Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-12-13 r89166) -- "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/2025-12-14/deps.csv", task.str = "151", release = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_master_1.17.99.6329d94b83b72bb1f05dc2a10374e84a61ff950d.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/25889513/R-devel/151" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/25889513/R-devel/151/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "CAST" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/25889513/R-devel/151/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] "2025-12-14 00:28:20 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/25889513/R-devel/151/library' (as 'lib' is unspecified) also installing the dependencies 'prodlim', 'geometries', 'rapidjsonr', 'sfheaders', 'later', 'promises', 'hardhat', 'ipred', 'geojsonsf', 'leaflet.providers', 'httpuv', 'spacesXYZ', 'jsonify', 'lwgeom', 'ModelMetrics', 'pROC', 'recipes', 'reshape2', 'Rcpp', 's2', 'units', 'xfun', 'yaml', 'htmlwidgets', 'leafem', 'leaflet', 'leafpop', 'raster', 'satellite', 'servr', 'cols4all', 'leafgl', 'leaflegend', 'leafsync', 'maptiles', 'tmaptools', 'caret', 'plyr', 'sf', 'twosamples', 'terra', 'knitr', 'geodata', 'mapview', 'rmarkdown', 'stars', 'rnaturalearth', 'tmap', 'PCAmixdata', 'clustMixType' trying URL 'http://cloud.r-project.org/src/contrib/prodlim_2025.04.28.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/geometries_0.2.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rapidjsonr_1.2.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/sfheaders_0.4.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/later_1.4.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/promises_1.5.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/hardhat_1.4.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/ipred_0.9-15.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/geojsonsf_2.0.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leaflet.providers_2.0.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/httpuv_1.6.16.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/spacesXYZ_1.6-0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/jsonify_1.2.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/lwgeom_0.2-14.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/ModelMetrics_1.2.2.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/pROC_1.19.0.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/recipes_1.3.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/reshape2_1.4.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/4.6.0/Other/Rcpp_1.1.0.8.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/s2_1.1.9.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/units_1.0-0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/xfun_0.54.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/yaml_2.3.12.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/htmlwidgets_1.6.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafem_0.2.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leaflet_2.2.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafpop_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/raster_3.6-32.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/satellite_1.0.6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/servr_0.32.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/cols4all_0.10.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafgl_0.2.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leaflegend_1.2.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafsync_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/maptiles_0.11.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tmaptools_3.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/caret_7.0-1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/plyr_1.8.9.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/sf_1.0-23.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/twosamples_2.0.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/terra_1.8-86.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/knitr_1.50.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/geodata_0.6-6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/mapview_2.11.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rmarkdown_2.30.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/stars_0.6-8.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rnaturalearth_1.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tmap_4.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/PCAmixdata_3.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/clustMixType_0.4-2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/CAST_1.0.3.tar.gz' * installing *source* package 'rapidjsonr' ... ** this is package 'rapidjsonr' version '1.2.1' ** package 'rapidjsonr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rapidjsonr) * installing *source* package 'hardhat' ... ** this is package 'hardhat' version '1.4.2' ** package 'hardhat' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/fansi/libs/fansi.so': /projects/genomic-ml/R/R-devel/library/fansi/libs/fansi.so: undefined symbol: R_nchar Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'hardhat' * removing '/tmp/th798/25889513/R-devel/151/library/hardhat' * installing *source* package 'leaflet.providers' ... ** this is package 'leaflet.providers' version '2.0.0' ** package 'leaflet.providers' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leaflet.providers) * installing *source* package 'spacesXYZ' ... ** this is package 'spacesXYZ' version '1.6-0' ** package 'spacesXYZ' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spacesXYZ) * installing *source* package 'Rcpp' ... ** this is package 'Rcpp' version '1.1.0.8.1' ** package 'Rcpp' 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/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 api.cpp -o api.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/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 attributes.cpp -o attributes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/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 barrier.cpp -o barrier.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/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 date.cpp -o date.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/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 module.cpp -o module.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/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 rcpp_init.cpp -o rcpp_init.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 Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-Rcpp/00new/Rcpp/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 (Rcpp) * installing *source* package 'xfun' ... ** this is package 'xfun' version '0.54' ** package 'xfun' successfully unpacked and MD5 sums checked ** using staged installation ** 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 -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.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 -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rand_lcg.c -o rand_lcg.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 xfun.so base64.o init.o rand_lcg.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-xfun/00new/xfun/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 (xfun) * installing *source* package 'yaml' ... ** this is package 'yaml' version '2.3.12' ** package 'yaml' successfully unpacked and MD5 sums checked ** using staged installation ** 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. -DNDEBUG -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 api.c -o api.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 dumper.c -o dumper.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 emitter.c -o emitter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 implicit.c -o implicit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 loader.c -o loader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 parser.c -o parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 r_emit.c -o r_emit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 r_ext.c -o r_ext.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 r_parse.c -o r_parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 reader.c -o reader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 scanner.c -o scanner.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -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 writer.c -o writer.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 yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-yaml/00new/yaml/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 (yaml) * installing *source* package 'twosamples' ... ** this is package 'twosamples' version '2.0.1' ** package 'twosamples' 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/cpp11/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 cpp11.cpp -o cpp11.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/cpp11/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 stat_functions.cpp -o stat_functions.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 twosamples.so cpp11.o stat_functions.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-twosamples/00new/twosamples/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** 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 (twosamples) * installing *source* package 'PCAmixdata' ... ** this is package 'PCAmixdata' version '3.1' ** package 'PCAmixdata' 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 (PCAmixdata) * installing *source* package 'clustMixType' ... ** this is package 'clustMixType' version '0.4-2' ** package 'clustMixType' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/fansi/libs/fansi.so': /projects/genomic-ml/R/R-devel/library/fansi/libs/fansi.so: undefined symbol: R_nchar Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'clustMixType' * removing '/tmp/th798/25889513/R-devel/151/library/clustMixType' * installing *source* package 'prodlim' ... ** this is package 'prodlim' version '2025.04.28' ** package 'prodlim' successfully unpacked and MD5 sums checked ** using staged installation ** 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'/tmp/th798/25889513/R-devel/151/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 GMLE.c -o GMLE.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 IntIndex.c -o IntIndex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 icens_prodlim.c -o icens_prodlim.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 icens_prodlim_ml.c -o icens_prodlim_ml.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 iindex.c -o iindex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 life_table.c -o life_table.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 loo.c -o loo.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 neighborhood.c -o neighborhood.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 predict.c -o predict.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 predict_individual_survival.c -o predict_individual_survival.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 prodlim.c -o prodlim.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 prodlim_clustersurv.c -o prodlim_clustersurv.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 prodlim_comprisk.c -o prodlim_comprisk.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 prodlim_multistates.c -o prodlim_multistates.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 prodlim_surv.c -o prodlim_surv.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 sindex.c -o sindex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 summary_prodlim.c -o summary_prodlim.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 prodlim.so GMLE.o IntIndex.o icens_prodlim.o icens_prodlim_ml.o iindex.o init.o life_table.o loo.o neighborhood.o predict.o predict_individual_survival.o prodlim.o prodlim_clustersurv.o prodlim_comprisk.o prodlim_multistates.o prodlim_surv.o sindex.o summary_prodlim.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-prodlim/00new/prodlim/libs ** R ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so': /projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so: undefined symbol: Rf_GetOption Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'prodlim' * removing '/tmp/th798/25889513/R-devel/151/library/prodlim' * installing *source* package 'geometries' ... ** this is package 'geometries' version '0.2.5' ** package 'geometries' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 bbox.cpp -o bbox.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 close.cpp -o close.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 columns.cpp -o columns.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 coordinates.cpp -o coordinates.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 geometries.cpp -o geometries.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 lines.cpp -o lines.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 lists.cpp -o lists.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 nest.cpp -o nest.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 shapes.cpp -o shapes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 tests.cpp -o tests.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 utils.cpp -o utils.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 geometries.so RcppExports.o bbox.o close.o columns.o coordinates.o geometries.o lines.o lists.o nest.o shapes.o tests.o utils.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-geometries/00new/geometries/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 (geometries) * installing *source* package 'later' ... ** this is package 'later' version '1.4.4' ** package 'later' successfully unpacked and MD5 sums checked ** using staged installation Running configure script -latomic linker flag not needed. ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' 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 -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 In file included from /tmp/th798/25889513/R-devel/151/library/Rcpp/include/RcppCommon.h:30, from /tmp/th798/25889513/R-devel/151/library/Rcpp/include/Rcpp.h:27, from RcppExports.cpp:5: /tmp/th798/25889513/R-devel/151/library/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: '#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410' 35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 callback_registry.cpp -o callback_registry.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 debug.cpp -o debug.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 fd.cpp -o fd.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 later.cpp -o later.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 later_posix.cpp -o later_posix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 later_win32.cpp -o later_win32.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 timer_posix.cpp -o timer_posix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 timestamp_unix.cpp -o timestamp_unix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 timestamp_win32.cpp -o timestamp_win32.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 tinycthread.c -o tinycthread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25889513/R-devel/151/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 wref.c -o wref.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 later.so RcppExports.o callback_registry.o debug.o fd.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o wref.o -pthread installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-later/00new/later/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 (later) * installing *source* package 'jsonify' ... ** this is package 'jsonify' version '1.2.3' ** package 'jsonify' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 from_json.cpp -o from_json.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 pretty.cpp -o pretty.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 read_json.cpp -o read_json.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 tests.cpp -o tests.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 to_json.cpp -o to_json.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 validate.cpp -o validate.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 jsonify.so RcppExports.o from_json.o pretty.o read_json.o tests.o to_json.o validate.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-jsonify/00new/jsonify/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 (jsonify) * installing *source* package 'ModelMetrics' ... ** this is package 'ModelMetrics' version '1.2.2.2' ** package 'ModelMetrics' 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'/tmp/th798/25889513/R-devel/151/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'/tmp/th798/25889513/R-devel/151/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 auc_.cpp -o auc_.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 confusionMatrix_.cpp -o confusionMatrix_.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 error.cpp -o error.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 gini_.cpp -o gini_.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 logLoss_.cpp -o logLoss_.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 ModelMetrics.so RcppExports.o auc_.o confusionMatrix_.o error.o gini_.o logLoss_.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-ModelMetrics/00new/ModelMetrics/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so': /projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so: undefined symbol: Rf_GetOption Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'ModelMetrics' * removing '/tmp/th798/25889513/R-devel/151/library/ModelMetrics' * installing *source* package 'pROC' ... ** this is package 'pROC' version '1.19.0.1' ** package 'pROC' 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'/tmp/th798/25889513/R-devel/151/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'/tmp/th798/25889513/R-devel/151/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 RcppVersion.cpp -o RcppVersion.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 delong.cpp -o delong.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 pROC.so RcppExports.o RcppVersion.o delong.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-pROC/00new/pROC/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pROC) * installing *source* package 's2' ... ** this is package 's2' version '1.1.9' ** package 's2' successfully unpacked and MD5 sums checked ** using staged installation Found OpenSSL pkg-config cflags and libs! Testing compiler OpenSSL configuration using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include ** Using PKG_CONFIG_PATH=/home/th798/.conda/envs/emacs1/lib/pkgconfig:/home/th798/lib/pkgconfig:/home/th798/lib64/pkgconfig:/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/pkgconfig ** Building abseil-cpp using cmake GNU Make 4.2.1 Built for x86_64-redhat-linux-gnu Copyright (C) 1988-2016 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Using MAKE=make cmake version 3.22.1 CMake suite maintained and supported by Kitware (kitware.com/cmake). Using CMAKE=/home/th798/.conda/envs/emacs1/bin/cmake Using MAKE=make -- The CXX compiler identification is GNU 12.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /packages/gcc/12.2.0-nnbserq/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test ABSL_INTERNAL_AT_LEAST_CXX17 -- Performing Test ABSL_INTERNAL_AT_LEAST_CXX17 - Success -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Configuring done -- Generating done -- Build files have been written to: /tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/build/abseil-cpp 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/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/lib64/pkgconfig/absl_bad_variant_access.pc -- Installing: /tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/lib64/libabsl_bad_variant_access.a -- Installing: /tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/lib64/pkgconfig/absl_variant.pc -- Installing: /tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/lib64/pkgconfig/absl_compare.pc -- Installing: /tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/lib64/pkgconfig/absl_utility.pc -- Installing: /tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/lib64/pkgconfig/absl_if_constexpr.pc ** Done! ** Using PKG_CONFIG_PATH=tools/dist/lib64/pkgconfig:/home/th798/.conda/envs/emacs1/lib/pkgconfig:/home/th798/lib/pkgconfig:/home/th798/lib64/pkgconfig:/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/pkgconfig Testing Abseil configuration using PKG_CFLAGS=-I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-Ltools/dist/lib64 -labsl_flags -labsl_flags_internal -labsl_flags_marshalling -labsl_flags_reflection -labsl_flags_private_handle_accessor -labsl_flags_commandlineflag -labsl_flags_commandlineflag_internal -labsl_flags_config -labsl_flags_program_name -labsl_raw_hash_set -labsl_hashtablez_sampler -labsl_log_internal_check_op -labsl_log_internal_conditions -labsl_log_internal_message -labsl_examine_stack -labsl_log_internal_format -labsl_log_internal_proto -labsl_log_internal_nullguard -labsl_log_internal_log_sink_set -labsl_log_internal_globals -labsl_log_globals -labsl_hash -labsl_city -labsl_bad_variant_access -labsl_low_level_hash -labsl_log_sink -labsl_log_entry -labsl_status -labsl_cord -labsl_cordz_info -labsl_cord_internal -labsl_cordz_functions -labsl_exponential_biased -labsl_cordz_handle -labsl_synchronization -labsl_graphcycles_internal -labsl_kernel_timeout_internal -labsl_time -labsl_civil_time -labsl_time_zone -labsl_crc_cord_state -labsl_crc32c -labsl_crc_internal -labsl_crc_cpu_detect -labsl_bad_optional_access -labsl_stacktrace -labsl_str_format_internal -labsl_strerror -labsl_symbolize -labsl_debugging_internal -labsl_demangle_internal -labsl_malloc_internal -labsl_strings -labsl_string_view -labsl_strings_internal -labsl_base -lrt -labsl_spinlock_wait -labsl_int128 -labsl_throw_delegate -labsl_raw_logging_internal -labsl_log_severity -L/home/th798/.conda/envs/emacs1/lib -lssl -lcrypto Using PKG_CFLAGS=-I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++17 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cpp-compat.cpp -o cpp-compat.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-accessors.cpp -o s2-accessors.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-bounds.cpp -o s2-bounds.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-cell.cpp -o s2-cell.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-cell-union.cpp -o s2-cell-union.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-constructors-formatters.cpp -o s2-constructors-formatters.o In file included from /tmp/th798/25889513/R-devel/151/library/Rcpp/include/RcppCommon.h:30, from /tmp/th798/25889513/R-devel/151/library/Rcpp/include/Rcpp.h:27, from geography.h:5, from s2-constructors-formatters.cpp:9: /tmp/th798/25889513/R-devel/151/library/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: '#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410' 27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/th798/25889513/R-devel/151/library/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: '#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410' 35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-predicates.cpp -o s2-predicates.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-transformers.cpp -o s2-transformers.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-geography.cpp -o s2-geography.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-lnglat.cpp -o s2-lnglat.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2-matrix.cpp -o s2-matrix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/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 wk-impl.c -o wk-impl.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/accessors-geog.cc -o s2geography/accessors-geog.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/accessors.cc -o s2geography/accessors.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/build.cc -o s2geography/build.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/coverings.cc -o s2geography/coverings.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/distance.cc -o s2geography/distance.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/geography.cc -o s2geography/geography.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/linear-referencing.cc -o s2geography/linear-referencing.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2geography/predicates.cc -o s2geography/predicates.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/encoded_s2cell_id_vector.cc -o s2/encoded_s2cell_id_vector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/encoded_s2point_vector.cc -o s2/encoded_s2point_vector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/encoded_s2shape_index.cc -o s2/encoded_s2shape_index.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/encoded_string_vector.cc -o s2/encoded_string_vector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/id_set_lexicon.cc -o s2/id_set_lexicon.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/mutable_s2shape_index.cc -o s2/mutable_s2shape_index.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/r2rect.cc -o s2/r2rect.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s1angle.cc -o s2/s1angle.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s1chord_angle.cc -o s2/s1chord_angle.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s1interval.cc -o s2/s1interval.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2boolean_operation.cc -o s2/s2boolean_operation.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2buffer_operation.cc -o s2/s2buffer_operation.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builder_graph.cc -o s2/s2builder_graph.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builder.cc -o s2/s2builder.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_closed_set_normalizer.cc -o s2/s2builderutil_closed_set_normalizer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_find_polygon_degeneracies.cc -o s2/s2builderutil_find_polygon_degeneracies.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_get_snapped_winding_delta.cc -o s2/s2builderutil_get_snapped_winding_delta.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_lax_polygon_layer.cc -o s2/s2builderutil_lax_polygon_layer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_lax_polyline_layer.cc -o s2/s2builderutil_lax_polyline_layer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_s2point_vector_layer.cc -o s2/s2builderutil_s2point_vector_layer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_s2polygon_layer.cc -o s2/s2builderutil_s2polygon_layer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_s2polyline_layer.cc -o s2/s2builderutil_s2polyline_layer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_s2polyline_vector_layer.cc -o s2/s2builderutil_s2polyline_vector_layer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2builderutil_snap_functions.cc -o s2/s2builderutil_snap_functions.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2cap.cc -o s2/s2cap.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2cell_id.cc -o s2/s2cell_id.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2cell_index.cc -o s2/s2cell_index.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2cell_union.cc -o s2/s2cell_union.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2cell.cc -o s2/s2cell.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2centroids.cc -o s2/s2centroids.