangles.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/random/random.c -o core/random/random.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg.c -o core/scg/scg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_approximate_methods.c -o core/scg/scg_approximate_methods.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_exact_scg.c -o core/scg/scg_exact_scg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_kmeans.c -o core/scg/scg_kmeans.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_optimal_method.c -o core/scg/scg_optimal_method.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/scg/scg_utils.c -o core/scg/scg_utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c core/version.c -o core/version.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_add.c -o vendor/cs/cs_add.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_amd.c -o vendor/cs/cs_amd.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_chol.c -o vendor/cs/cs_chol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_cholsol.c -o vendor/cs/cs_cholsol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_compress.c -o vendor/cs/cs_compress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_counts.c -o vendor/cs/cs_counts.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_cumsum.c -o vendor/cs/cs_cumsum.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dfs.c -o vendor/cs/cs_dfs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dmperm.c -o vendor/cs/cs_dmperm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_droptol.c -o vendor/cs/cs_droptol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dropzeros.c -o vendor/cs/cs_dropzeros.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_dupl.c -o vendor/cs/cs_dupl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_entry.c -o vendor/cs/cs_entry.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_ereach.c -o vendor/cs/cs_ereach.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_etree.c -o vendor/cs/cs_etree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_fkeep.c -o vendor/cs/cs_fkeep.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_gaxpy.c -o vendor/cs/cs_gaxpy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_happly.c -o vendor/cs/cs_happly.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_house.c -o vendor/cs/cs_house.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_ipvec.c -o vendor/cs/cs_ipvec.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_leaf.c -o vendor/cs/cs_leaf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_load.c -o vendor/cs/cs_load.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_lsolve.c -o vendor/cs/cs_lsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_ltsolve.c -o vendor/cs/cs_ltsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_lu.c -o vendor/cs/cs_lu.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_lusol.c -o vendor/cs/cs_lusol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_malloc.c -o vendor/cs/cs_malloc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_maxtrans.c -o vendor/cs/cs_maxtrans.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_multiply.c -o vendor/cs/cs_multiply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_norm.c -o vendor/cs/cs_norm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_permute.c -o vendor/cs/cs_permute.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_pinv.c -o vendor/cs/cs_pinv.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_post.c -o vendor/cs/cs_post.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_print.c -o vendor/cs/cs_print.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_pvec.c -o vendor/cs/cs_pvec.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_qr.c -o vendor/cs/cs_qr.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_qrsol.c -o vendor/cs/cs_qrsol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_randperm.c -o vendor/cs/cs_randperm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_reach.c -o vendor/cs/cs_reach.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_scatter.c -o vendor/cs/cs_scatter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_scc.c -o vendor/cs/cs_scc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_schol.c -o vendor/cs/cs_schol.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_spsolve.c -o vendor/cs/cs_spsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_sqr.c -o vendor/cs/cs_sqr.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_symperm.c -o vendor/cs/cs_symperm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_tdfs.c -o vendor/cs/cs_tdfs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_transpose.c -o vendor/cs/cs_transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_updown.c -o vendor/cs/cs_updown.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_usolve.c -o vendor/cs/cs_usolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_util.c -o vendor/cs/cs_util.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/cs/cs_utsolve.c -o vendor/cs/cs_utsolve.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/mini-gmp/mini-gmp.c -o vendor/mini-gmp/mini-gmp.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/gss.c -o vendor/plfit/gss.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/hzeta.c -o vendor/plfit/hzeta.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/kolmogorov.c -o vendor/plfit/kolmogorov.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/lbfgs.c -o vendor/plfit/lbfgs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/mt.c -o vendor/plfit/mt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/options.c -o vendor/plfit/options.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/platform.c -o vendor/plfit/platform.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/plfit.c -o vendor/plfit/plfit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/plfit_error.c -o vendor/plfit/plfit_error.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/rbinom.c -o vendor/plfit/rbinom.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/plfit/sampling.c -o vendor/plfit/sampling.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/second.f -o vendor/arpack/second.o /packages/gcc/12.2.0-nnbserq/bin/gfortran -fpic -g -O2 -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Color.cpp -o vendor/simpleraytracer/Color.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Light.cpp -o vendor/simpleraytracer/Light.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Point.cpp -o vendor/simpleraytracer/Point.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/RIgraphRay.cpp -o vendor/simpleraytracer/RIgraphRay.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Ray.cpp -o vendor/simpleraytracer/Ray.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/RayTracer.cpp -o vendor/simpleraytracer/RayTracer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/RayVector.cpp -o vendor/simpleraytracer/RayVector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Shape.cpp -o vendor/simpleraytracer/Shape.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Sphere.cpp -o vendor/simpleraytracer/Sphere.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/Triangle.cpp -o vendor/simpleraytracer/Triangle.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vendor/simpleraytracer/unit_limiter.cpp -o vendor/simpleraytracer/unit_limiter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/R.c -o vendor/uuid/R.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/clear.c -o vendor/uuid/clear.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/compare.c -o vendor/uuid/compare.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/copy.c -o vendor/uuid/copy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/gen_uuid.c -o vendor/uuid/gen_uuid.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/isnull.c -o vendor/uuid/isnull.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/pack.c -o vendor/uuid/pack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/parse.c -o vendor/uuid/parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/unpack.c -o vendor/uuid/unpack.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c vendor/uuid/unparse.c -o vendor/uuid/unparse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c rinterface.c -o rinterface.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c rinterface_extra.c -o rinterface_extra.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c rrandom.c -o rrandom.