Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-03-27 r88065) -- "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/2025-03-28/deps.csv", task.str = "972", release = "/scratch/th798/data.table-revdeps/2025-03-28/data.table_release_1.17.0.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-03-28/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/16170527/R-devel/972" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/16170527/R-devel/972/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "pagoda2" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/16170527/R-devel/972/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] "2025-03-28 01:06:38 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/16170527/R-devel/972/library' (as 'lib' is unspecified) Warning: dependency 'scde' is not available also installing the dependencies 'RcppSpdlog', 'dendsort', 'drat', 'N2R', 'sccore' trying URL 'http://cloud.r-project.org/src/contrib/RcppSpdlog_0.0.20.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/dendsort_0.3.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/drat_0.2.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/N2R_1.0.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/sccore_1.0.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/pagoda2_1.0.12.tar.gz' * installing *source* package 'RcppSpdlog' ... ** this is package 'RcppSpdlog' version '0.0.20' ** package 'RcppSpdlog' 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../inst/include/ -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -I../inst/include/ -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c exampleRsink.cpp -o exampleRsink.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c formatter.cpp -o formatter.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c interface.cpp -o interface.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 RcppSpdlog.so RcppExports.o exampleRsink.o formatter.o interface.o installing to /tmp/th798/16170527/R-devel/972/library/00LOCK-RcppSpdlog/00new/RcppSpdlog/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 (RcppSpdlog) * installing *source* package 'dendsort' ... ** this is package 'dendsort' version '0.3.4' ** package 'dendsort' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dendsort) * installing *source* package 'drat' ... ** this is package 'drat' version '0.2.5' ** package 'drat' 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 ** installing vignettes ** 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 (drat) * installing *source* package 'sccore' ... ** this is package 'sccore' version '1.0.5' ** 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: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; | ^~~~~~~~~~~~~~~~ /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/th798/16170527/R-devel/972/library/00LOCK-sccore/00new/sccore/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading 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 'N2R' ... ** this is package 'N2R' version '1.0.3' ** package 'N2R' 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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/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"./n2/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:4: /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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/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"./n2/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 check_openmp.cpp -o check_openmp.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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/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"./n2/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 n2knn.cpp -o n2knn.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 n2knn.cpp:24: /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/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/Eigen/src/SparseCore/SparseMatrix.h:1040:66: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' n2knn.cpp:80:22: 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] /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/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' n2knn.cpp:80:22: 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, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:79:45: required from 'void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename SrcXprType::Scalar = double; typename DstXprType::Scalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:38:16: required from 'Derived& Eigen::SparseMatrixBase::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; Derived = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1239:27: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' n2knn.cpp:80:22: 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] (cd n2 && CFLAGS="-I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " CXXFLAGS="-I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " MAKE="make -f \"/home/th798/R/R-devel/etc/Makeconf\" -f Makefile" make -f "/home/th798/R/R-devel/etc/Makeconf" -f Makefile lib) || exit 1; make[1]: Entering directory '/tmp/th798/16170527/RtmpO8LrWR/R.INSTALL54f2936e8340/N2R/src/n2' /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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base.cc -o base.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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hnsw.cc -o hnsw.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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hnsw_node.cc -o hnsw_node.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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c distance.cc -o distance.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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c heuristic.cc -o heuristic.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'/tmp/th798/16170527/R-devel/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-devel/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mmap.cc -o mmap.o ar rvs ../libn2.a base.o hnsw.o hnsw_node.o distance.o heuristic.o mmap.o ar: creating ../libn2.a a - base.o a - hnsw.o a - hnsw_node.o a - distance.o a - heuristic.o a - mmap.o make[1]: Leaving directory '/tmp/th798/16170527/RtmpO8LrWR/R.INSTALL54f2936e8340/N2R/src/n2' /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 N2R.so RcppExports.o check_openmp.o n2knn.o -L. -lpthread -ln2 -lm -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp installing to /tmp/th798/16170527/R-devel/972/library/00LOCK-N2R/00new/N2R/libs ** 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 ** 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 (N2R) * installing *source* package 'pagoda2' ... ** this is package 'pagoda2' version '1.0.12' ** package 'pagoda2' 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"./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: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; | ^~~~~~~~~~~~~~~~ /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"./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 binaryExport.cpp -o binaryExport.