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2closest_cell_query.cc -o s2/s2closest_cell_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2closest_edge_query.cc -o s2/s2closest_edge_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2closest_point_query.cc -o s2/s2closest_point_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2contains_vertex_query.cc -o s2/s2contains_vertex_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2convex_hull_query.cc -o s2/s2convex_hull_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2coords.cc -o s2/s2coords.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2crossing_edge_query.cc -o s2/s2crossing_edge_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2debug.cc -o s2/s2debug.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2earth.cc -o s2/s2earth.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2edge_clipping.cc -o s2/s2edge_clipping.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2edge_crosser.cc -o s2/s2edge_crosser.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2edge_crossings.cc -o s2/s2edge_crossings.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2edge_distances.cc -o s2/s2edge_distances.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2edge_tessellator.cc -o s2/s2edge_tessellator.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2error.cc -o s2/s2error.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2furthest_edge_query.cc -o s2/s2furthest_edge_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2hausdorff_distance_query.cc -o s2/s2hausdorff_distance_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2latlng_rect_bounder.cc -o s2/s2latlng_rect_bounder.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2latlng_rect.cc -o s2/s2latlng_rect.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2latlng.cc -o s2/s2latlng.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2lax_loop_shape.cc -o s2/s2lax_loop_shape.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2lax_polygon_shape.cc -o s2/s2lax_polygon_shape.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2lax_polyline_shape.cc -o s2/s2lax_polyline_shape.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2loop_measures.cc -o s2/s2loop_measures.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2loop.cc -o s2/s2loop.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2max_distance_targets.cc -o s2/s2max_distance_targets.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2measures.cc -o s2/s2measures.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2memory_tracker.cc -o s2/s2memory_tracker.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2metrics.cc -o s2/s2metrics.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2min_distance_targets.cc -o s2/s2min_distance_targets.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2padded_cell.cc -o s2/s2padded_cell.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2point_compression.cc -o s2/s2point_compression.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2point_region.cc -o s2/s2point_region.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2pointutil.cc -o s2/s2pointutil.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2polygon.cc -o s2/s2polygon.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2polyline_alignment.cc -o s2/s2polyline_alignment.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2polyline_measures.cc -o s2/s2polyline_measures.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2polyline_simplifier.cc -o s2/s2polyline_simplifier.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2polyline.cc -o s2/s2polyline.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2predicates.cc -o s2/s2predicates.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2projections.cc -o s2/s2projections.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2r2rect.cc -o s2/s2r2rect.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2region_coverer.cc -o s2/s2region_coverer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2region_intersection.cc -o s2/s2region_intersection.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2region_term_indexer.cc -o s2/s2region_term_indexer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2region_union.cc -o s2/s2region_union.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2region.cc -o s2/s2region.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shape_index_buffered_region.cc -o s2/s2shape_index_buffered_region.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shape_index_measures.cc -o s2/s2shape_index_measures.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shape_index.cc -o s2/s2shape_index.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shape_measures.cc -o s2/s2shape_measures.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shape_nesting_query.cc -o s2/s2shape_nesting_query.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_build_polygon_boundaries.cc -o s2/s2shapeutil_build_polygon_boundaries.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_coding.cc -o s2/s2shapeutil_coding.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_contains_brute_force.cc -o s2/s2shapeutil_contains_brute_force.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_conversion.cc -o s2/s2shapeutil_conversion.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_edge_iterator.cc -o s2/s2shapeutil_edge_iterator.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_get_reference_point.cc -o s2/s2shapeutil_get_reference_point.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2shapeutil_visit_crossing_edge_pairs.cc -o s2/s2shapeutil_visit_crossing_edge_pairs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2text_format.cc -o s2/s2text_format.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2wedge_relations.cc -o s2/s2wedge_relations.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/s2winding_operation.cc -o s2/s2winding_operation.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/util/bits/bit-interleave.cc -o s2/util/bits/bit-interleave.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/util/coding/coder.cc -o s2/util/coding/coder.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/util/coding/varint.cc -o s2/util/coding/varint.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/util/math/exactfloat/exactfloat.cc -o s2/util/math/exactfloat/exactfloat.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/util/math/mathutil.cc -o s2/util/math/mathutil.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../src -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/wk/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I/tmp/th798/25889513/RtmpxxGla0/R.INSTALL26f333301e76bf/s2/tools/dist/include -I/home/th798/.conda/envs/emacs1/include -pthread -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c s2/util/units/length-units.cc -o s2/util/units/length-units.o ar rcs s2/libs2static.a s2/encoded_s2cell_id_vector.o s2/encoded_s2point_vector.o s2/encoded_s2shape_index.o s2/encoded_string_vector.o s2/id_set_lexicon.o s2/mutable_s2shape_index.o s2/r2rect.o s2/s1angle.o s2/s1chord_angle.o s2/s1interval.o s2/s2boolean_operation.o s2/s2buffer_operation.o s2/s2builder_graph.o s2/s2builder.o s2/s2builderutil_closed_set_normalizer.o s2/s2builderutil_find_polygon_degeneracies.o s2/s2builderutil_get_snapped_winding_delta.o s2/s2builderutil_lax_polygon_layer.o s2/s2builderutil_lax_polyline_layer.o s2/s2builderutil_s2point_vector_layer.o s2/s2builderutil_s2polygon_layer.o s2/s2builderutil_s2polyline_layer.o s2/s2builderutil_s2polyline_vector_layer.o s2/s2builderutil_snap_functions.o s2/s2cap.o s2/s2cell_id.o s2/s2cell_index.o s2/s2cell_union.o s2/s2cell.o s2/s2centroids.o s2/s2closest_cell_query.o s2/s2closest_edge_query.o s2/s2closest_point_query.o s2/s2contains_vertex_query.o s2/s2convex_hull_query.o s2/s2coords.o s2/s2crossing_edge_query.o s2/s2debug.o s2/s2earth.o s2/s2edge_clipping.o s2/s2edge_crosser.o s2/s2edge_crossings.o s2/s2edge_distances.o s2/s2edge_tessellator.o s2/s2error.o s2/s2furthest_edge_query.o s2/s2hausdorff_distance_query.o s2/s2latlng_rect_bounder.o s2/s2latlng_rect.o s2/s2latlng.o s2/s2lax_loop_shape.o s2/s2lax_polygon_shape.o s2/s2lax_polyline_shape.o s2/s2loop_measures.o s2/s2loop.o s2/s2max_distance_targets.o s2/s2measures.o s2/s2memory_tracker.o s2/s2metrics.o s2/s2min_distance_targets.o s2/s2padded_cell.o s2/s2point_compression.o s2/s2point_region.o s2/s2pointutil.o s2/s2polygon.o s2/s2polyline_alignment.o s2/s2polyline_measures.o s2/s2polyline_simplifier.o s2/s2polyline.o s2/s2predicates.o s2/s2projections.o s2/s2r2rect.o s2/s2region_coverer.o s2/s2region_intersection.o s2/s2region_term_indexer.o s2/s2region_union.o s2/s2region.o s2/s2shape_index_buffered_region.o s2/s2shape_index_measures.o s2/s2shape_index.o s2/s2shape_measures.o s2/s2shape_nesting_query.o s2/s2shapeutil_build_polygon_boundaries.o s2/s2shapeutil_coding.o s2/s2shapeutil_contains_brute_force.o s2/s2shapeutil_conversion.o s2/s2shapeutil_edge_iterator.o s2/s2shapeutil_get_reference_point.o s2/s2shapeutil_visit_crossing_edge_pairs.o s2/s2text_format.o s2/s2wedge_relations.o s2/s2winding_operation.o s2/util/bits/bit-interleave.o s2/util/coding/coder.o s2/util/coding/varint.o s2/util/math/exactfloat/exactfloat.o s2/util/math/mathutil.o s2/util/units/length-units.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 s2.so cpp-compat.o s2-accessors.o s2-bounds.o s2-cell.o s2-cell-union.o s2-constructors-formatters.o s2-predicates.o s2-transformers.o init.o RcppExports.o s2-geography.o s2-lnglat.o s2-matrix.o wk-impl.o s2geography/accessors-geog.o s2geography/accessors.o s2geography/build.o s2geography/coverings.o s2geography/distance.o s2geography/geography.o s2geography/linear-referencing.o s2geography/predicates.o -Ls2 -ls2static -Ltools/dist/lib64 -labsl_flags -labsl_flags_internal -labsl_flags_marshalling -labsl_flags_reflection -labsl_flags_private_handle_accessor -labsl_flags_commandlineflag -labsl_flags_commandlineflag_internal -labsl_flags_config -labsl_flags_program_name -labsl_raw_hash_set -labsl_hashtablez_sampler -labsl_log_internal_check_op -labsl_log_internal_conditions -labsl_log_internal_message -labsl_examine_stack -labsl_log_internal_format -labsl_log_internal_proto -labsl_log_internal_nullguard -labsl_log_internal_log_sink_set -labsl_log_internal_globals -labsl_log_globals -labsl_hash -labsl_city -labsl_bad_variant_access -labsl_low_level_hash -labsl_log_sink -labsl_log_entry -labsl_status -labsl_cord -labsl_cordz_info -labsl_cord_internal -labsl_cordz_functions -labsl_exponential_biased -labsl_cordz_handle -labsl_synchronization -labsl_graphcycles_internal -labsl_kernel_timeout_internal -labsl_time -labsl_civil_time -labsl_time_zone -labsl_crc_cord_state -labsl_crc32c -labsl_crc_internal -labsl_crc_cpu_detect -labsl_bad_optional_access -labsl_stacktrace -labsl_str_format_internal -labsl_strerror -labsl_symbolize -labsl_debugging_internal -labsl_demangle_internal -labsl_malloc_internal -labsl_strings -labsl_string_view -labsl_strings_internal -labsl_base -lrt -labsl_spinlock_wait -labsl_int128 -labsl_throw_delegate -labsl_raw_logging_internal -labsl_log_severity -L/home/th798/.conda/envs/emacs1/lib -lssl -lcrypto /usr/bin/ld: cannot find -labsl_flags /usr/bin/ld: cannot find -labsl_flags_internal /usr/bin/ld: cannot find -labsl_flags_marshalling /usr/bin/ld: cannot find -labsl_flags_reflection /usr/bin/ld: cannot find -labsl_flags_private_handle_accessor /usr/bin/ld: cannot find -labsl_flags_commandlineflag /usr/bin/ld: cannot find -labsl_flags_commandlineflag_internal /usr/bin/ld: cannot find -labsl_flags_config /usr/bin/ld: cannot find -labsl_flags_program_name /usr/bin/ld: cannot find -labsl_raw_hash_set /usr/bin/ld: cannot find -labsl_hashtablez_sampler /usr/bin/ld: cannot find -labsl_log_internal_check_op /usr/bin/ld: cannot find -labsl_log_internal_conditions /usr/bin/ld: cannot find -labsl_log_internal_message /usr/bin/ld: cannot find -labsl_examine_stack /usr/bin/ld: cannot find -labsl_log_internal_format /usr/bin/ld: cannot find -labsl_log_internal_proto /usr/bin/ld: cannot find -labsl_log_internal_nullguard /usr/bin/ld: cannot find -labsl_log_internal_log_sink_set /usr/bin/ld: cannot find -labsl_log_internal_globals /usr/bin/ld: cannot find -labsl_log_globals /usr/bin/ld: cannot find -labsl_hash /usr/bin/ld: cannot find -labsl_city /usr/bin/ld: cannot find -labsl_bad_variant_access /usr/bin/ld: cannot find -labsl_low_level_hash /usr/bin/ld: cannot find -labsl_log_sink /usr/bin/ld: cannot find -labsl_log_entry /usr/bin/ld: cannot find -labsl_status /usr/bin/ld: cannot find -labsl_cord /usr/bin/ld: cannot find -labsl_cordz_info /usr/bin/ld: cannot find -labsl_cord_internal /usr/bin/ld: cannot find -labsl_cordz_functions /usr/bin/ld: cannot find -labsl_exponential_biased /usr/bin/ld: cannot find -labsl_cordz_handle /usr/bin/ld: cannot find -labsl_synchronization /usr/bin/ld: cannot find -labsl_graphcycles_internal /usr/bin/ld: cannot find -labsl_kernel_timeout_internal /usr/bin/ld: cannot find -labsl_time /usr/bin/ld: cannot find -labsl_civil_time /usr/bin/ld: cannot find -labsl_time_zone /usr/bin/ld: cannot find -labsl_crc_cord_state /usr/bin/ld: cannot find -labsl_crc32c /usr/bin/ld: cannot find -labsl_crc_internal /usr/bin/ld: cannot find -labsl_crc_cpu_detect /usr/bin/ld: cannot find -labsl_bad_optional_access /usr/bin/ld: cannot find -labsl_stacktrace /usr/bin/ld: cannot find -labsl_str_format_internal /usr/bin/ld: cannot find -labsl_strerror /usr/bin/ld: cannot find -labsl_symbolize /usr/bin/ld: cannot find -labsl_debugging_internal /usr/bin/ld: cannot find -labsl_demangle_internal /usr/bin/ld: cannot find -labsl_malloc_internal /usr/bin/ld: cannot find -labsl_strings /usr/bin/ld: cannot find -labsl_string_view /usr/bin/ld: cannot find -labsl_strings_internal /usr/bin/ld: cannot find -labsl_base /usr/bin/ld: cannot find -labsl_spinlock_wait /usr/bin/ld: cannot find -labsl_int128 /usr/bin/ld: cannot find -labsl_throw_delegate /usr/bin/ld: cannot find -labsl_raw_logging_internal /usr/bin/ld: cannot find -labsl_log_severity collect2: error: ld returned 1 exit status make: *** [/home/th798/R/R-devel/share/make/shlib.mk:10: s2.so] Error 1 ERROR: compilation failed for package 's2' * removing '/tmp/th798/25889513/R-devel/151/library/s2' * installing *source* package 'units' ... ** this is package 'units' version '1.0-0' ** package 'units' successfully unpacked and MD5 sums checked ** using staged installation configure: units: 1.0-0 checking for default C++ standard... 