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -I"./include" -I"../rigraph/include" -fpic -O3 -c lazyeval.c -o lazyeval.o ar rvs ../librigraph.a core/centrality/betweenness.o core/centrality/centrality_other.o core/centrality/centralization.o core/centrality/closeness.o core/centrality/coreness.o core/centrality/prpack/prpack_base_graph.o core/centrality/prpack/prpack_igraph_graph.o core/centrality/prpack/prpack_preprocessed_ge_graph.o core/centrality/prpack/prpack_preprocessed_gs_graph.o core/centrality/prpack/prpack_preprocessed_scc_graph.o core/centrality/prpack/prpack_preprocessed_schur_graph.o core/centrality/prpack/prpack_result.o core/centrality/prpack/prpack_solver.o core/centrality/prpack/prpack_utils.o core/cliques/cliquer/cliquer.o core/cliques/cliquer/cliquer_graph.o core/cliques/cliquer/reorder.o core/cliques/cliquer_wrapper.o core/cliques/cliques.o core/cliques/glet.o core/cliques/maximal_cliques.o core/community/community_misc.o core/community/edge_betweenness.o core/community/fast_modularity.o core/community/fluid.o core/community/infomap/infomap.o core/community/infomap/infomap_FlowGraph.o core/community/infomap/infomap_Greedy.o core/community/infomap/infomap_Node.o core/community/label_propagation.o core/community/leading_eigenvector.o core/community/leiden.o core/community/louvain.o core/community/modularity.o core/community/optimal_modularity.o core/community/spinglass/NetDataTypes.o core/community/spinglass/NetRoutines.o core/community/spinglass/clustertool.o core/community/spinglass/pottsmodel_2.o core/community/walktrap/walktrap.o core/community/walktrap/walktrap_communities.o core/community/walktrap/walktrap_graph.o core/community/walktrap/walktrap_heap.o core/connectivity/cohesive_blocks.o core/connectivity/components.o core/connectivity/separators.o core/constructors/adjacency.o core/constructors/atlas.o core/constructors/basic_constructors.o core/constructors/de_bruijn.o core/constructors/famous.o core/constructors/full.o core/constructors/kautz.o core/constructors/lcf.o core/constructors/linegraph.o core/constructors/prufer.o core/constructors/regular.o core/core/array.o core/core/buckets.o core/core/cutheap.o core/core/dqueue.o core/core/error.o core/core/estack.o core/core/fixed_vectorlist.o core/core/grid.o core/core/heap.o core/core/indheap.o core/core/interruption.o core/core/marked_queue.o core/core/matrix.o core/core/memory.o core/core/printing.o core/core/progress.o core/core/psumtree.o core/core/set.o core/core/sparsemat.o core/core/spmatrix.o core/core/stack.o core/core/statusbar.o core/core/strvector.o core/core/trie.o core/core/vector.o core/core/vector_ptr.o core/flow/flow.o core/flow/st-cuts.o core/games/barabasi.o core/games/callaway_traits.o core/games/citations.o core/games/correlated.o core/games/degree_sequence.o core/games/degree_sequence_vl/gengraph_box_list.o core/games/degree_sequence_vl/gengraph_degree_sequence.o core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o core/games/degree_sequence_vl/gengraph_mr-connected.o core/games/degree_sequence_vl/gengraph_powerlaw.o core/games/degree_sequence_vl/gengraph_random.o core/games/dotproduct.o core/games/erdos_renyi.o core/games/establishment.o core/games/forestfire.o core/games/grg.o core/games/growing_random.o core/games/islands.o core/games/k_regular.o core/games/preference.o core/games/recent_degree.o core/games/sbm.o core/games/static_fitness.o core/games/tree.o core/games/watts_strogatz.o core/graph/adjlist.o core/graph/attributes.o core/graph/basic_query.o core/graph/cattributes.o core/graph/iterators.o core/graph/type_indexededgelist.o core/graph/visitors.o core/hrg/hrg.o core/hrg/hrg_types.o core/internal/glpk_support.o core/internal/hacks.o core/internal/lsap.o core/internal/qsort.o core/internal/qsort_r.o core/internal/zeroin.o core/io/dimacs.o core/io/dl-lexer.o core/io/dl-parser.o core/io/dl.o core/io/dot.o core/io/edgelist.o core/io/gml-lexer.o core/io/gml-parser.o core/io/gml-tree.o core/io/gml.o core/io/graphdb.o core/io/graphml.o core/io/leda.o core/io/lgl-lexer.o core/io/lgl-parser.o core/io/lgl.o core/io/ncol-lexer.o core/io/ncol-parser.o core/io/ncol.o core/io/pajek-lexer.o core/io/pajek-parser.o core/io/pajek.o core/isomorphism/bliss.o core/isomorphism/bliss/defs.o core/isomorphism/bliss/graph.o core/isomorphism/bliss/heap.o core/isomorphism/bliss/orbit.o core/isomorphism/bliss/partition.o core/isomorphism/bliss/uintseqhash.o core/isomorphism/bliss/utils.o core/isomorphism/isoclasses.o core/isomorphism/isomorphism_misc.o core/isomorphism/lad.o core/isomorphism/queries.o core/isomorphism/vf2.o core/layout/circular.o core/layout/davidson_harel.o core/layout/drl/DensityGrid.o core/layout/drl/DensityGrid_3d.o core/layout/drl/drl_graph.o core/layout/drl/drl_graph_3d.o core/layout/drl/drl_layout.o core/layout/drl/drl_layout_3d.o core/layout/drl/drl_parse.o core/layout/fruchterman_reingold.o core/layout/gem.o core/layout/graphopt.o core/layout/kamada_kawai.o core/layout/large_graph.o core/layout/layout_bipartite.o core/layout/layout_grid.o core/layout/layout_random.o core/layout/mds.o core/layout/merge_dla.o core/layout/merge_grid.o core/layout/reingold_tilford.o core/layout/sugiyama.o core/linalg/arpack.o core/linalg/blas.o core/linalg/eigen.o core/linalg/lapack.o core/math/bfgs.o core/math/complex.o core/math/utils.o core/misc/bipartite.o core/misc/chordality.o core/misc/cocitation.o core/misc/coloring.o core/misc/conversion.o core/misc/degree_sequence.o core/misc/embedding.o core/misc/feedback_arc_set.o core/misc/graphicality.o core/misc/matching.o core/misc/microscopic_update.o core/misc/mixing.o core/misc/motifs.o core/misc/other.o core/misc/scan.o core/misc/sir.o core/misc/spanning_trees.o core/operators/add_edge.o core/operators/complementer.o core/operators/compose.o core/operators/connect_neighborhood.o core/operators/contract.o core/operators/difference.o core/operators/disjoint_union.o core/operators/intersection.o core/operators/misc_internal.o core/operators/permute.o core/operators/rewire.o core/operators/rewire_edges.o core/operators/simplify.o core/operators/subgraph.o core/operators/union.o core/paths/all_shortest_paths.o core/paths/bellman_ford.o core/paths/dijkstra.o core/paths/distances.o core/paths/eulerian.o core/paths/histogram.o core/paths/johnson.o core/paths/random_walk.o core/paths/shortest_paths.o core/paths/simple_paths.o core/paths/unweighted.o core/properties/basic_properties.o core/properties/constraint.o core/properties/convergence_degree.o core/properties/dag.o core/properties/degrees.o core/properties/girth.o core/properties/loops.o core/properties/multiplicity.o core/properties/neighborhood.o core/properties/spectral.o core/properties/trees.o core/properties/triangles.o core/random/random.o core/scg/scg.o core/scg/scg_approximate_methods.o core/scg/scg_exact_scg.o core/scg/scg_kmeans.o core/scg/scg_optimal_method.o core/scg/scg_utils.o core/version.o vendor/cs/cs_add.o vendor/cs/cs_amd.o vendor/cs/cs_chol.o vendor/cs/cs_cholsol.o vendor/cs/cs_compress.o vendor/cs/cs_counts.o vendor/cs/cs_cumsum.o vendor/cs/cs_dfs.o vendor/cs/cs_dmperm.o vendor/cs/cs_droptol.o vendor/cs/cs_dropzeros.o vendor/cs/cs_dupl.o vendor/cs/cs_entry.o vendor/cs/cs_ereach.o vendor/cs/cs_etree.o vendor/cs/cs_fkeep.o vendor/cs/cs_gaxpy.o vendor/cs/cs_happly.o vendor/cs/cs_house.o vendor/cs/cs_ipvec.o vendor/cs/cs_leaf.o vendor/cs/cs_load.o vendor/cs/cs_lsolve.o vendor/cs/cs_ltsolve.o vendor/cs/cs_lu.o vendor/cs/cs_lusol.o vendor/cs/cs_malloc.o vendor/cs/cs_maxtrans.o vendor/cs/cs_multiply.o vendor/cs/cs_norm.o vendor/cs/cs_permute.o vendor/cs/cs_pinv.o vendor/cs/cs_post.o vendor/cs/cs_print.o vendor/cs/cs_pvec.o vendor/cs/cs_qr.o vendor/cs/cs_qrsol.o vendor/cs/cs_randperm.o vendor/cs/cs_reach.o vendor/cs/cs_scatter.o vendor/cs/cs_scc.o vendor/cs/cs_schol.o vendor/cs/cs_spsolve.o vendor/cs/cs_sqr.o vendor/cs/cs_symperm.o vendor/cs/cs_tdfs.o vendor/cs/cs_transpose.o vendor/cs/cs_updown.o vendor/cs/cs_usolve.o vendor/cs/cs_util.o vendor/cs/cs_utsolve.o vendor/mini-gmp/mini-gmp.o vendor/plfit/gss.o vendor/plfit/hzeta.o vendor/plfit/kolmogorov.o vendor/plfit/lbfgs.o vendor/plfit/mt.o vendor/plfit/options.o vendor/plfit/platform.o vendor/plfit/plfit.o vendor/plfit/plfit_error.o vendor/plfit/rbinom.o vendor/plfit/sampling.o vendor/arpack/dgetv0.o vendor/arpack/dlaqrb.o vendor/arpack/dmout.o vendor/arpack/dnaitr.o vendor/arpack/dnapps.o vendor/arpack/dnaup2.o vendor/arpack/dnaupd.o vendor/arpack/dnconv.o vendor/arpack/dneigh.o vendor/arpack/dneupd.o vendor/arpack/dngets.o vendor/arpack/dsaitr.o vendor/arpack/dsapps.o vendor/arpack/dsaup2.o vendor/arpack/dsaupd.o vendor/arpack/dsconv.o vendor/arpack/dseigt.o vendor/arpack/dsesrt.o vendor/arpack/dseupd.o vendor/arpack/dsgets.o vendor/arpack/dsortc.o vendor/arpack/dsortr.o vendor/arpack/dstatn.o vendor/arpack/dstats.o vendor/arpack/dstqrb.o vendor/arpack/dvout.o vendor/arpack/ivout.o vendor/arpack/second.o vendor/arpack/wrap.o vendor/simpleraytracer/Color.o vendor/simpleraytracer/Light.o vendor/simpleraytracer/Point.o vendor/simpleraytracer/RIgraphRay.o vendor/simpleraytracer/Ray.o vendor/simpleraytracer/RayTracer.o vendor/simpleraytracer/RayVector.o vendor/simpleraytracer/Shape.o vendor/simpleraytracer/Sphere.o vendor/simpleraytracer/Triangle.o vendor/simpleraytracer/unit_limiter.o vendor/uuid/R.o vendor/uuid/clear.o vendor/uuid/compare.o vendor/uuid/copy.o vendor/uuid/gen_uuid.o vendor/uuid/isnull.o vendor/uuid/pack.o vendor/uuid/parse.o vendor/uuid/unpack.o vendor/uuid/unparse.o rinterface.o rinterface_extra.o rrandom.o lazyeval.o ar: creating ../librigraph.a a - core/centrality/betweenness.o a - core/centrality/centrality_other.o a - core/centrality/centralization.o a - core/centrality/closeness.o a - core/centrality/coreness.o a - core/centrality/prpack/prpack_base_graph.o a - core/centrality/prpack/prpack_igraph_graph.o a - core/centrality/prpack/prpack_preprocessed_ge_graph.o a - core/centrality/prpack/prpack_preprocessed_gs_graph.o a - core/centrality/prpack/prpack_preprocessed_scc_graph.o a - core/centrality/prpack/prpack_preprocessed_schur_graph.o a - core/centrality/prpack/prpack_result.o a - core/centrality/prpack/prpack_solver.o a - core/centrality/prpack/prpack_utils.o a - core/cliques/cliquer/cliquer.o a - core/cliques/cliquer/cliquer_graph.o a - core/cliques/cliquer/reorder.o a - core/cliques/cliquer_wrapper.o a - core/cliques/cliques.o a - core/cliques/glet.o a - core/cliques/maximal_cliques.o a - core/community/community_misc.o a - core/community/edge_betweenness.o a - core/community/fast_modularity.o a - core/community/fluid.o a - core/community/infomap/infomap.o a - core/community/infomap/infomap_FlowGraph.o a - core/community/infomap/infomap_Greedy.o a - core/community/infomap/infomap_Node.o a - core/community/label_propagation.o a - core/community/leading_eigenvector.o a - core/community/leiden.o a - core/community/louvain.o a - core/community/modularity.o a - core/community/optimal_modularity.o a - core/community/spinglass/NetDataTypes.o a - core/community/spinglass/NetRoutines.o a - core/community/spinglass/clustertool.o a - core/community/spinglass/pottsmodel_2.o a - core/community/walktrap/walktrap.o a - core/community/walktrap/walktrap_communities.o a - core/community/walktrap/walktrap_graph.o a - core/community/walktrap/walktrap_heap.o a - core/connectivity/cohesive_blocks.o a - core/connectivity/components.o a - core/connectivity/separators.o a - core/constructors/adjacency.o a - core/constructors/atlas.o a - core/constructors/basic_constructors.o a - core/constructors/de_bruijn.o a - core/constructors/famous.o a - core/constructors/full.o a - core/constructors/kautz.o a - core/constructors/lcf.o a - core/constructors/linegraph.o a - core/constructors/prufer.o a - core/constructors/regular.o a - core/core/array.o a - core/core/buckets.o a - core/core/cutheap.o a - core/core/dqueue.o a - core/core/error.o a - core/core/estack.o a - core/core/fixed_vectorlist.o a - core/core/grid.o a - core/core/heap.o a - core/core/indheap.o a - core/core/interruption.o a - core/core/marked_queue.o a - core/core/matrix.o a - core/core/memory.o a - core/core/printing.o a - core/core/progress.o a - core/core/psumtree.o a - core/core/set.o a - core/core/sparsemat.o a - core/core/spmatrix.o a - core/core/stack.o a - core/core/statusbar.o a - core/core/strvector.o a - core/core/trie.o a - core/core/vector.o a - core/core/vector_ptr.o a - core/flow/flow.o a - core/flow/st-cuts.o a - core/games/barabasi.o a - core/games/callaway_traits.o a - core/games/citations.o a - core/games/correlated.o a - core/games/degree_sequence.o a - core/games/degree_sequence_vl/gengraph_box_list.o a - core/games/degree_sequence_vl/gengraph_degree_sequence.o a - core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o a - core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o a - core/games/degree_sequence_vl/gengraph_mr-connected.o a - core/games/degree_sequence_vl/gengraph_powerlaw.o a - core/games/degree_sequence_vl/gengraph_random.o a - core/games/dotproduct.o a - core/games/erdos_renyi.o a - core/games/establishment.o a - core/games/forestfire.o a - core/games/grg.o a - core/games/growing_random.o a - core/games/islands.o a - core/games/k_regular.o a - core/games/preference.o a - core/games/recent_degree.o a - core/games/sbm.o a - core/games/static_fitness.o a - core/games/tree.o a - core/games/watts_strogatz.o a - core/graph/adjlist.o a - core/graph/attributes.o a - core/graph/basic_query.o a - core/graph/cattributes.o a - core/graph/iterators.o a - core/graph/type_indexededgelist.o a - core/graph/visitors.o a - core/hrg/hrg.o a - core/hrg/hrg_types.o a - core/internal/glpk_support.o a - core/internal/hacks.o a - core/internal/lsap.o a - core/internal/qsort.o a - core/internal/qsort_r.o a - core/internal/zeroin.o a - core/io/dimacs.o a - core/io/dl-lexer.o a - core/io/dl-parser.o a - core/io/dl.o a - core/io/dot.o a - core/io/edgelist.o a - core/io/gml-lexer.o a - core/io/gml-parser.o a - core/io/gml-tree.o a - core/io/gml.o a - core/io/graphdb.o a - core/io/graphml.o a - core/io/leda.o a - core/io/lgl-lexer.o a - core/io/lgl-parser.o a - core/io/lgl.o a - core/io/ncol-lexer.o a - core/io/ncol-parser.o a - core/io/ncol.o a - core/io/pajek-lexer.o a - core/io/pajek-parser.o a - core/io/pajek.o a - core/isomorphism/bliss.o a - core/isomorphism/bliss/defs.o a - core/isomorphism/bliss/graph.o a - core/isomorphism/bliss/heap.o a - core/isomorphism/bliss/orbit.o a - core/isomorphism/bliss/partition.o a - core/isomorphism/bliss/uintseqhash.o a - core/isomorphism/bliss/utils.o a - core/isomorphism/isoclasses.o a - core/isomorphism/isomorphism_misc.o a - core/isomorphism/lad.o a - core/isomorphism/queries.o a - core/isomorphism/vf2.o a - core/layout/circular.o a - core/layout/davidson_harel.o a - core/layout/drl/DensityGrid.o a - core/layout/drl/DensityGrid_3d.o a - core/layout/drl/drl_graph.o a - core/layout/drl/drl_graph_3d.o a - core/layout/drl/drl_layout.o a - core/layout/drl/drl_layout_3d.o a - core/layout/drl/drl_parse.o a - core/layout/fruchterman_reingold.o a - core/layout/gem.o a - core/layout/graphopt.o a - core/layout/kamada_kawai.o a - core/layout/large_graph.o a - core/layout/layout_bipartite.o a - core/layout/layout_grid.o a - core/layout/layout_random.o a - core/layout/mds.o a - core/layout/merge_dla.o a - core/layout/merge_grid.o a - core/layout/reingold_tilford.o a - core/layout/sugiyama.o a - core/linalg/arpack.o a - core/linalg/blas.o a - core/linalg/eigen.o a - core/linalg/lapack.o a - core/math/bfgs.o a - core/math/complex.o a - core/math/utils.o a - core/misc/bipartite.o a - core/misc/chordality.o a - core/misc/cocitation.o a - core/misc/coloring.o a - core/misc/conversion.o a - core/misc/degree_sequence.o a - core/misc/embedding.o a - core/misc/feedback_arc_set.o a - core/misc/graphicality.o a - core/misc/matching.o a - core/misc/microscopic_update.o a - core/misc/mixing.o a - core/misc/motifs.o a - core/misc/other.o a - core/misc/scan.o a - core/misc/sir.o a - core/misc/spanning_trees.o a - core/operators/add_edge.o a - core/operators/complementer.o a - core/operators/compose.o a - core/operators/connect_neighborhood.o a - core/operators/contract.o a - core/operators/difference.o a - core/operators/disjoint_union.o a - core/operators/intersection.o a - core/operators/misc_internal.o a - core/operators/permute.o a - core/operators/rewire.o a - core/operators/rewire_edges.o a - core/operators/simplify.o a - core/operators/subgraph.o a - core/operators/union.o a - core/paths/all_shortest_paths.o a - core/paths/bellman_ford.o a - core/paths/dijkstra.o a - core/paths/distances.o a - core/paths/eulerian.o a - core/paths/histogram.o a - core/paths/johnson.o a - core/paths/random_walk.o a - core/paths/shortest_paths.o a - core/paths/simple_paths.o a - core/paths/unweighted.o a - core/properties/basic_properties.o a - core/properties/constraint.o a - core/properties/convergence_degree.o a - core/properties/dag.o a - core/properties/degrees.o a - core/properties/girth.o a - core/properties/loops.o a - core/properties/multiplicity.o a - core/properties/neighborhood.o a - core/properties/spectral.o a - core/properties/trees.o a - core/properties/triangles.o a - core/random/random.o a - core/scg/scg.o a - core/scg/scg_approximate_methods.o a - core/scg/scg_exact_scg.o a - core/scg/scg_kmeans.o a - core/scg/scg_optimal_method.o a - core/scg/scg_utils.o a - core/version.o a - vendor/cs/cs_add.o a - vendor/cs/cs_amd.o a - vendor/cs/cs_chol.o a - vendor/cs/cs_cholsol.o a - vendor/cs/cs_compress.o a - vendor/cs/cs_counts.o a - vendor/cs/cs_cumsum.o a - vendor/cs/cs_dfs.o a - vendor/cs/cs_dmperm.o a - vendor/cs/cs_droptol.o a - vendor/cs/cs_dropzeros.o a - vendor/cs/cs_dupl.o a - vendor/cs/cs_entry.o a - vendor/cs/cs_ereach.o a - vendor/cs/cs_etree.o a - vendor/cs/cs_fkeep.o a - vendor/cs/cs_gaxpy.o a - vendor/cs/cs_happly.o a - vendor/cs/cs_house.o a - vendor/cs/cs_ipvec.o a - vendor/cs/cs_leaf.o a - vendor/cs/cs_load.o a - vendor/cs/cs_lsolve.o a - vendor/cs/cs_ltsolve.o a - vendor/cs/cs_lu.o a - vendor/cs/cs_lusol.o a - vendor/cs/cs_malloc.o a - vendor/cs/cs_maxtrans.o a - vendor/cs/cs_multiply.o a - vendor/cs/cs_norm.o a - vendor/cs/cs_permute.o a - vendor/cs/cs_pinv.o a - vendor/cs/cs_post.o a - vendor/cs/cs_print.o a - vendor/cs/cs_pvec.o a - vendor/cs/cs_qr.o a - vendor/cs/cs_qrsol.o a - vendor/cs/cs_randperm.o a - vendor/cs/cs_reach.o a - vendor/cs/cs_scatter.o a - vendor/cs/cs_scc.o a - vendor/cs/cs_schol.o a - vendor/cs/cs_spsolve.o a - vendor/cs/cs_sqr.o a - vendor/cs/cs_symperm.o a - vendor/cs/cs_tdfs.o a - vendor/cs/cs_transpose.o a - vendor/cs/cs_updown.o a - vendor/cs/cs_usolve.o a - vendor/cs/cs_util.o a - vendor/cs/cs_utsolve.o a - vendor/mini-gmp/mini-gmp.o a - vendor/plfit/gss.o a - vendor/plfit/hzeta.o a - vendor/plfit/kolmogorov.o a - vendor/plfit/lbfgs.o a - vendor/plfit/mt.o a - vendor/plfit/options.o a - vendor/plfit/platform.o a - vendor/plfit/plfit.o a - vendor/plfit/plfit_error.o a - vendor/plfit/rbinom.o a - vendor/plfit/sampling.o a - vendor/arpack/dgetv0.o a - vendor/arpack/dlaqrb.o a - vendor/arpack/dmout.o a - vendor/arpack/dnaitr.o a - vendor/arpack/dnapps.o a - vendor/arpack/dnaup2.o a - vendor/arpack/dnaupd.o a - vendor/arpack/dnconv.o a - vendor/arpack/dneigh.o a - vendor/arpack/dneupd.o a - vendor/arpack/dngets.o a - vendor/arpack/dsaitr.o a - vendor/arpack/dsapps.o a - vendor/arpack/dsaup2.o a - vendor/arpack/dsaupd.o a - vendor/arpack/dsconv.o a - vendor/arpack/dseigt.o a - vendor/arpack/dsesrt.o a - vendor/arpack/dseupd.o a - vendor/arpack/dsgets.o a - vendor/arpack/dsortc.o a - vendor/arpack/dsortr.o a - vendor/arpack/dstatn.o a - vendor/arpack/dstats.o a - vendor/arpack/dstqrb.o a - vendor/arpack/dvout.o a - vendor/arpack/ivout.o a - vendor/arpack/second.o a - vendor/arpack/wrap.o a - vendor/simpleraytracer/Color.o a - vendor/simpleraytracer/Light.o a - vendor/simpleraytracer/Point.o a - vendor/simpleraytracer/RIgraphRay.o a - vendor/simpleraytracer/Ray.o a - vendor/simpleraytracer/RayTracer.o a - vendor/simpleraytracer/RayVector.o a - vendor/simpleraytracer/Shape.o a - vendor/simpleraytracer/Sphere.o a - vendor/simpleraytracer/Triangle.o a - vendor/simpleraytracer/unit_limiter.o a - vendor/uuid/R.o a - vendor/uuid/clear.o a - vendor/uuid/compare.o a - vendor/uuid/copy.o a - vendor/uuid/gen_uuid.o a - vendor/uuid/isnull.o a - vendor/uuid/pack.o a - vendor/uuid/parse.o a - vendor/uuid/unpack.o a - vendor/uuid/unparse.o a - rinterface.o a - rinterface_extra.o a - rrandom.o a - lazyeval.o make[1]: Leaving directory '/tmp/th798/17408827/RtmpVczuMa/R.INSTALL112c6f5e5ceebf/leidenAlg/src/rigraph' make[1]: Entering directory '/tmp/th798/17408827/RtmpVczuMa/R.INSTALL112c6f5e5ceebf/leidenAlg/src/leidenalg' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c CPMVertexPartition.cpp -o CPMVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c LinearResolutionParameterVertexPartition.cpp -o LinearResolutionParameterVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RBConfigurationVertexPartition.cpp -o RBConfigurationVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c SurpriseVertexPartition.cpp -o SurpriseVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ModularityVertexPartition.cpp -o ModularityVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RBERVertexPartition.cpp -o RBERVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c GraphHelper.cpp -o GraphHelper.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c MutableVertexPartition.cpp -o MutableVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ResolutionParameterVertexPartition.cpp -o ResolutionParameterVertexPartition.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c Optimiser.cpp -o Optimiser.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DUSING_R -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -O3 -pthread -fPIC -fopenmp -I"./include" -I"../rigraph/include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c SignificanceVertexPartition.cpp -o SignificanceVertexPartition.o ar rvs ../libleidenalg.a CPMVertexPartition.o LinearResolutionParameterVertexPartition.o RBConfigurationVertexPartition.o SurpriseVertexPartition.o ModularityVertexPartition.o RBERVertexPartition.o GraphHelper.o MutableVertexPartition.o ResolutionParameterVertexPartition.o Optimiser.o SignificanceVertexPartition.o ar: creating ../libleidenalg.a a - CPMVertexPartition.o a - LinearResolutionParameterVertexPartition.o a - RBConfigurationVertexPartition.o a - SurpriseVertexPartition.o a - ModularityVertexPartition.o a - RBERVertexPartition.o a - GraphHelper.o a - MutableVertexPartition.o a - ResolutionParameterVertexPartition.o a - Optimiser.o a - SignificanceVertexPartition.o make[1]: Leaving directory '/tmp/th798/17408827/RtmpVczuMa/R.INSTALL112c6f5e5ceebf/leidenAlg/src/leidenalg' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o leidenAlg.so RcppExports.o leiden.o -L. -lpthread -lleidenalg -lrigraph -lm -L/home/th798/R/R-release/lib -lRlapack -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath -fopenmp installing to /tmp/th798/17408827/R-release/1274/library/00LOCK-leidenAlg/00new/leidenAlg/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leidenAlg) * installing *source* package 'RcppPlanc' ... ** this is package 'RcppPlanc' version '2.0.10' ** package 'RcppPlanc' successfully unpacked and MD5 sums checked ** using staged installation -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /packages/gcc/12.2.0-nnbserq/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /packages/gcc/12.2.0-nnbserq/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done This is libplanc 1.0.2 containing component nmflib 1.0.1 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") CMake Debug Log at cmake/FindR.cmake:38 (find_program): find_program called with the following settings: VAR: R_EXECUTABLE NAMES: "R" Documentation: Path to a program. Framework Only Search Frameworks: 0 Search Frameworks Last: 0 Search Frameworks First: 0 AppBundle Only Search AppBundle: 0 Search AppBundle Last: 0 Search AppBundle First: 0 CMAKE_FIND_USE_CMAKE_PATH: 1 CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH: 0 CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH: 0 CMAKE_FIND_USE_CMAKE_SYSTEM_PATH: 0 find_program considered the following locations: The item was found at /home/th798/R/R-release/bin/R Call Stack (most recent call first): CMakeLists.txt:73 (find_package) CMake Debug Log at cmake/FindR.cmake:64 (find_program): find_program called with the following settings: VAR: RSCRIPT_EXECUTABLE NAMES: "Rscript" Documentation: Rscript executable. Framework Only Search Frameworks: 0 Search Frameworks Last: 0 Search Frameworks First: 0 AppBundle Only Search AppBundle: 0 Search AppBundle Last: 0 Search AppBundle First: 0 CMAKE_FIND_USE_CMAKE_PATH: 1 CMAKE_FIND_USE_CMAKE_ENVIRONMENT_PATH: 1 CMAKE_FIND_USE_SYSTEM_ENVIRONMENT_PATH: 1 CMAKE_FIND_USE_CMAKE_SYSTEM_PATH: 1 find_program considered the following locations: /packages/gcc/12.2.0-nnbserq/bin/Rscript /packages/gcc/12.2.0-nnbserq/sbin/Rscript /packages/gcc/12.2.0-nnbserq/Rscript /packages/zstd/1.5.2-cs5ansz/bin/Rscript /packages/zstd/1.5.2-cs5ansz/sbin/Rscript /packages/zstd/1.5.2-cs5ansz/Rscript /packages/zlib/1.2.13-po6bkge/bin/Rscript /packages/zlib/1.2.13-po6bkge/sbin/Rscript /packages/zlib/1.2.13-po6bkge/Rscript /packages/mpc/1.2.1-nnfoiwh/bin/Rscript /packages/mpc/1.2.1-nnfoiwh/sbin/Rscript /packages/mpc/1.2.1-nnfoiwh/Rscript /packages/mpfr/4.1.0-yfsqqka/bin/Rscript /packages/mpfr/4.1.0-yfsqqka/sbin/Rscript /packages/mpfr/4.1.0-yfsqqka/Rscript /packages/gmp/6.2.1-7ydtie6/bin/Rscript /packages/gmp/6.2.1-7ydtie6/sbin/Rscript /packages/gmp/6.2.1-7ydtie6/Rscript /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/bin/Rscript /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/sbin/Rscript /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/Rscript /packages/gcc-8.3.1/proj/7.1.0/bin/Rscript /packages/gcc-8.3.1/proj/7.1.0/sbin/Rscript /packages/gcc-8.3.1/proj/7.1.0/Rscript /packages/gdal/3.3.1/bin/Rscript /packages/gdal/3.3.1/sbin/Rscript /packages/gdal/3.3.1/Rscript The item was found at /home/th798/R/R-release/bin/Rscript Call Stack (most recent call first): CMakeLists.txt:73 (find_package) -- Found R: /home/th798/R/R-release/bin/R (found version "4.5.0") CMake Debug Log at CMakeLists.txt:73 (find_package): find_package considered the following paths for R.cmake /projects/genomic-ml/.conda/envs/emacs1/share/cmake-3.22/Modules/FindR.cmake The file was found at /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/cmake/FindR.cmake -- Could NOT find MKL (missing: MKL_DIR) -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /projects/genomic-ml/.conda/envs/emacs1/lib/libopenblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /projects/genomic-ml/.conda/envs/emacs1/lib/libopenblas.so;-lpthread;-lm;-ldl -- Could NOT find OpenBLAS (missing: OpenBLAS_DIR) -- Looking for openblas/cblas.h -- Looking for openblas/cblas.h - not found -- Found HDF5: /home/th798/.conda/envs/emacs1/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libpthread.so;/packages/zlib/1.2.13-po6bkge/lib/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.2") -- Performing Test HDF5_LINKS CMake Warning at /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles/CMakeTmp/CMakeLists.txt:17 (add_executable): Cannot generate a safe runtime search path for target cmTC_8ac24 because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /packages/zlib/1.2.13-po6bkge/lib may be hidden by files in: /home/th798/.conda/envs/emacs1/lib Some of these libraries may not be found correctly. -- Performing Test HDF5_LINKS - Success -- Found R_Rcpp: /projects/genomic-ml/R/R-release/library/Rcpp -- Found R_RcppArmadillo: /projects/genomic-ml/R/R-release/library/RcppArmadillo -- Found R_RcppProgress: /projects/genomic-ml/R/R-release/library/RcppProgress -- Performing Test UNSAFE_MATH -- Performing Test UNSAFE_MATH - Success -- Performing Test FINITE_MATH -- Performing Test FINITE_MATH - Success -- Performing Test TRAPPING_MATH -- Performing Test TRAPPING_MATH - Success -- Performing Test ERRNO_MATH -- Performing Test ERRNO_MATH - Success -- Performing Test UNSIGNED_ZERO -- Performing Test UNSIGNED_ZERO - Success -- Performing Test