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"./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 checkfunctions.cpp -o checkfunctions.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 ./include/largeVis.h:9, from checkfunctions.cpp:2: /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"./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 edgeweights.cpp -o edgeweights.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 ./include/largeVis.h:9, from edgeweights.cpp:9: /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/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/Eigen/src/SparseCore/SparseMatrix.h:1040:66: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' edgeweights.cpp:155:24: 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] /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/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' edgeweights.cpp:155:24: 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, 0>': /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:79:45: required from 'void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename SrcXprType::Scalar = double; typename DstXprType::Scalar = double]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:38:16: required from 'Derived& Eigen::SparseMatrixBase::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; Derived = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1239:27: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-devel/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' edgeweights.cpp:155:24: 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] /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"./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 gradients.cpp -o gradients.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 ./include/largeVis.h:9, from gradients.cpp:3: /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"./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 largeVis.cpp -o largeVis.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 ./include/largeVis.h:9, from largeVis.cpp:4: /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"./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 misc2.cpp -o misc2.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"./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 pagoda1_liftover.cpp -o pagoda1_liftover.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"./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 rank.cpp -o rank.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 pagoda2.so RcppExports.o binaryExport.o checkfunctions.o edgeweights.o gradients.o largeVis.o misc2.o pagoda1_liftover.o rank.o -L. -lpthread -lm -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -fopenmp installing to /tmp/th798/16170527/R-devel/972/library/00LOCK-pagoda2/00new/pagoda2/libs ** 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 ** 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 (pagoda2) The downloaded source packages are in '/tmp/th798/16170527/RtmprjHN4l/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 181.717 12.589 207.060 > print(Sys.time()) [1] "2025-03-28 01:10:05 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] "2025-03-28 01:10:05 MST" Installing package into '/tmp/th798/16170527/R-devel/972/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.0' ** 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/th798/16170527/R-devel/972/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] "2025-03-28 01:10:33 MST" * using log directory '/tmp/th798/16170527/R-devel/972/pagoda2.Rcheck' * using R Under development (unstable) (2025-03-27 r88065) * 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 'pagoda2/DESCRIPTION' ... OK * this is package 'pagoda2' version '1.0.12' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'scde' * 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 'pagoda2' can be installed ... OK * used C++ compiler: 'g++ (Spack GCC) 12.2.0' * 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 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-03-28 01:14:06 MST" [1] "2025-03-28 01:14:06 MST" Installing package into '/tmp/th798/16170527/R-devel/972/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/th798/16170527/R-devel/972/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] "2025-03-28 01:14:34 MST" * using log directory '/tmp/th798/16170527/R-devel/972/pagoda2.Rcheck' * using R Under development (unstable) (2025-03-27 r88065) * 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 'pagoda2/DESCRIPTION' ... OK * this is package 'pagoda2' version '1.0.12' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'scde' * 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 'pagoda2' can be installed ... OK * used C++ compiler: 'g++ (Spack GCC) 12.2.0' * 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 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-03-28 01:18:00 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$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 4.4.3 (2025-02-28) -- "Trophy Case" 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/2025-03-28/deps.csv", task.str = "972", release = "/scratch/th798/data.table-revdeps/2025-03-28/data.table_release_1.17.0.