201703 checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 option to enable C++11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for _Bool... no checking for stdbool.h that conforms to C99 or later... yes checking for error_at_line... yes checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the compiler supports GNU C... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed checking for brew... no checking for XML_ParserCreate in -lexpat... yes checking for udunits2.h... no checking for udunits2/udunits2.h... yes checking for ut_read_xml in -ludunits2... yes configure: creating ./config.status config.status: creating src/Makevars ** 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 -DUDUNITS2_DIR=1 -I'/tmp/th798/25889513/R-devel/151/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 -DUDUNITS2_DIR=1 -I'/tmp/th798/25889513/R-devel/151/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 tokenizer.cpp -o tokenizer.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DUDUNITS2_DIR=1 -I'/tmp/th798/25889513/R-devel/151/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 udunits.cpp -o udunits.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 units.so RcppExports.o tokenizer.o udunits.o -lexpat -lexpat -ludunits2 installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-units/00new/units/libs ** R ** demo ** 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 (units) * installing *source* package 'cols4all' ... ** this is package 'cols4all' version '0.10' ** package 'cols4all' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cols4all) * installing *source* package 'plyr' ... ** this is package 'plyr' version '1.8.9' ** package 'plyr' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' 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'/tmp/th798/25889513/R-devel/151/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/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 loop_apply.c -o loop_apply.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 split-numeric.cpp -o split-numeric.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 plyr.so RcppExports.o loop_apply.o split-numeric.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-plyr/00new/plyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (plyr) * installing *source* package 'terra' ... ** this is package 'terra' version '1.8-86' ** package 'terra' successfully unpacked and MD5 sums checked ** using staged installation configure: CC: /packages/gcc/12.2.0-nnbserq/bin/gcc configure: CXX: /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 checking for gdal-config... /packages/gdal/3.3.1/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.3.1 checking GDAL version >= 2.0.1... yes checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for gdal.h... yes checking GDAL: linking with --libs only... yes checking GDAL: /packages/gdal/3.3.1/share/gdal/pcs.csv readable... no checking GDAL: checking whether PROJ is available for linking:... yes checking GDAL: checking whether PROJ is available for running:... yes configure: GDAL: 3.3.1 checking for proj.h... yes checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes checking for geos-config... /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/bin/geos-config checking geos-config usability... yes configure: GEOS: 3.8.1 checking GEOS version >= 3.4.0... yes checking for geos_c.h... yes checking geos: linking with -L/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/lib -lgeos_c... yes checking Intel TBB exists:... no configure: WARNING: to support parallel processing install TBB devel or update the PKG_CONFIG_PATH environment variable configure: Package CPP flags: -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include configure: Package LIBS: -L/packages/gdal/3.3.1/lib -lgdal -lproj -L/packages/gdal/3.3.1/lib -lgdal -L/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/lib -lgeos_c configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++17 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 RcppFunctions.cpp -o RcppFunctions.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 RcppModule.cpp -o RcppModule.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 arith.cpp -o arith.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 crs.cpp -o crs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 distRaster.cpp -o distRaster.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 distValueRaster.cpp -o distValueRaster.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 distVector.cpp -o distVector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 distance.cpp -o distance.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 extract.cpp -o extract.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 file_utils.cpp -o file_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 focal.cpp -o focal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 gcp.cpp -o gcp.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 gdal_algs.cpp -o gdal_algs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 gdal_multidimensional.cpp -o gdal_multidimensional.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 gdalio.cpp -o gdalio.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 geodesic.c -o geodesic.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 geos_methods.cpp -o geos_methods.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 geosphere.cpp -o geosphere.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 math_utils.cpp -o math_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 mediancut.cpp -o mediancut.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 memory.cpp -o memory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 movingWindow.cpp -o movingWindow.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 ncdf.cpp -o ncdf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 nearest.cpp -o nearest.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 patches.cpp -o patches.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 ram.cpp -o ram.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 raster_methods.cpp -o raster_methods.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 raster_stats.cpp -o raster_stats.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 rasterize.cpp -o rasterize.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 read.cpp -o read.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 read_gdal.cpp -o read_gdal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 read_ogr.cpp -o read_ogr.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 sample.cpp -o sample.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 sort.cpp -o sort.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatBase.cpp -o spatBase.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatDataframe.cpp -o spatDataframe.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatFactor.cpp -o spatFactor.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatRaster.cpp -o spatRaster.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatRasterMultiple.cpp -o spatRasterMultiple.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatSources.cpp -o spatSources.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatTime.cpp -o spatTime.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatVector.cpp -o spatVector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 spatVector2.cpp -o spatVector2.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 string_utils.cpp -o string_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 surfArea.cpp -o surfArea.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 table_utils.cpp -o table_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 vecmath.cpp -o vecmath.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 vecmathse.cpp -o vecmathse.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 vector_methods.cpp -o vector_methods.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 watershed_internal.cpp -o watershed_internal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 write.cpp -o write.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 write_gdal.cpp -o write_gdal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-devel/151/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 write_ogr.cpp -o write_ogr.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 terra.so RcppExports.o RcppFunctions.o RcppModule.o arith.o crs.o distRaster.o distValueRaster.o distVector.o distance.o extract.o file_utils.o focal.o gcp.o gdal_algs.o gdal_multidimensional.o gdalio.o geodesic.o geos_methods.o geosphere.o math_utils.o mediancut.o memory.o movingWindow.o ncdf.o nearest.o patches.o ram.o raster_methods.o raster_stats.o rasterize.o read.o read_gdal.o read_ogr.o sample.o sort.o spatBase.o spatDataframe.o spatFactor.o spatRaster.o spatRasterMultiple.o spatSources.o spatTime.o spatVector.o spatVector2.o string_utils.o surfArea.o table_utils.o vecmath.o vecmathse.o vector_methods.o watershed_internal.o write.o write_gdal.o write_ogr.o -L/packages/gdal/3.3.1/lib -lgdal -lproj -L/packages/gdal/3.3.1/lib -lgdal -L/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/lib -lgeos_c installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-terra/00new/terra/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'sds' with signature 'x="stars"': no definition for class "stars" in method for 'sds' with signature 'x="stars_proxy"': no definition for class "stars_proxy" in method for 'svc' with signature 'x="sf"': no definition for class "sf" in method for 'coerce' with signature '"stars","SpatRasterDataset"': no definition for class "stars" in method for 'coerce' with signature '"ggmap","SpatRaster"': no definition for class "ggmap" in method for 'coerce' with signature '"sf","SpatRaster"': no definition for class "sf" in method for 'coerce' with signature '"sf","SpatVector"': no definition for class "sf" in method for 'coerce' with signature '"sfc","SpatVector"': no definition for class "sfc" in method for 'coerce' with signature '"sfg","SpatVector"': no definition for class "sfg" in method for 'coerce' with signature '"XY","SpatVector"': no definition for class "XY" in method for 'coerce' with signature '"im","SpatRaster"': no definition for class "im" in method for 'coerce' with signature '"SpatVector","Spatial"': no definition for class "Spatial" in method for 'coerce' with signature '"Spatial","SpatVector"': no definition for class "Spatial" in method for 'coerce' with signature '"SpatialGrid","SpatRaster"': no definition for class "SpatialGrid" in method for 'coerce' with signature '"SpatialPixels","SpatRaster"': no definition for class "SpatialPixels" in method for 'crs' with signature '"sf"': no definition for class "sf" Creating a generic function for 'ncol' from package 'base' in package 'terra' in method for 'distance' with signature 'x="SpatRaster",y="sf"': no definition for class "sf" in method for 'ext' with signature 'x="sf"': no definition for class "sf" in method for 'ext' with signature 'x="bbox"': no definition for class "bbox" in method for 'ext' with signature 'x="Extent"': no definition for class "Extent" in method for 'ext' with signature 'x="Raster"': no definition for class "Raster" in method for 'ext' with signature 'x="Spatial"': no definition for class "Spatial" in method for 'extract' with signature 'x="SpatRaster",y="sf"': no definition for class "sf" in method for 'mask' with signature 'x="SpatRaster",mask="sf"': no definition for class "sf" in method for 'points' with signature 'x="sf"': no definition for class "sf" in method for 'lines' with signature 'x="sf"': no definition for class "sf" in method for 'polys' with signature 'x="sf"': no definition for class "sf" in method for 'polys' with signature 'x="leaflet"': no definition for class "leaflet" in method for 'lines' with signature 'x="leaflet"': no definition for class "leaflet" in method for 'points' with signature 'x="leaflet"': no definition for class "leaflet" in method for 'rast' with signature 'x="stars"': no definition for class "stars" in method for 'rast' with signature 'x="stars_proxy"': no definition for class "stars_proxy" in method for 'rasterize' with signature 'x="sf",y="SpatRaster"': no definition for class "sf" Creating a generic function for 'rowSums' from package 'base' in package 'terra' Creating a generic function for 'colSums' from package 'base' in package 'terra' Creating a generic function for 'rowMeans' from package 'base' in package 'terra' Creating a generic function for 'colMeans' from package 'base' in package 'terra' in method for 'show' with signature '"Rcpp_SpatDataFrame"': no definition for class "Rcpp_SpatDataFrame" in method for 'show' with signature '"Rcpp_SpatCategories"': no definition for class "Rcpp_SpatCategories" in method for 'geomtype' with signature 'x="Spatial"': no definition for class "Spatial" Creating a generic function for 'identical' from package 'base' in package 'terra' in method for 'vect' with signature 'x="Spatial"': no definition for class "Spatial" in method for 'vect' with signature 'x="sf"': no definition for class "sf" in method for 'vect' with signature 'x="sfc"': no definition for class "sfc" in method for 'vect' with signature 'x="XY"': no definition for class "XY" Creating a generic function for 'unserialize' from package 'base' in package 'terra' Creating a generic function for 'readRDS' from package 'base' in package 'terra' ** help *** installing help indices *** copying figures ** 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 (terra) * installing *source* package 'knitr' ... ** this is package 'knitr' version '1.50' ** package 'knitr' 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 (knitr) * installing *source* package 'sfheaders' ... ** this is package 'sfheaders' version '0.4.5' ** package 'sfheaders' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 bbox.cpp -o bbox.