RECIPROCAL_MATH -- Performing Test RECIPROCAL_MATH - Success -- Performing Test ARCH_AVX -- Performing Test ARCH_AVX - Success -- Performing Test HAS_POPCNT -- Performing Test HAS_POPCNT - Success -- Looking for cblas.h -- Looking for cblas.h - not found -- Looking for flexiblas/cblas.h -- Looking for flexiblas/cblas.h - not found -- A cache variable, namely HWLOC_DIR, has been set to specify the install directory of HWLOC -- Checking for one of the modules 'hwloc' -- Looking for HWLOC - not found using PkgConfig. Perhaps you should add the directory containing hwloc.pc to the PKG_CONFIG_PATH environment variable. -- Looking for HWLOC - PkgConfig not used -- Looking for hwloc -- hwloc.h not found -- Looking for hwloc -- lib hwloc not found -- Could NOT find HWLOC (missing: HWLOC_LIBRARIES HWLOC_WORKS) -- Looking for dlfcn.h -- Looking for dlfcn.h - found -- NNLS_SOURCE_DIR = /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nnls -- NMF_SOURCE_DIR = /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf -- NMFLIB_COMMON = /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/common -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done CMake Warning at nmf/CMakeLists.txt:12 (add_library): Cannot generate a safe runtime search path for target nmflib because files in some directories may conflict with libraries in implicit directories: runtime library [libz.so.1] in /packages/zlib/1.2.13-po6bkge/lib may be hidden by files in: /projects/genomic-ml/.conda/envs/emacs1/lib /home/th798/.conda/envs/emacs1/lib Some of these libraries may not be found correctly. -- Generating done CMake Warning: Manually-specified variables were not used by the project: R_SHLIB_EXT -- Build files have been written to: /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -S/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc -B/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build --check-build-system CMakeFiles/Makefile.cmake 0 /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_progress_start /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles/utils.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make -f CMakeFiles/utils.dir/build.make CMakeFiles/utils.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 5%] Building CXX object CMakeFiles/utils.dir/common/utils.cpp.o /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/R/R-release/include -I/projects/genomic-ml/R/R-release/library/Rcpp/include -I/projects/genomic-ml/R/R-release/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-release/library/RcppProgress/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -MD -MT CMakeFiles/utils.dir/common/utils.cpp.o -MF CMakeFiles/utils.dir/common/utils.cpp.o.d -o CMakeFiles/utils.dir/common/utils.cpp.o -c /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/common/utils.cpp make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 5%] Built target utils make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles/hwloc.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make -f CMakeFiles/hwloc.dir/build.make CMakeFiles/hwloc.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 11%] Creating directories for 'hwloc' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/tmp /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-mkdir [ 17%] Performing download step (download, verify and extract) for 'hwloc' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -P /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/download-hwloc.cmake -- Downloading... dst='/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.11.2.tar.gz' timeout='none' inactivity timeout='none' -- Using src='https://download.open-mpi.org/release/hwloc/v2.11/hwloc-2.11.2.tar.gz' -- [download 0% complete] -- [download 1% complete] -- [download 2% complete] -- [download 3% complete] -- [download 4% complete] -- [download 5% complete] -- [download 6% complete] -- [download 7% complete] -- [download 8% complete] -- [download 9% complete] -- [download 10% complete] -- [download 11% complete] -- [download 12% complete] -- [download 13% complete] -- [download 14% complete] -- [download 15% complete] -- [download 16% complete] -- [download 17% complete] -- [download 18% complete] -- [download 19% complete] -- [download 20% complete] -- [download 21% complete] -- [download 22% complete] -- [download 23% complete] -- [download 24% complete] -- [download 25% complete] -- [download 26% complete] -- [download 27% complete] -- [download 28% complete] -- [download 29% complete] -- [download 30% complete] -- [download 31% complete] -- [download 32% complete] -- [download 33% complete] -- [download 34% complete] -- [download 35% complete] -- [download 36% complete] -- [download 37% complete] -- [download 38% complete] -- [download 39% complete] -- [download 40% complete] -- [download 41% complete] -- [download 42% complete] -- [download 43% complete] -- [download 44% complete] -- [download 45% complete] -- [download 46% complete] -- [download 47% complete] -- [download 48% complete] -- [download 49% complete] -- [download 50% complete] -- [download 51% complete] -- [download 52% complete] -- [download 53% complete] -- [download 54% complete] -- [download 55% complete] -- [download 56% complete] -- [download 57% complete] -- [download 58% complete] -- [download 59% complete] -- [download 60% complete] -- [download 61% complete] -- [download 62% complete] -- [download 63% complete] -- [download 64% complete] -- [download 65% complete] -- [download 66% complete] -- [download 67% complete] -- [download 68% complete] -- [download 69% complete] -- [download 70% complete] -- [download 71% complete] -- [download 72% complete] -- [download 73% complete] -- [download 74% complete] -- [download 75% complete] -- [download 76% complete] -- [download 77% complete] -- [download 78% complete] -- [download 79% complete] -- [download 80% complete] -- [download 81% complete] -- [download 82% complete] -- [download 83% complete] -- [download 84% complete] -- [download 85% complete] -- [download 86% complete] -- [download 87% complete] -- [download 88% complete] -- [download 89% complete] -- [download 90% complete] -- [download 91% complete] -- [download 92% complete] -- [download 93% complete] -- [download 94% complete] -- [download 95% complete] -- [download 96% complete] -- [download 97% complete] -- [download 98% complete] -- [download 99% complete] -- [download 100% complete] -- verifying file... file='/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.11.2.tar.gz' -- Downloading... done cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -P /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/verify-hwloc.cmake cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -P /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/extract-hwloc.cmake -- extracting... src='/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-2.11.2.tar.gz' dst='/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc' -- extracting... [tar xfz] -- extracting... [analysis] -- extracting... [rename] -- extracting... [clean up] -- extracting... done cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-download [ 23%] No update step for 'hwloc' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E echo_append /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-update [ 29%] Performing patch step for 'hwloc' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cat /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/../../tools/patches/00_remove_stdio.patch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/../../tools/patches/01_remove_sprintf.patch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/../../tools/patches/02_adjust_windows_types.patch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/../../tools/patches/03_remove_abort.patch | /usr/bin/patch -p1 -l patching file hwloc/components.c patching file hwloc/distances.c patching file hwloc/memattrs.c patching file hwloc/pci-common.c patching file hwloc/topology-aix.c patching file hwloc/topology-bgq.c patching file hwloc/topology-cuda.c patching file hwloc/topology-darwin.c patching file hwloc/topology-levelzero.c patching file hwloc/topology-linux.c patching file hwloc/topology-nvml.c patching file hwloc/topology-opencl.c patching file hwloc/topology-pci.c patching file hwloc/topology-rsmi.c patching file hwloc/topology-solaris.c patching file hwloc/topology-synthetic.c patching file hwloc/topology-windows.c patching file hwloc/topology-x86.c patching file hwloc/topology-xml-libxml.c patching file hwloc/topology-xml-nolibxml.c patching file hwloc/topology-xml.c patching file hwloc/topology.c patching file hwloc/cpukinds.c patching file hwloc/topology-freebsd.c patching file hwloc/topology-linux.c patching file hwloc/topology-rsmi.c patching file hwloc/topology-windows.c patching file hwloc/topology-xml.c patching file include/hwloc/cuda.h patching file include/hwloc/cudart.h patching file include/hwloc/levelzero.h patching file include/hwloc/nvml.h patching file include/hwloc/opencl.h patching file include/hwloc/openfabrics-verbs.h patching file include/hwloc/rsmi.h patching file hwloc/topology-windows.c patching file hwloc/distances.c