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-03-28/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/16170527/R-release/972" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/16170527/R-release/972/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "pagoda2" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/16170527/R-release/972/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] "2025-03-28 01:18:07 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/16170527/R-release/972/library' (as 'lib' is unspecified) also installing the dependencies 'RcppSpdlog', 'dendsort', 'drat', 'N2R', 'sccore' trying URL 'http://cloud.r-project.org/src/contrib/RcppSpdlog_0.0.20.tar.gz' Content type 'application/x-gzip' length 287317 bytes (280 KB) ================================================== downloaded 280 KB trying URL 'http://cloud.r-project.org/src/contrib/dendsort_0.3.4.tar.gz' Content type 'application/x-gzip' length 1913330 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'http://cloud.r-project.org/src/contrib/drat_0.2.5.tar.gz' Content type 'application/x-gzip' length 181199 bytes (176 KB) ================================================== downloaded 176 KB trying URL 'http://cloud.r-project.org/src/contrib/N2R_1.0.3.tar.gz' Content type 'application/x-gzip' length 26278 bytes (25 KB) ================================================== downloaded 25 KB trying URL 'http://cloud.r-project.org/src/contrib/sccore_1.0.5.tar.gz' Content type 'application/x-gzip' length 378722 bytes (369 KB) ================================================== downloaded 369 KB trying URL 'http://cloud.r-project.org/src/contrib/pagoda2_1.0.12.tar.gz' Content type 'application/x-gzip' length 544445 bytes (531 KB) ================================================== downloaded 531 KB * installing *source* package 'RcppSpdlog' ... ** package 'RcppSpdlog' 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../inst/include/ -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -I../inst/include/ -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c exampleRsink.cpp -o exampleRsink.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include/ -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c formatter.cpp -o formatter.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include/ -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c interface.cpp -o interface.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 RcppSpdlog.so RcppExports.o exampleRsink.o formatter.o interface.o installing to /tmp/th798/16170527/R-release/972/library/00LOCK-RcppSpdlog/00new/RcppSpdlog/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 (RcppSpdlog) * installing *source* package 'dendsort' ... ** package 'dendsort' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dendsort) * installing *source* package 'drat' ... ** package 'drat' 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 ** installing vignettes ** 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 (drat) * installing *source* package 'sccore' ... ** 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: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; | ^~~~~~~~~~~~~~~~ /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/th798/16170527/R-release/972/library/00LOCK-sccore/00new/sccore/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading 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 'N2R' ... ** package 'N2R' 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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/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"./n2/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:4: /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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/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"./n2/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 check_openmp.cpp -o check_openmp.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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/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"./n2/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 n2knn.cpp -o n2knn.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 n2knn.cpp:24: /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/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/Eigen/src/SparseCore/SparseMatrix.h:1040:66: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' n2knn.cpp:80:22: 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] /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/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' n2knn.cpp:80:22: 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, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:79:45: required from 'void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename SrcXprType::Scalar = double; typename DstXprType::Scalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:38:16: required from 'Derived& Eigen::SparseMatrixBase::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; Derived = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1239:27: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' n2knn.cpp:80:22: 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] (cd n2 && CFLAGS="-I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " CXXFLAGS="-I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " MAKE="make -f \"/home/th798/R/R-release/etc/Makeconf\" -f Makefile" make -f "/home/th798/R/R-release/etc/Makeconf" -f Makefile lib) || exit 1; make[1]: Entering directory '/tmp/th798/16170527/RtmpVE4kHp/R.INSTALL693d2436bd44f/N2R/src/n2' /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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base.cc -o base.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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hnsw.cc -o hnsw.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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hnsw_node.cc -o hnsw_node.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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c distance.cc -o distance.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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c heuristic.cc -o heuristic.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'/tmp/th798/16170527/R-release/972/library/RcppSpdlog/include' -I'/projects/genomic-ml/R/R-release/library/RcppEigen/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I"./include" -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mmap.cc -o mmap.o ar rvs ../libn2.a base.o hnsw.o hnsw_node.o distance.o heuristic.o mmap.o ar: creating ../libn2.a a - base.o a - hnsw.o a - hnsw_node.o a - distance.o a - heuristic.o a - mmap.o make[1]: Leaving directory '/tmp/th798/16170527/RtmpVE4kHp/R.INSTALL693d2436bd44f/N2R/src/n2' /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 N2R.so RcppExports.o check_openmp.o n2knn.o -L. -lpthread -ln2 -lm -L/home/th798/R/R-release/lib -lRlapack -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath -fopenmp installing to /tmp/th798/16170527/R-release/972/library/00LOCK-N2R/00new/N2R/libs ** 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 ** 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 (N2R) * installing *source* package 'pagoda2' ... ** package 'pagoda2' 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"./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: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; | ^~~~~~~~~~~~~~~~ /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"./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 binaryExport.cpp -o binaryExport.