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 cast.cpp -o cast.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 lists.cpp -o lists.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 sfg_dimension.cpp -o sfg_dimension.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 shapes.cpp -o shapes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 to_df.cpp -o to_df.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 to_sf.cpp -o to_sf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 to_sfc.cpp -o to_sfc.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 to_sfg.cpp -o to_sfg.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/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 utils.cpp -o utils.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 sfheaders.so RcppExports.o bbox.o cast.o lists.o sfg_dimension.o shapes.o to_df.o to_sf.o to_sfc.o to_sfg.o utils.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-sfheaders/00new/sfheaders/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 (sfheaders) * installing *source* package 'promises' ... ** this is package 'promises' version '1.5.0' ** package 'promises' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (promises) ERROR: dependency 'prodlim' is not available for package 'ipred' Perhaps try a variation of: install.packages('prodlim') * removing '/tmp/th798/25889513/R-devel/151/library/ipred' * installing *source* package 'reshape2' ... ** this is package 'reshape2' version '1.4.5' ** package 'reshape2' 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'/tmp/th798/25889513/R-devel/151/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'/tmp/th798/25889513/R-devel/151/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 melt.cpp -o melt.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 reshape2.so RcppExports.o melt.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-reshape2/00new/reshape2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (reshape2) * installing *source* package 'raster' ... ** this is package 'raster' version '3.6-32' ** package 'raster' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' 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'/tmp/th798/25889513/R-devel/151/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 RasterModule.cpp -o RasterModule.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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'/tmp/th798/25889513/R-devel/151/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 aggregate.cpp -o aggregate.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 bilinear.cpp -o bilinear.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 broom.cpp -o broom.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 cellRowCol.cpp -o cellRowCol.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 clamp.cpp -o clamp.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 distance.cpp -o distance.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 edge.cpp -o edge.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 focal_fun.cpp -o focal_fun.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 focal_get.cpp -o focal_get.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 focal_sum.cpp -o focal_sum.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 geodesic.c -o geodesic.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 getPolygons.cpp -o getPolygons.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 layerize.cpp -o layerize.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 memory.cpp -o memory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 modal.cpp -o modal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 ppmin.cpp -o ppmin.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 raster_aggregate.cpp -o raster_aggregate.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 raster_distance.cpp -o raster_distance.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 rasterize.cpp -o rasterize.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 reclass.cpp -o reclass.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 terrain.cpp -o terrain.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 util.cpp -o util.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25889513/R-devel/151/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 xyCell.cpp -o xyCell.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 raster.so RasterModule.o RcppExports.o aggregate.o bilinear.o broom.o cellRowCol.o clamp.o distance.o edge.o focal_fun.o focal_get.o focal_sum.o geodesic.o getPolygons.o layerize.o memory.o modal.o ppmin.o raster_aggregate.o raster_distance.o rasterize.o reclass.o terrain.o util.o xyCell.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-raster/00new/raster/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'initialize' with signature '"BasicRaster"': no definition for class "BasicRaster" in method for 'brick' with signature 'x="kasc"': no definition for class "kasc" in method for 'brick' with signature 'x="grf"': no definition for class "grf" in method for 'coerce' with signature '"STFDF","RasterBrick"': no definition for class "STFDF" in method for 'coerce' with signature '"STSDF","RasterBrick"': no definition for class "STSDF" in method for 'coerce' with signature '"asc","RasterLayer"': no definition for class "asc" in method for 'coerce' with signature '"RasterLayer","asc"': no definition for class "asc" in method for 'coerce' with signature '"kasc","RasterBrick"': no definition for class "kasc" in method for 'coerce' with signature '"kasc","RasterStack"': no definition for class "kasc" in method for 'coerce' with signature '"kde","RasterLayer"': no definition for class "kde" in method for 'coerce' with signature '"grf","RasterBrick"': no definition for class "grf" in method for 'coerce' with signature '"grf","RasterLayer"': no definition for class "grf" in method for 'extent' with signature 'x="bbox"': no definition for class "bbox" in method for 'extent' with signature 'x="sf"': no definition for class "sf" in method for 'extract' with signature 'x="Raster",y="sf"': no definition for class "sf" in method for 'mask' with signature 'x="Raster",mask="sf"': no definition for class "sf" in method for 'raster' with signature 'x="sf"': no definition for class "sf" in method for 'raster' with signature 'x="kasc"': no definition for class "kasc" in method for 'raster' with signature 'x="asc"': no definition for class "asc" in method for 'raster' with signature 'x="kde"': no definition for class "kde" in method for 'raster' with signature 'x="grf"': no definition for class "grf" in method for 'rasterize' with signature 'x="sf",y="Raster"': no definition for class "sf" in method for 'setValues' with signature 'x="RasterLayerSparse"': no definition for class "RasterLayerSparse" in method for 'stack' with signature 'x="kasc"': no definition for class "kasc" ** 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 (raster) ERROR: dependency 's2' is not available for package 'sf' Perhaps try a variation of: install.packages('s2') * removing '/tmp/th798/25889513/R-devel/151/library/sf' * installing *source* package 'geodata' ... ** this is package 'geodata' version '0.6-6' ** package 'geodata' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geodata) * installing *source* package 'rmarkdown' ... ** this is package 'rmarkdown' version '2.30' ** package 'rmarkdown' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (rmarkdown) * installing *source* package 'geojsonsf' ... ** this is package 'geojsonsf' version '2.0.5' ** package 'geojsonsf' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 df_geojson.cpp -o df_geojson.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 geojson_to_sf.cpp -o geojson_to_sf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 geojson_to_wkt.cpp -o geojson_to_wkt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 geojson_wkt.cpp -o geojson_wkt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 read_geojson.cpp -o read_geojson.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-devel/151/library/geometries/include' -I'/tmp/th798/25889513/R-devel/151/library/jsonify/include' -I'/tmp/th798/25889513/R-devel/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-devel/151/library/sfheaders/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 sf_geojson.cpp -o sf_geojson.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 geojsonsf.so RcppExports.o df_geojson.o geojson_to_sf.o geojson_to_wkt.o geojson_wkt.o read_geojson.o sf_geojson.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-geojsonsf/00new/geojsonsf/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geojsonsf) * installing *source* package 'httpuv' ... ** this is package 'httpuv' version '1.6.16' ** package 'httpuv' successfully unpacked and MD5 sums checked ** using staged installation ** Using bundled copy of libuv ** PKG_CFLAGS=-Ilibuv/include ** PKG_LIBS=./libuv/.libs/libuv.b ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' 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 -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c callback.cpp -o callback.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c callbackqueue.cpp -o callbackqueue.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c filedatasource-unix.cpp -o filedatasource-unix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c filedatasource-win.cpp -o filedatasource-win.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fs.cpp -o fs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gzipdatasource.cpp -o gzipdatasource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c http.cpp -o http.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c httprequest.cpp -o httprequest.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c httpresponse.cpp -o httpresponse.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c httpuv.cpp -o httpuv.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c md5.c -o md5.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mime.cpp -o mime.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c socket.cpp -o socket.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c staticpath.cpp -o staticpath.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c thread.cpp -o thread.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c timegm.cpp -o timegm.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uvutil.cpp -o uvutil.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c webapplication.cpp -o webapplication.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c websockets-base.cpp -o websockets-base.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c websockets-hixie76.cpp -o websockets-hixie76.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c websockets-hybi03.cpp -o websockets-hybi03.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c websockets-ietf.cpp -o websockets-ietf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c websockets.cpp -o websockets.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c winutils.cpp -o winutils.o cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4 ignoring -p /usr/bin/cp -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4 cd libuv; \ if ! command -v automake >/dev/null 2>&1 ; then \ echo "automake not found. Touching files so configure will not try to run automake."; \ touch aclocal.m4; \ touch -r aclocal.m4 configure Makefile.in; \ else \ echo "automake found. Running autoupdate and autogen.sh."; \ autoupdate; \ sh autogen.sh; \ fi; \ chmod +x configure; \ CC="/packages/gcc/12.2.0-nnbserq/bin/gcc" 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 -fpic -fvisibility=hidden -DNDEBUG" CPPFLAGS="-I/home/th798/.conda/envs/emacs1/include -I/home/th798/include" AR="ar" RANLIB="ranlib" LDFLAGS="-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" ./configure "--quiet" automake not found. Touching files so configure will not try to run automake. /usr/bin/cp .//depcomp conftest.dir make --directory=libuv \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/th798/25889513/RtmpmyIiy5/R.INSTALL2880fe211b1bde/httpuv/src/libuv' CC src/libuv_la-fs-poll.lo CC src/libuv_la-idna.lo CC src/libuv_la-inet.lo CC src/libuv_la-random.lo CC src/libuv_la-strscpy.lo CC src/libuv_la-threadpool.lo CC src/libuv_la-timer.lo CC src/libuv_la-uv-data-getter-setters.lo CC src/libuv_la-uv-common.lo CC src/libuv_la-version.lo CC src/unix/libuv_la-async.lo CC src/unix/libuv_la-core.lo CC src/unix/libuv_la-dl.lo CC src/unix/libuv_la-fs.lo CC src/unix/libuv_la-getaddrinfo.lo CC src/unix/libuv_la-getnameinfo.lo CC src/unix/libuv_la-loop-watcher.lo CC src/unix/libuv_la-loop.lo CC src/unix/libuv_la-pipe.lo CC src/unix/libuv_la-poll.lo CC src/unix/libuv_la-process.lo CC src/unix/libuv_la-random-devurandom.lo CC src/unix/libuv_la-signal.lo CC src/unix/libuv_la-stream.lo CC src/unix/libuv_la-tcp.lo CC src/unix/libuv_la-thread.lo CC src/unix/libuv_la-tty.lo CC src/unix/libuv_la-udp.lo CC src/unix/libuv_la-linux-core.lo CC src/unix/libuv_la-linux-inotify.lo CC src/unix/libuv_la-linux-syscalls.lo CC src/unix/libuv_la-procfs-exepath.lo CC src/unix/libuv_la-proctitle.lo CC src/unix/libuv_la-random-getrandom.lo CC src/unix/libuv_la-random-sysctl-linux.lo CC src/unix/libuv_la-epoll.lo CCLD libuv.la make[1]: Leaving directory '/tmp/th798/25889513/RtmpmyIiy5/R.INSTALL2880fe211b1bde/httpuv/src/libuv' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c http-parser/http_parser.c -o http-parser/http_parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha1/sha1.c -o sha1/sha1.