patching file hwloc/topology-linux.c cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-patch [ 35%] Performing configure step for 'hwloc' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E env LD= "CFLAGS=-DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " sh ../hwloc/configure --with-pic --prefix=/out/ --disable-picky --enable-shared=no --enable-static=yes --disable-cairo --disable-libxml2 --disable-io --disable-plugin-dlopen --disable-plugin-ltdl --enable-embedded-mode && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate ../hwloc/aclocal.m4 && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate ../hwloc/Makefile.in && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate ../hwloc/configure && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch_nocreate config.status ### ### Configuring hwloc distribution tarball ### Startup tests ### checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '682419' is supported by ustar format... yes checking whether GID '3301' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports nested variables... (cached) yes checking whether make supports the include directive... yes (GNU style) checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc understands -c and -o together... yes checking dependency style of /packages/gcc/12.2.0-nnbserq/bin/gcc... /usr/bin/cp ../hwloc/./config//depcomp conftest.dir gcc3 checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for wchar.h... yes checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking for ar... ar checking the archiver (ar) interface... ar checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by /packages/gcc/12.2.0-nnbserq/bin/gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from /packages/gcc/12.2.0-nnbserq/bin/gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -fno-rtti -fno-exceptions... no checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to produce PIC... -fPIC -DPIC checking if /packages/gcc/12.2.0-nnbserq/bin/gcc PIC flag -fPIC -DPIC works... yes checking if /packages/gcc/12.2.0-nnbserq/bin/gcc static flag -static works... no checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -c -o file.o... yes checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -c -o file.o... (cached) yes checking whether the /packages/gcc/12.2.0-nnbserq/bin/gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking whether the compiler supports GNU C++... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/g++ accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/g++ option to enable C++11 features... none needed checking dependency style of /packages/gcc/12.2.0-nnbserq/bin/g++... /usr/bin/cp ../hwloc/./config//depcomp conftest.dir gcc3 checking how to run the C++ preprocessor... /packages/gcc/12.2.0-nnbserq/bin/g++ -E checking for ld used by /packages/gcc/12.2.0-nnbserq/bin/g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the /packages/gcc/12.2.0-nnbserq/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for /packages/gcc/12.2.0-nnbserq/bin/g++ option to produce PIC... -fPIC -DPIC checking if /packages/gcc/12.2.0-nnbserq/bin/g++ PIC flag -fPIC -DPIC works... yes checking if /packages/gcc/12.2.0-nnbserq/bin/g++ static flag -static works... no checking if /packages/gcc/12.2.0-nnbserq/bin/g++ supports -c -o file.o... yes checking if /packages/gcc/12.2.0-nnbserq/bin/g++ supports -c -o file.o... (cached) yes checking whether the /packages/gcc/12.2.0-nnbserq/bin/g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the compiler supports GNU C... (cached) yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... (cached) yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... (cached) none needed checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc understands -c and -o together... (cached) yes checking dependency style of /packages/gcc/12.2.0-nnbserq/bin/gcc... (cached) gcc3 checking for /packages/gcc/12.2.0-nnbserq/bin/gcc options needed to detect all undeclared functions... none needed checking for pkg-config... /home/th798/.conda/envs/emacs1/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking how to run the C preprocessor... /packages/gcc/12.2.0-nnbserq/bin/gcc -E checking for X... libraries , headers ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build configure: hwloc srcdir: /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc configure: Detected VPATH build checking for hwloc version... 2.11.2 checking if want hwloc maintainer support... disabled (embedded mode) checking for hwloc directory prefix... (none) checking for hwloc symbol prefix... hwloc_ checking for the C compiler vendor... gnu checking size of void *... 8 checking which OS support to include... Linux checking which CPU support to include... x86_64 checking size of unsigned long... 8 checking size of unsigned int... 4 checking for __attribute__... yes checking for __attribute__(aligned)... yes checking for __attribute__(always_inline)... yes checking for __attribute__(cold)... yes checking for __attribute__(const)... yes checking for __attribute__(deprecated)... yes checking for __attribute__(constructor)... yes checking for __attribute__(format)... yes checking for __attribute__(hot)... yes checking for __attribute__(malloc)... yes checking for __attribute__(may_alias)... yes checking for __attribute__(no_instrument_function)... yes checking for __attribute__(nonnull)... yes checking for __attribute__(noreturn)... yes checking for __attribute__(packed)... yes checking for __attribute__(pure)... yes checking for __attribute__(sentinel)... yes checking for __attribute__(unused)... yes checking for __attribute__(warn_unused_result)... yes checking for __attribute__(weak_alias)... yes checking if /packages/gcc/12.2.0-nnbserq/bin/gcc supports -fvisibility=hidden... yes checking whether to enable symbol visibility... yes (via -fvisibility=hidden) configure: WARNING: "-fvisibility=hidden" has been added to the hwloc CFLAGS checking whether the C compiler rejects function calls with too many arguments... yes checking whether the C compiler rejects function calls with too few arguments... yes checking for unistd.h... (cached) yes checking for dirent.h... yes checking for strings.h... (cached) yes checking for ctype.h... yes checking for strcasecmp... yes checking whether strcasecmp is declared... yes checking whether function strcasecmp has a complete prototype... yes checking for strncasecmp... yes checking whether strncasecmp is declared... yes checking whether function strncasecmp has a complete prototype... yes checking for strftime... yes checking for setlocale... yes checking for stdint.h... (cached) yes checking for sys/mman.h... yes **** Linux-specific checks checking whether sched_getcpu is declared... yes checking whether sched_setaffinity is declared... yes checking whether function sched_setaffinity has a complete prototype... yes checking for old prototype of sched_setaffinity... no checking for working CPU_SET... yes checking for working CPU_SET_S... yes checking for working syscall with 6 parameters... yes checking for libudev.h... no **** end of Linux-specific checks checking whether pthread_setaffinity_np is declared... yes checking whether pthread_getaffinity_np is declared... yes checking whether fabsf is declared... yes checking for fabsf in -lm... yes checking whether modff is declared... yes checking for modff in -lm... yes checking whether _SC_NPROCESSORS_ONLN is declared... yes checking whether _SC_NPROCESSORS_CONF is declared... yes checking whether _SC_NPROC_ONLN is declared... no checking whether _SC_NPROC_CONF is declared... no checking whether _SC_PAGESIZE is declared... yes checking whether _SC_PAGE_SIZE is declared... yes checking whether _SC_LARGE_PAGESIZE is declared... no checking for mach/mach_init.h... no checking for mach_init.h... no checking for mach/mach_host.h... no checking whether strtoull is declared... yes checking for ssize_t... yes checking whether snprintf is declared... yes checking whether _strdup is declared... no checking whether _putenv is declared... no checking whether snprintf is correct... yes checking whether getprogname is declared... no checking whether getexecname is declared... no checking for program_invocation_name... yes checking for __progname... yes checking for pthread_t... yes checking for ffs... yes checking whether ffs is declared... yes checking whether function ffs has a complete prototype... yes checking for ffsl... yes checking whether ffsl is declared... yes checking whether function ffsl has a complete prototype... yes checking for fls... no checking for flsl... no checking for clz... no checking for clzl... no checking for openat... yes checking for malloc.h... yes checking for getpagesize... yes checking for memalign... yes checking for posix_memalign... yes checking for sys/utsname.h... yes checking for uname... yes checking for pthread_mutex_lock... yes **** x86 CPUID configuration checking for x86 cpuid... yes **** end of x86 CPUID configuration **** component and plugin-specific configuration checking if plugin support is enabled... no checking components to build statically... noos xml synthetic xml_nolibxml linux