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"./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 checkfunctions.cpp -o checkfunctions.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 ./include/largeVis.h:9, from checkfunctions.cpp:2: /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"./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 edgeweights.cpp -o edgeweights.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 ./include/largeVis.h:9, from edgeweights.cpp:9: /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/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/Eigen/src/SparseCore/SparseMatrix.h:1040:66: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' edgeweights.cpp:155:24: 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] /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/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1181:93: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' edgeweights.cpp:155:24: 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, 0>': /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseCompressedBase.h:336:80: required from 'struct Eigen::internal::evaluator > >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1505:8: required from 'struct Eigen::internal::evaluator >' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:79:45: required from 'void Eigen::internal::assign_sparse_to_sparse(DstXprType&, const SrcXprType&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:132:28: required from 'static void Eigen::internal::Assignment::run(DstXprType&, const SrcXprType&, const Eigen::internal::assign_op&) [with DstXprType = Eigen::SparseMatrix; SrcXprType = Eigen::SparseMatrix; Functor = Eigen::internal::assign_op; typename SrcXprType::Scalar = double; typename DstXprType::Scalar = double]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseAssign.h:38:16: required from 'Derived& Eigen::SparseMatrixBase::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; Derived = Eigen::SparseMatrix]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1239:27: required from 'Eigen::SparseMatrix<_Scalar, _Options, _StorageIndex>& Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::operator=(const Eigen::SparseMatrixBase&) [with OtherDerived = Eigen::SparseMatrix; _Scalar = double; int _Options = 0; _StorageIndex = int]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1063:7: required from 'void Eigen::internal::set_from_triplets(const InputIterator&, const InputIterator&, SparseMatrixType&, DupFunctor) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; SparseMatrixType = Eigen::SparseMatrix; DupFunctor = scalar_sum_op]' /projects/genomic-ml/R/R-release/library/RcppEigen/include/Eigen/src/SparseCore/SparseMatrix.h:1110:92: required from 'void Eigen::SparseMatrix<_Scalar, _Flags, _StorageIndex>::setFromTriplets(const InputIterators&, const InputIterators&) [with InputIterators = __gnu_cxx::__normal_iterator*, std::vector > >; _Scalar = double; int _Options = 0; _StorageIndex = int]' edgeweights.cpp:155:24: 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] /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"./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 gradients.cpp -o gradients.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 ./include/largeVis.h:9, from gradients.cpp:3: /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"./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 largeVis.cpp -o largeVis.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 ./include/largeVis.h:9, from largeVis.cpp:4: /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"./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 misc2.cpp -o misc2.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"./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 pagoda1_liftover.cpp -o pagoda1_liftover.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"./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 rank.cpp -o rank.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 pagoda2.so RcppExports.o binaryExport.o checkfunctions.o edgeweights.o gradients.o largeVis.o misc2.o pagoda1_liftover.o rank.o -L. -lpthread -lm -L/home/th798/R/R-release/lib -lRlapack -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath -fopenmp installing to /tmp/th798/16170527/R-release/972/library/00LOCK-pagoda2/00new/pagoda2/libs ** 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 ** 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 (pagoda2) The downloaded source packages are in '/tmp/th798/16170527/RtmpqY6O9J/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 205.494 13.138 229.045 > print(Sys.time()) [1] "2025-03-28 01:21:56 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] "2025-03-28 01:21:56 MST" Installing package into '/tmp/th798/16170527/R-release/972/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** 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/th798/16170527/R-release/972/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] "2025-03-28 01:22:21 MST" * using log directory '/tmp/th798/16170527/R-release/972/pagoda2.Rcheck' * using R version 4.4.3 (2025-02-28) * 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 'pagoda2/DESCRIPTION' ... OK * this is package 'pagoda2' version '1.0.12' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 'pagoda2' can be installed ... OK * used C++ compiler: 'g++ (Spack GCC) 12.2.0' * 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 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-03-28 01:26:06 MST" [1] "2025-03-28 01:26:06 MST" Installing package into '/tmp/th798/16170527/R-release/972/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** 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/th798/16170527/R-release/972/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] "2025-03-28 01:26:34 MST" * using log directory '/tmp/th798/16170527/R-release/972/pagoda2.Rcheck' * using R version 4.4.3 (2025-02-28) * 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 'pagoda2/DESCRIPTION' ... OK * this is package 'pagoda2' version '1.0.12' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * 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 'pagoda2' can be installed ... OK * used C++ compiler: 'g++ (Spack GCC) 12.2.0' * 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 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2025-03-28 01:30:39 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$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) + } >