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilibuv/include -pthread -I'/tmp/th798/25889513/R-devel/151/library/later/include' -I'/tmp/th798/25889513/R-devel/151/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64/base64.cpp -o base64/base64.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 httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o ./libuv/.libs/libuv.b ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-httpuv/00new/httpuv/libs ** R ** demo ** 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 (httpuv) ERROR: dependency 'sf' is not available for package 'lwgeom' Perhaps try a variation of: install.packages('sf') * removing '/tmp/th798/25889513/R-devel/151/library/lwgeom' ERROR: dependency 'ipred' is not available for package 'recipes' Perhaps try a variation of: install.packages('ipred') * removing '/tmp/th798/25889513/R-devel/151/library/recipes' * installing *source* package 'htmlwidgets' ... ** this is package 'htmlwidgets' version '1.6.4' ** package 'htmlwidgets' 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 (htmlwidgets) * installing *source* package 'satellite' ... ** this is package 'satellite' version '1.0.6' ** package 'satellite' 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'/tmp/th798/25889513/R-devel/151/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'/tmp/th798/25889513/R-devel/151/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 SatelliteCppFun.cpp -o SatelliteCppFun.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 satellite.so RcppExports.o SatelliteCppFun.o installing to /tmp/th798/25889513/R-devel/151/library/00LOCK-satellite/00new/satellite/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (satellite) ERROR: dependency 'sf' is not available for package 'maptiles' Perhaps try a variation of: install.packages('sf') * removing '/tmp/th798/25889513/R-devel/151/library/maptiles' ERROR: dependency 'sf' is not available for package 'stars' Perhaps try a variation of: install.packages('sf') * removing '/tmp/th798/25889513/R-devel/151/library/stars' ERROR: dependency 'sf' is not available for package 'rnaturalearth' Perhaps try a variation of: install.packages('sf') * removing '/tmp/th798/25889513/R-devel/151/library/rnaturalearth' ERROR: dependency 'sf' is not available for package 'leaflet' Perhaps try a variation of: install.packages('sf') * removing '/tmp/th798/25889513/R-devel/151/library/leaflet' ERROR: dependency 'sf' is not available for package 'leafpop' Perhaps try a variation of: install.packages('sf') * removing '/tmp/th798/25889513/R-devel/151/library/leafpop' * installing *source* package 'servr' ... ** this is package 'servr' version '0.32' ** package 'servr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (servr) ERROR: dependencies 'sf', 'lwgeom', 'stars' are not available for package 'tmaptools' Perhaps try a variation of: install.packages(c('sf', 'lwgeom', 'stars')) * removing '/tmp/th798/25889513/R-devel/151/library/tmaptools' ERROR: dependencies 'ModelMetrics', 'recipes' are not available for package 'caret' Perhaps try a variation of: install.packages(c('ModelMetrics', 'recipes')) * removing '/tmp/th798/25889513/R-devel/151/library/caret' ERROR: dependencies 'leaflet', 'sf' are not available for package 'leafem' Perhaps try a variation of: install.packages(c('leaflet', 'sf')) * removing '/tmp/th798/25889513/R-devel/151/library/leafem' ERROR: dependencies 'leaflet', 'sf' are not available for package 'leafgl' Perhaps try a variation of: install.packages(c('leaflet', 'sf')) * removing '/tmp/th798/25889513/R-devel/151/library/leafgl' ERROR: dependency 'leaflet' is not available for package 'leaflegend' Perhaps try a variation of: install.packages('leaflet') * removing '/tmp/th798/25889513/R-devel/151/library/leaflegend' ERROR: dependency 'leaflet' is not available for package 'leafsync' Perhaps try a variation of: install.packages('leaflet') * removing '/tmp/th798/25889513/R-devel/151/library/leafsync' ERROR: dependencies 'caret', 'sf' are not available for package 'CAST' Perhaps try a variation of: install.packages(c('caret', 'sf')) * removing '/tmp/th798/25889513/R-devel/151/library/CAST' ERROR: dependencies 'leafem', 'leaflet', 'leafpop', 'sf' are not available for package 'mapview' Perhaps try a variation of: install.packages(c('leafem', 'leaflet', 'leafpop', 'sf')) * removing '/tmp/th798/25889513/R-devel/151/library/mapview' ERROR: dependencies 'leafem', 'leafgl', 'leaflegend', 'leaflet', 'leafsync', 'maptiles', 'sf', 'stars', 's2', 'tmaptools' are not available for package 'tmap' Perhaps try a variation of: install.packages(c('leafem', 'leafgl', 'leaflegend', 'leaflet', 'leafsync', 'maptiles', 'sf', 'stars', 's2', 'tmaptools')) * removing '/tmp/th798/25889513/R-devel/151/library/tmap' The downloaded source packages are in '/tmp/th798/25889513/RtmpC0lhRp/downloaded_packages' There were 23 warnings (use warnings() to see them) > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 966.753 86.017 1076.990 > print(Sys.time()) [1] "2025-12-14 00:46:17 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] "2025-12-14 00:46:17 MST" Installing package into '/tmp/th798/25889513/R-devel/151/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.8' ** 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/th798/25889513/R-devel/151/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] "2025-12-14 00:46:36 MST" * using log directory '/tmp/th798/25889513/R-devel/151/CAST.Rcheck' * using R Under development (unstable) (2025-12-13 r89166) * 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 'CAST/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CAST' version '1.0.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR Packages required but not available: 'caret', 'sf' Packages suggested but not available for checking: 'mapview', 'stars', 'rnaturalearth', 'tmap', 'clustMixType' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. * DONE Status: 1 ERROR See '/tmp/th798/25889513/R-devel/151/CAST.Rcheck/00check.log' for details. [1] "2025-12-14 00:46:41 MST" [1] "2025-12-14 00:46:41 MST" Installing package into '/tmp/th798/25889513/R-devel/151/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 frollapply.c -o frollapply.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 mergelist.c -o mergelist.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 shellsort.c -o shellsort.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 frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.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/th798/25889513/R-devel/151/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] "2025-12-14 00:47:02 MST" * using log directory '/tmp/th798/25889513/R-devel/151/CAST.Rcheck' * using R Under development (unstable) (2025-12-13 r89166) * 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 'CAST/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CAST' version '1.0.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR Packages required but not available: 'caret', 'sf' Packages suggested but not available for checking: 'mapview', 'stars', 'rnaturalearth', 'tmap', 'clustMixType' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. * DONE Status: 1 ERROR See '/tmp/th798/25889513/R-devel/151/CAST.Rcheck/00check.log' for details. [1] "2025-12-14 00:47:06 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) Error: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so': /projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so: undefined symbol: Rf_GetOption Execution halted WARNING: ignoring environment value of R_HOME R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 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/2025-12-14/deps.csv", task.str = "151", release = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_master_1.17.99.6329d94b83b72bb1f05dc2a10374e84a61ff950d.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/25889513/R-release/151" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/25889513/R-release/151/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "CAST" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/25889513/R-release/151/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] "2025-12-14 00:47:12 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/25889513/R-release/151/library' (as 'lib' is unspecified) also installing the dependencies 'Rcpp', 'geometries', 'rapidjsonr', 'sfheaders', 'geojsonsf', 'xfun', 'spacesXYZ', 'jsonify', 'terra', 'leafem', 'leafpop', 'satellite', 'servr', 'cols4all', 'leafgl', 'leaflegend', 'leafsync', 'maptiles', 'tmaptools', 'twosamples', 'geodata', 'mapview', 'rnaturalearth', 'tmap', 'PCAmixdata', 'clustMixType' trying URL 'http://cloud.r-project.org/src/contrib/Rcpp_1.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/geometries_0.2.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rapidjsonr_1.2.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/sfheaders_0.4.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/geojsonsf_2.0.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/xfun_0.54.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/spacesXYZ_1.6-0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/jsonify_1.2.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/terra_1.8-86.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafem_0.2.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafpop_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/satellite_1.0.6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/servr_0.32.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/cols4all_0.10.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafgl_0.2.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leaflegend_1.2.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/leafsync_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/maptiles_0.11.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tmaptools_3.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/twosamples_2.0.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/geodata_0.6-6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/mapview_2.11.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rnaturalearth_1.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tmap_4.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/PCAmixdata_3.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/clustMixType_0.4-2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/CAST_1.0.3.tar.gz' * installing *source* package 'Rcpp' ... ** this is package 'Rcpp' version '1.1.0' ** package 'Rcpp' 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/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 api.cpp -o api.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 attributes.cpp -o attributes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 barrier.cpp -o barrier.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 date.cpp -o date.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 module.cpp -o module.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 rcpp_init.cpp -o rcpp_init.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 Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-Rcpp/00new/Rcpp/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 (Rcpp) * installing *source* package 'rapidjsonr' ... ** this is package 'rapidjsonr' version '1.2.1' ** package 'rapidjsonr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rapidjsonr) * installing *source* package 'xfun' ... ** this is package 'xfun' version '0.54' ** package 'xfun' successfully unpacked and MD5 sums checked ** using staged installation ** 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 -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.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 -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rand_lcg.c -o rand_lcg.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 xfun.so base64.o init.o rand_lcg.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-xfun/00new/xfun/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 (xfun) * installing *source* package 'spacesXYZ' ... ** this is package 'spacesXYZ' version '1.6-0' ** package 'spacesXYZ' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spacesXYZ) * installing *source* package 'leafpop' ... ** this is package 'leafpop' version '0.1.0' ** package 'leafpop' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leafpop) * installing *source* package 'leaflegend' ... ** this is package 'leaflegend' version '1.2.1' ** package 'leaflegend' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leaflegend) * installing *source* package 'leafsync' ... ** this is package 'leafsync' version '0.1.0' ** package 'leafsync' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leafsync) * installing *source* package 'tmaptools' ... ** this is package 'tmaptools' version '3.3' ** package 'tmaptools' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tmaptools) * installing *source* package 'twosamples' ... ** this is package 'twosamples' version '2.0.1' ** package 'twosamples' 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/cpp11/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 cpp11.cpp -o cpp11.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/cpp11/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 stat_functions.cpp -o stat_functions.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 twosamples.so cpp11.o stat_functions.