x86 checking components to build as plugins... **** end of component and plugin configuration checking for diff... /usr/bin/diff ### ### Performing final hwloc configuration ### checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating hwloc/Makefile config.status: creating include/private/autogen/config.h config.status: creating include/hwloc/autogen/config.h config.status: executing depfiles commands config.status: executing libtool commands ----------------------------------------------------------------------------- Hwloc optional build support status (more details can be found above): Probe / display I/O devices: no Graphical output: no (disabled in embedded mode) XML input / output: basic Plugin support: no ----------------------------------------------------------------------------- cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-configure [ 41%] Performing build step for 'hwloc' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && make make[3]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' /bin/sh ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating hwloc/Makefile config.status: creating include/private/autogen/config.h config.status: include/private/autogen/config.h is unchanged config.status: creating include/hwloc/autogen/config.h config.status: include/hwloc/autogen/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands Making all in include make[4]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' Making all in hwloc make[4]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' CC topology.lo CC traversal.lo CC distances.lo CC memattrs.lo CC cpukinds.lo CC components.lo CC bind.lo CC bitmap.lo CC pci-common.lo CC diff.lo CC shmem.lo CC misc.lo CC base64.lo CC topology-noos.lo CC topology-synthetic.lo CC topology-xml.lo CC topology-xml-nolibxml.lo CC topology-linux.lo CC topology-hardwired.lo CC topology-x86.lo CCLD libhwloc_embedded.la make[4]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[4]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[3]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-build [ 47%] Performing install step for 'hwloc' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && make install make[3]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' Making install in include make[4]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[5]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' make[4]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include' Making install in hwloc make[4]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make install-exec-hook make[6]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[6]: Nothing to be done for 'install-exec-hook'. make[6]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[5]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[4]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/hwloc' make[4]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[5]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[4]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' make[3]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-install [ 52%] Completed 'hwloc' /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E make_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles/hwloc-complete /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E touch /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-stamp/hwloc-done /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E remove_directory /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc/utils/lstopo make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 52%] Built target hwloc make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles/hw_detect.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make -f CMakeFiles/hw_detect.dir/build.make CMakeFiles/hw_detect.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 58%] Building C object CMakeFiles/hw_detect.dir/common/hw_detect.c.o /packages/gcc/12.2.0-nnbserq/bin/gcc -DUSING_R -I/home/th798/R/R-release/include -I/projects/genomic-ml/R/R-release/library/Rcpp/include -I/projects/genomic-ml/R/R-release/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-release/library/RcppProgress/include -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc-build/include -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/hwloc-prefix/src/hwloc/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -std=gnu99 -MD -MT CMakeFiles/hw_detect.dir/common/hw_detect.c.o -MF CMakeFiles/hw_detect.dir/common/hw_detect.c.o.d -o CMakeFiles/hw_detect.dir/common/hw_detect.c.o -c /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/common/hw_detect.c make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 58%] Built target hw_detect make -f CMakeFiles/detect_blas.dir/build.make CMakeFiles/detect_blas.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/CMakeFiles/detect_blas.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make -f CMakeFiles/detect_blas.dir/build.make CMakeFiles/detect_blas.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 64%] Building C object CMakeFiles/detect_blas.dir/common/detect_blas.c.o /packages/gcc/12.2.0-nnbserq/bin/gcc -DUSING_R -I/home/th798/R/R-release/include -I/projects/genomic-ml/R/R-release/library/Rcpp/include -I/projects/genomic-ml/R/R-release/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-release/library/RcppProgress/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -std=gnu99 -MD -MT CMakeFiles/detect_blas.dir/common/detect_blas.c.o -MF CMakeFiles/detect_blas.dir/common/detect_blas.c.o.d -o CMakeFiles/detect_blas.dir/common/detect_blas.c.o -c /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/common/detect_blas.c make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 64%] Built target detect_blas make -f nmf/CMakeFiles/nmflib.dir/build.make nmf/CMakeFiles/nmflib.dir/depend make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build && /projects/genomic-ml/.conda/envs/emacs1/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf/CMakeFiles/nmflib.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make -f nmf/CMakeFiles/nmflib.dir/build.make nmf/CMakeFiles/nmflib.dir/build make[2]: Entering directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' [ 70%] Building CXX object nmf/CMakeFiles/nmflib.dir/nmf_lib.cpp.o cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-release/include -I/projects/genomic-ml/R/R-release/library/Rcpp/include -I/projects/genomic-ml/R/R-release/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-release/library/RcppProgress/include -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/nmf_lib.cpp.o -MF CMakeFiles/nmflib.dir/nmf_lib.cpp.o.d -o CMakeFiles/nmflib.dir/nmf_lib.cpp.o -c /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/nmf_lib.cpp [ 76%] Building CXX object nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o cd /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf && /packages/gcc/12.2.0-nnbserq/bin/g++ -DUSING_R -Dnmflib_EXPORTS -I/home/th798/R/R-release/include -I/projects/genomic-ml/R/R-release/library/Rcpp/include -I/projects/genomic-ml/R/R-release/library/RcppArmadillo/include -I/projects/genomic-ml/R/R-release/library/RcppProgress/include -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/common -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nnls -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf -I/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/_deps/highfive-src/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -g -DNDEBUG -fPIC -fvisibility-inlines-hidden -fopenmp -funsafe-math-optimizations -ffinite-math-only -fno-trapping-math -fno-math-errno -fno-signed-zeros -freciprocal-math -mavx -mpopcnt -MD -MT nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o -MF CMakeFiles/nmflib.dir/bppnmf.cpp.o.d -o CMakeFiles/nmflib.dir/bppnmf.cpp.o -c /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.cpp In file included from /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.cpp:4: /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp: In member function 'void planc::BPPNMF::updateOtherGivenOneMultipleRHS(const T&, const arma::mat&, char, arma::mat*, arma::fvec)': /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:56:30: error: 'unique_ptr' is not a member of 'std' 56 | std::vector>> subproblems; | ^~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:10:1: note: 'std::unique_ptr' is defined in header ''; did you forget to '#include '? 