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-twosamples/00new/twosamples/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** 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 (twosamples) * installing *source* package 'PCAmixdata' ... ** this is package 'PCAmixdata' version '3.1' ** package 'PCAmixdata' 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 (PCAmixdata) * installing *source* package 'clustMixType' ... ** this is package 'clustMixType' version '0.4-2' ** package 'clustMixType' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clustMixType) * installing *source* package 'geometries' ... ** this is package 'geometries' version '0.2.5' ** package 'geometries' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 bbox.cpp -o bbox.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 close.cpp -o close.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 columns.cpp -o columns.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 coordinates.cpp -o coordinates.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 geometries.cpp -o geometries.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 lines.cpp -o lines.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 lists.cpp -o lists.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 nest.cpp -o nest.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 shapes.cpp -o shapes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 tests.cpp -o tests.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 utils.cpp -o utils.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 geometries.so RcppExports.o bbox.o close.o columns.o coordinates.o geometries.o lines.o lists.o nest.o shapes.o tests.o utils.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-geometries/00new/geometries/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 (geometries) * installing *source* package 'jsonify' ... ** this is package 'jsonify' version '1.2.3' ** package 'jsonify' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 from_json.cpp -o from_json.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 pretty.cpp -o pretty.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 read_json.cpp -o read_json.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 tests.cpp -o tests.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 to_json.cpp -o to_json.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 validate.cpp -o validate.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 jsonify.so RcppExports.o from_json.o pretty.o read_json.o tests.o to_json.o validate.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-jsonify/00new/jsonify/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 (jsonify) * installing *source* package 'terra' ... ** this is package 'terra' version '1.8-86' ** package 'terra' successfully unpacked and MD5 sums checked ** using staged installation configure: CC: /packages/gcc/12.2.0-nnbserq/bin/gcc configure: CXX: /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 checking for gdal-config... /packages/gdal/3.3.1/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.3.1 checking GDAL version >= 2.0.1... yes checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for gdal.h... yes checking GDAL: linking with --libs only... yes checking GDAL: /packages/gdal/3.3.1/share/gdal/pcs.csv readable... no checking GDAL: checking whether PROJ is available for linking:... yes checking GDAL: checking whether PROJ is available for running:... yes configure: GDAL: 3.3.1 checking for proj.h... yes checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes checking for geos-config... /packages/gcc-8.3.1/geos/3.8.1-j7t4spf/bin/geos-config checking geos-config usability... yes configure: GEOS: 3.8.1 checking GEOS version >= 3.4.0... yes checking for geos_c.h... yes checking geos: linking with -L/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/lib -lgeos_c... yes checking Intel TBB exists:... no configure: WARNING: to support parallel processing install TBB devel or update the PKG_CONFIG_PATH environment variable configure: Package CPP flags: -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include configure: Package LIBS: -L/packages/gdal/3.3.1/lib -lgdal -lproj -L/packages/gdal/3.3.1/lib -lgdal -L/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/lib -lgeos_c configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++17 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 RcppFunctions.cpp -o RcppFunctions.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 RcppModule.cpp -o RcppModule.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 arith.cpp -o arith.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 crs.cpp -o crs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 distRaster.cpp -o distRaster.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 distValueRaster.cpp -o distValueRaster.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 distVector.cpp -o distVector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 distance.cpp -o distance.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 extract.cpp -o extract.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 file_utils.cpp -o file_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 focal.cpp -o focal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 gcp.cpp -o gcp.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 gdal_algs.cpp -o gdal_algs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 gdal_multidimensional.cpp -o gdal_multidimensional.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 gdalio.cpp -o gdalio.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 geodesic.c -o geodesic.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 geos_methods.cpp -o geos_methods.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 geosphere.cpp -o geosphere.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 math_utils.cpp -o math_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 mediancut.cpp -o mediancut.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 memory.cpp -o memory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 movingWindow.cpp -o movingWindow.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 ncdf.cpp -o ncdf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 nearest.cpp -o nearest.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 patches.cpp -o patches.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 ram.cpp -o ram.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 raster_methods.cpp -o raster_methods.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 raster_stats.cpp -o raster_stats.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 rasterize.cpp -o rasterize.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 read.cpp -o read.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 read_gdal.cpp -o read_gdal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 read_ogr.cpp -o read_ogr.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 sample.cpp -o sample.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 sort.cpp -o sort.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatBase.cpp -o spatBase.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatDataframe.cpp -o spatDataframe.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatFactor.cpp -o spatFactor.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatRaster.cpp -o spatRaster.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatRasterMultiple.cpp -o spatRasterMultiple.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatSources.cpp -o spatSources.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatTime.cpp -o spatTime.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatVector.cpp -o spatVector.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 spatVector2.cpp -o spatVector2.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 string_utils.cpp -o string_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 surfArea.cpp -o surfArea.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 table_utils.cpp -o table_utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 vecmath.cpp -o vecmath.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 vecmathse.cpp -o vecmathse.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 vector_methods.cpp -o vector_methods.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 watershed_internal.cpp -o watershed_internal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 write.cpp -o write.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 write_gdal.cpp -o write_gdal.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DHAVE_PROJ_H -I/packages/gdal/3.3.1/include -I/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/include -I'/tmp/th798/25889513/R-release/151/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 write_ogr.cpp -o write_ogr.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 terra.so RcppExports.o RcppFunctions.o RcppModule.o arith.o crs.o distRaster.o distValueRaster.o distVector.o distance.o extract.o file_utils.o focal.o gcp.o gdal_algs.o gdal_multidimensional.o gdalio.o geodesic.o geos_methods.o geosphere.o math_utils.o mediancut.o memory.o movingWindow.o ncdf.o nearest.o patches.o ram.o raster_methods.o raster_stats.o rasterize.o read.o read_gdal.o read_ogr.o sample.o sort.o spatBase.o spatDataframe.o spatFactor.o spatRaster.o spatRasterMultiple.o spatSources.o spatTime.o spatVector.o spatVector2.o string_utils.o surfArea.o table_utils.o vecmath.o vecmathse.o vector_methods.o watershed_internal.o write.o write_gdal.o write_ogr.o -L/packages/gdal/3.3.1/lib -lgdal -lproj -L/packages/gdal/3.3.1/lib -lgdal -L/packages/gcc-8.3.1/geos/3.8.1-j7t4spf/lib -lgeos_c installing to /tmp/th798/25889513/R-release/151/library/00LOCK-terra/00new/terra/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'sds' with signature 'x="stars"': no definition for class "stars" in method for 'sds' with signature 'x="stars_proxy"': no definition for class "stars_proxy" in method for 'svc' with signature 'x="sf"': no definition for class "sf" in method for 'coerce' with signature '"stars","SpatRasterDataset"': no definition for class "stars" in method for 'coerce' with signature '"ggmap","SpatRaster"': no definition for class "ggmap" in method for 'coerce' with signature '"sf","SpatRaster"': no definition for class "sf" in method for 'coerce' with signature '"sf","SpatVector"': no definition for class "sf" in method for 'coerce' with signature '"sfc","SpatVector"': no definition for class "sfc" in method for 'coerce' with signature '"sfg","SpatVector"': no definition for class "sfg" in method for 'coerce' with signature '"XY","SpatVector"': no definition for class "XY" in method for 'coerce' with signature '"im","SpatRaster"': no definition for class "im" in method for 'coerce' with signature '"SpatVector","Spatial"': no definition for class "Spatial" in method for 'coerce' with signature '"Spatial","SpatVector"': no definition for class "Spatial" in method for 'coerce' with signature '"SpatialGrid","SpatRaster"': no definition for class "SpatialGrid" in method for 'coerce' with signature '"SpatialPixels","SpatRaster"': no definition for class "SpatialPixels" in method for 'crs' with signature '"sf"': no definition for class "sf" Creating a generic function for 'ncol' from package 'base' in package 'terra' in method for 'distance' with signature 'x="SpatRaster",y="sf"': no definition for class "sf" in method for 'ext' with signature 'x="sf"': no definition for class "sf" in method for 'ext' with signature 'x="bbox"': no definition for class "bbox" in method for 'ext' with signature 'x="Extent"': no definition for class "Extent" in method for 'ext' with signature 'x="Raster"': no definition for class "Raster" in method for 'ext' with signature 'x="Spatial"': no definition for class "Spatial" in method for 'extract' with signature 'x="SpatRaster",y="sf"': no definition for class "sf" in method for 'mask' with signature 'x="SpatRaster",mask="sf"': no definition for class "sf" in method for 'points' with signature 'x="sf"': no definition for class "sf" in method for 'lines' with signature 'x="sf"': no definition for class "sf" in method for 'polys' with signature 'x="sf"': no definition for class "sf" in method for 'polys' with signature 'x="leaflet"': no definition for class "leaflet" in method for 'lines' with signature 'x="leaflet"': no definition for class "leaflet" in method for 'points' with signature 'x="leaflet"': no definition for class "leaflet" in method for 'rast' with signature 'x="stars"': no definition for class "stars" in method for 'rast' with signature 'x="stars_proxy"': no definition for class "stars_proxy" in method for 'rasterize' with signature 'x="sf",y="SpatRaster"': no definition for class "sf" Creating a generic function for 'rowSums' from package 'base' in package 'terra' Creating a generic function for 'colSums' from package 'base' in package 'terra' Creating a generic function for 'rowMeans' from package 'base' in package 'terra' Creating a generic function for 'colMeans' from package 'base' in package 'terra' in method for 'show' with signature '"Rcpp_SpatDataFrame"': no definition for class "Rcpp_SpatDataFrame" in method for 'show' with signature '"Rcpp_SpatCategories"': no definition for class "Rcpp_SpatCategories" in method for 'geomtype' with signature 'x="Spatial"': no definition for class "Spatial" Creating a generic function for 'identical' from package 'base' in package 'terra' in method for 'vect' with signature 'x="Spatial"': no definition for class "Spatial" in method for 'vect' with signature 'x="sf"': no definition for class "sf" in method for 'vect' with signature 'x="sfc"': no definition for class "sfc" in method for 'vect' with signature 'x="XY"': no definition for class "XY" Creating a generic function for 'unserialize' from package 'base' in package 'terra' Creating a generic function for 'readRDS' from package 'base' in package 'terra' ** help *** installing help indices *** copying figures ** 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 (terra) * installing *source* package 'servr' ... ** this is package 'servr' version '0.32' ** package 'servr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (servr) * installing *source* package 'cols4all' ... ** this is package 'cols4all' version '0.10' ** package 'cols4all' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cols4all) * installing *source* package 'sfheaders' ... ** this is package 'sfheaders' version '0.4.5' ** package 'sfheaders' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 bbox.cpp -o bbox.