9 | #include "hals.hpp" +++ |+#include 10 | /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:56:69: error: template argument 1 is invalid 56 | std::vector>> subproblems; | ^~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:56:69: error: template argument 2 is invalid /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:56:71: error: expected unqualified-id before '>' token 56 | std::vector>> subproblems; | ^ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:58:86: error: 'subproblems' has not been declared 58 | #pragma omp parallel default(none) shared(othermat, input, giventInput, giventGiven, subproblems, indices, numChunks) num_threads(this->ncores) | ^~~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:67:26: error: 'unique_ptr' is not a member of 'std' 67 | std::unique_ptr> subProblem(new BPPNNLS( | ^~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:67:26: note: 'std::unique_ptr' is defined in header ''; did you forget to '#include '? /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:67:65: error: expected primary-expression before '>' token 67 | std::unique_ptr> subProblem(new BPPNNLS( | ^~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:67:68: error: there are no arguments to 'subProblem' that depend on a template parameter, so a declaration of 'subProblem' must be available [-fpermissive] 67 | std::unique_ptr> subProblem(new BPPNNLS( | ^~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:67:68: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:73:25: error: 'subproblems' was not declared in this scope 73 | subproblems.push_back(std::move(subProblem)); | ^~~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:73:57: error: 'subProblem' was not declared in this scope 73 | subproblems.push_back(std::move(subProblem)); | ^~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:91:37: error: 'subproblems' was not declared in this scope 91 | for (int i = 0; i < subproblems.size(); i++) { | ^~~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:91:17: error: invalid controlling predicate 91 | for (int i = 0; i < subproblems.size(); i++) { | ^~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:105:33: error: 'subproblems' was not declared in this scope 105 | for (int i = 0; i < subproblems.size(); i++) { | ^~~~~~~~~~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:105:13: error: invalid controlling predicate 105 | for (int i = 0; i < subproblems.size(); i++) { | ^~~ /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp: In instantiation of 'void planc::BPPNMF::updateOtherGivenOneMultipleRHS(const T&, const arma::mat&, char, arma::mat*, arma::fvec) [with T = arma::SpMat; arma::mat = arma::Mat; arma::fvec = arma::Col]': /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:129:17: required from 'void planc::BPPNMF::commonSolve() [with T = arma::SpMat]' /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.cpp:29:22: required from here /tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/planc/nmf/bppnmf.hpp:67:78: error: 'subProblem' was not declared in this scope 67 | std::unique_ptr> subProblem(new BPPNNLS( | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | giventGiven, | ~~~~~~~~~~~~ 69 | static_cast(giventInput.cols(spanStart, spanEnd)), true)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [nmf/CMakeFiles/nmflib.dir/build.make:93: nmf/CMakeFiles/nmflib.dir/bppnmf.cpp.o] Error 1 make[2]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make[1]: *** [CMakeFiles/Makefile2:215: nmf/CMakeFiles/nmflib.dir/all] Error 2 make[1]: Leaving directory '/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build' make: *** [Makefile:139: all] Error 2 -- Install configuration: "RelWithDebInfo" CMake Error at cmake_install.cmake:65 (file): file INSTALL cannot find "/tmp/th798/17408827/RtmpLcCdBm/R.INSTALL1145113f7cada/RcppPlanc/src/build/nmf/libnmflib.so": No such file or directory. ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++17 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rcppplanc_nmf.cpp -o rcppplanc_nmf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -Iplanc/common -Iplanc/nmf -Iplanc/nnls -Ibuild/_deps/highfive-src/include -Ibuild/nmf -DUSING_R -DHIGHFIVE_HAS_CONCEPTS=0 -DMPI_NO_CPPBIND -DRcppPlanc_EXPORTS -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rcppplanc_nnls.cpp -o rcppplanc_nnls.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o RcppPlanc.so RcppExports.o rcppplanc_nmf.o rcppplanc_nnls.o -L./ -lnmflib -fopenmp -Wl,-rpath,$ORIGIN/../libs,--enable-new-dtags /usr/bin/ld: cannot find -lnmflib collect2: error: ld returned 1 exit status make: *** [/home/th798/R/R-release/share/make/shlib.mk:10: RcppPlanc.so] Error 1 ERROR: compilation failed for package 'RcppPlanc' * removing '/tmp/th798/17408827/R-release/1274/library/RcppPlanc' ERROR: dependency 'RcppPlanc' is not available for package 'rliger' Perhaps try a variation of: install.packages('RcppPlanc') * removing '/tmp/th798/17408827/R-release/1274/library/rliger' The downloaded source packages are in '/tmp/th798/17408827/RtmpK6QZEU/downloaded_packages' Warning messages: 1: In install.packages(rev.dep, dep = TRUE) : installation of package 'RcppPlanc' had non-zero exit status 2: In install.packages(rev.dep, dep = TRUE) : installation of package 'rliger' had non-zero exit status > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 394.717 40.204 454.309 > print(Sys.time()) [1] "2025-05-21 03:57:00 MST" > downloaded_packages <- file.path( + tempdir(), + "downloaded_packages") > dl.glob <- file.path( + downloaded_packages, + paste0(rev.dep,"_*.tar.gz")) > rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob)) > colnames(rev.dep.dl.row) <- c("pkg","path") > rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE) > pkg.Rcheck <- paste0(rev.dep, ".Rcheck") > > proj.dir <- "~/genomic-ml/data.table-revdeps" > source(file.path(proj.dir, "myStatus.R")) > Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]])) > dir.create(Rvers, showWarnings=FALSE) > Rcheck.list <- list() > for(dt.version.short in c("release", "master")){ + dt.tar.gz <- cargs[[dt.version.short]] + dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz) + print(Sys.time()) + install.packages(dt.tar.gz, repos=NULL) + print(Sys.time()) + check.cmd <- get_check_cmd(rev.dep.release.tar.gz) + system(check.cmd) + print(Sys.time()) + dest.Rcheck <- file.path( + Rvers, + paste0(dt.version, ".Rcheck")) + unlink(dest.Rcheck, recursive=TRUE) + file.rename(pkg.Rcheck, dest.Rcheck) + Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log") + } [1] "2025-05-21 03:57:00 MST" Installing package into '/tmp/th798/17408827/R-release/1274/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.2' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/17408827/R-release/1274/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2025-05-21 03:57:31 MST" * using log directory '/tmp/th798/17408827/R-release/1274/scCustomize.Rcheck' * using R version 4.5.0 (2025-04-11) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * checking for file 'scCustomize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scCustomize' version '3.0.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'rliger' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'scCustomize' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-05-21 04:04:07 MST" [1] "2025-05-21 04:04:07 MST" Installing package into '/tmp/th798/17408827/R-release/1274/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.99' ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/17408827/R-release/1274/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2025-05-21 04:04:38 MST" * using log directory '/tmp/th798/17408827/R-release/1274/scCustomize.Rcheck' * using R version 4.5.0 (2025-04-11) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * checking for file 'scCustomize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'scCustomize' version '3.0.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'rliger' * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'scCustomize' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-05-21 04:11:22 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$checking), + sig.diff.row$release, + rev.dep.release.tar.gz, + release.tag) + print(bisect.cmd) + bisect.out <- system(bisect.cmd, intern=TRUE) + cat(bisect.out,sep="\n") + if(is.null(attr(bisect.out,"status"))){ + first.bad.sha <- nc::capture_all_str( + bisect.out, + sha="[0-9a-f]+", + " is the first new commit")$sha + parent.cmd <- paste( + "cd ~/R/data.table && git log --pretty=%P -n 1", + first.bad.sha) + parent.sha <- system(parent.cmd, intern=TRUE) + sig.diff.dt[diff.i, first.bad.commit := first.bad.sha] + parent.msg <- paste0("parent=", parent.sha) + this.comment <- if(parent.sha==old.sha){ + paste(parent.msg, "same as git bisect old") + }else if(first.bad.sha==master.sha){ + paste("same as git bisect new=master,", parent.msg) + }else{ + parent.msg + } + sig.diff.dt[diff.i, comments := this.comment] + } + } + ## add CRAN column. + sig.diff.dt[, CRAN := { + flavor <- get_flavor(Rvers) + details <- data.table(flavor=unique(flavor))[, { + base <- "https://www.r-project.org/nosvn/R.check/" + u <- paste0(base, flavor, "/", rev.dep, "-00check.txt") + check.txt <- tempfile() + tryCatch({ + download.file(u, check.txt, quiet=TRUE) + }, error=function(e){ + NULL + }) + check.lines <- if(file.exists(check.txt)){ + readLines(check.txt,encoding="UTF-8") + }else{ + "" + } + repl.lines <- gsub("[\u2018\u2019]", "'", check.lines) + ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C. + myStatus(line.vec=repl.lines) + }, by=flavor] + select.dt <- data.table(flavor, checking) + details[select.dt, msg, on=.(flavor, checking)] + }] + dir.create(file.path(job.dir, Rvers)) + diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv") + data.table::fwrite(sig.diff.dt, diffs.csv) + print(sig.diff.dt) + } >