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 cast.cpp -o cast.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 lists.cpp -o lists.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 sfg_dimension.cpp -o sfg_dimension.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 shapes.cpp -o shapes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 to_df.cpp -o to_df.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 to_sf.cpp -o to_sf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 to_sfc.cpp -o to_sfc.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 to_sfg.cpp -o to_sfg.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/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 utils.cpp -o utils.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 sfheaders.so RcppExports.o bbox.o cast.o lists.o sfg_dimension.o shapes.o to_df.o to_sf.o to_sfc.o to_sfg.o utils.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-sfheaders/00new/sfheaders/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 (sfheaders) * installing *source* package 'satellite' ... ** this is package 'satellite' version '1.0.6' ** package 'satellite' 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'/tmp/th798/25889513/R-release/151/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'/tmp/th798/25889513/R-release/151/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 SatelliteCppFun.cpp -o SatelliteCppFun.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 satellite.so RcppExports.o SatelliteCppFun.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-satellite/00new/satellite/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (satellite) * installing *source* package 'maptiles' ... ** this is package 'maptiles' version '0.11.0' ** package 'maptiles' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maptiles) * installing *source* package 'geodata' ... ** this is package 'geodata' version '0.6-6' ** package 'geodata' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geodata) * installing *source* package 'rnaturalearth' ... ** this is package 'rnaturalearth' version '1.1.0' ** package 'rnaturalearth' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (rnaturalearth) * installing *source* package 'CAST' ... ** this is package 'CAST' version '1.0.3' ** package 'CAST' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (CAST) * installing *source* package 'geojsonsf' ... ** this is package 'geojsonsf' version '2.0.5' ** package 'geojsonsf' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 df_geojson.cpp -o df_geojson.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 geojson_to_sf.cpp -o geojson_to_sf.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 geojson_to_wkt.cpp -o geojson_to_wkt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 geojson_wkt.cpp -o geojson_wkt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 read_geojson.cpp -o read_geojson.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/25889513/R-release/151/library/geometries/include' -I'/tmp/th798/25889513/R-release/151/library/jsonify/include' -I'/tmp/th798/25889513/R-release/151/library/rapidjsonr/include' -I'/tmp/th798/25889513/R-release/151/library/Rcpp/include' -I'/tmp/th798/25889513/R-release/151/library/sfheaders/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 sf_geojson.cpp -o sf_geojson.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 geojsonsf.so RcppExports.o df_geojson.o geojson_to_sf.o geojson_to_wkt.o geojson_wkt.o read_geojson.o sf_geojson.o installing to /tmp/th798/25889513/R-release/151/library/00LOCK-geojsonsf/00new/geojsonsf/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geojsonsf) * installing *source* package 'leafem' ... ** this is package 'leafem' version '0.2.5' ** package 'leafem' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leafem) * installing *source* package 'leafgl' ... ** this is package 'leafgl' version '0.2.2' ** package 'leafgl' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leafgl) * installing *source* package 'mapview' ... ** this is package 'mapview' version '2.11.4' ** package 'mapview' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB Warning in load(file, envir = tmp_env) : strings not representable in native encoding will be translated to UTF-8 Warning in load(file, envir = tmp_env) : strings not representable in native encoding will be translated to UTF-8 ** inst ** byte-compile and prepare package for lazy loading Error in setOldClass("XYZ") : inconsistent old-style class information for "XYZ"; the class is defined but does not extend "oldClass" and is not valid as the data part Error: unable to load R code in package 'mapview' Execution halted ERROR: lazy loading failed for package 'mapview' * removing '/tmp/th798/25889513/R-release/151/library/mapview' * installing *source* package 'tmap' ... ** this is package 'tmap' version '4.2' ** package 'tmap' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tmap) The downloaded source packages are in '/tmp/th798/25889513/Rtmp2FRawQ/downloaded_packages' Warning message: In install.packages(rev.dep, dep = TRUE) : installation of package 'mapview' had non-zero exit status > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 538.118 28.331 581.180 > print(Sys.time()) [1] "2025-12-14 00:56:53 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] "2025-12-14 00:56:53 MST" Installing package into '/tmp/th798/25889513/R-release/151/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.8' ** 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/th798/25889513/R-release/151/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] "2025-12-14 00:57:12 MST" * using log directory '/tmp/th798/25889513/R-release/151/CAST.Rcheck' * using R version 4.5.2 (2025-10-31) * 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 'CAST/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CAST' version '1.0.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'mapview' * 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 'CAST' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 ... WARNING Warning in readLines(conn, n = last - first + 1L, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(CAST) > > test_check("CAST") Loading required package: ggplot2 Loading required package: lattice note: variables were not weighted either because no weights or model were given, no variable importance could be retrieved from the given model, or the model has a single feature. Check caret::varImp(model) note: No model and no CV folds were given. The DI threshold is therefore based on all training data note: variables were not weighted either because no weights or model were given, no variable importance could be retrieved from the given model, or the model has a single feature. Check caret::varImp(model) note: No model and no CV folds were given. The DI threshold is therefore based on all training data [1] "model using Sepal.Length,Sepal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 8" [1] "model using Sepal.Length,Petal.Length will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 7" [1] "model using Sepal.Length,Petal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 6" [1] "model using Sepal.Width,Petal.Length will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 5" [1] "model using Sepal.Width,Petal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 4" [1] "model using Petal.Length,Petal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 3" [1] "vars selected: Petal.Length,Petal.Width with Accuracy 0.953" [1] "model using additional variable Sepal.Length will be trained now..." note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . [1] "maximum number of models that still need to be trained: 2" [1] "model using additional variable Sepal.Width will be trained now..." note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . [1] "maximum number of models that still need to be trained: 1" [1] "vars selected: Petal.Length,Petal.Width,Sepal.Width with Accuracy 0.954" [1] "model using additional variable Sepal.Length will be trained now..." [1] "maximum number of models that still need to be trained: 0" [1] "vars selected: Petal.Length,Petal.Width,Sepal.Width with Accuracy 0.954" Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched off Spherical geometry (s2) switched on features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched off features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched on features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched off variable(s) 'fct' is (are) treated as categorical variables time variable that has been selected: Date time variable that has been selected: Date time variable that has been selected: Date note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . Spherical geometry (s2) switched on although coordinates are longitude/latitude, st_sample assumes that they are planar although coordinates are longitude/latitude, st_sample assumes that they are planar 1000 prediction points are sampled from the modeldomain Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points Gij <= Gj; a random CV assignment is returned variable(s) 'fct' is (are) treated as categorical variables some prediction points contain NAs, which will be removed Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points variable(s) 'fct' is (are) treated as categorical variables 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points variable(s) 'fct' is (are) treated as categorical variables 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points 1000 prediction points are sampled from the modeldomain 1000 prediction points are sampled from the modeldomain 1000 prediction points are sampled from the modeldomain 1000 prediction points are sampled from the modeldomain [ FAIL 3 | WARN 199 | SKIP 10 | PASS 110 ] == Skipped tests (10) ========================================================== * On CRAN (10): 'test-errorProfiles.R:3:3', 'test-errorProfiles.R:36:3', 'test-errorProfiles.R:67:3', 'test-fss.R:3:3', 'test-fss.R:27:3', 'test-fss.R:47:3', 'test-fss.R:70:3', 'test-fss.R:120:5', 'test-fss.R:135:5', 'test-fss.R:152:5' == Failed tests ================================================================ -- Failure ('test-geodist.R:250:3'): geodist works with categorical variables in feature space -- `mean_prediction2sample` (`actual`) not equal to 0.1625 (`expected`). `actual`: 0.1626 `expected`: 0.1625 -- Error ('test-knndm.R:261:3'): kNNDM works in feature space with clustered training points -- Error in `wk_handle.wk_wkb(wkb, s2_geography_writer(oriented = oriented, check = check, tessellate_tol = if (planar) { tessellate_tol_m/s2_earth_radius_meters() } else { Inf }))`: Loop 9 is not valid: Edge 568 crosses edge 571 Backtrace: x 1. \-CAST::knndm(...) at test-knndm.R:261:3 2. +-sf::st_union(...) 3. \-sf:::st_union.sf(...) 4. +-sf::st_union(st_geometry(x), ..., by_feature = by_feature, is_coverage = is_coverage) 5. \-sf:::st_union.sfc(...) 6. +-sf::st_as_sfc(s2::s2_union_agg(x, ...), crs = st_crs(x)) 7. \-s2::s2_union_agg(x, ...) 8. +-s2:::new_s2_geography(...) 9. | \-base::structure(x, class = c("s2_geography", "wk_vctr")) 10. +-s2:::cpp_s2_union_agg(...) 11. \-s2::s2_union(x, options = options) 12. +-s2::as_s2_geography(x) 13. \-sf:::as_s2_geography.sfc(x) 14. \-sf:::st_as_s2.sfc(x, ..., oriented = oriented) 15. +-s2::as_s2_geography(st_as_binary(x), ..., oriented = oriented) 16. \-s2:::as_s2_geography.WKB(st_as_binary(x), ..., oriented = oriented) 17. \-s2::s2_geog_from_wkb(x, oriented = oriented, check = check) 18. +-wk::wk_handle(...) 19. \-wk:::wk_handle.wk_wkb(...) -- Error ('test-knndm.R:339:3'): kNNDM works in feature space with Mahalanobis distance -- Error in `wk_handle.wk_wkb(wkb, s2_geography_writer(oriented = oriented, check = check, tessellate_tol = if (planar) { tessellate_tol_m/s2_earth_radius_meters() } else { Inf }))`: Loop 9 is not valid: Edge 568 crosses edge 571 Backtrace: x 1. \-CAST::knndm(...) at test-knndm.R:339:3 2. +-sf::st_union(...) 3. \-sf:::st_union.sf(...) 4. +-sf::st_union(st_geometry(x), ..., by_feature = by_feature, is_coverage = is_coverage) 5. \-sf:::st_union.sfc(...) 6. +-sf::st_as_sfc(s2::s2_union_agg(x, ...), crs = st_crs(x)) 7. \-s2::s2_union_agg(x, ...) 8. +-s2:::new_s2_geography(...) 9. | \-base::structure(x, class = c("s2_geography", "wk_vctr")) 10. +-s2:::cpp_s2_union_agg(...) 11. \-s2::s2_union(x, options = options) 12. +-s2::as_s2_geography(x) 13. \-sf:::as_s2_geography.sfc(x) 14. \-sf:::st_as_s2.sfc(x, ..., oriented = oriented) 15. +-s2::as_s2_geography(st_as_binary(x), ..., oriented = oriented) 16. \-s2:::as_s2_geography.WKB(st_as_binary(x), ..., oriented = oriented) 17. \-s2::s2_geog_from_wkb(x, oriented = oriented, check = check) 18. +-wk::wk_handle(...) 19. \-wk:::wk_handle.wk_wkb(...) [ FAIL 3 | WARN 199 | SKIP 10 | PASS 110 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'cast01-CAST-intro.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") CAST package:CAST R Documentation '_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s _D_e_s_c_r_i_p_t_i_o_n: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models by analysing the similarity between new data and training data. Methods are described in Meyer et al. (2018); Meyer et al. (2019); Meyer and Pebesma (2021); Mil et al. (2022); Meyer and Pebesma (2022); Linnenbrink et al. (2023). The package is described in detail in Meyer et al. (2024). _D_e_t_a_i_l_s: 'caret' Applications for Spatio-Temporal models _A_u_t_h_o_r(_s): Hanna Meyer, Carles Mil, Marvin Ludwig, Jan Linnenbrink, Fabian Schumacher _R_e_f_e_r_e_n_c_e_s: * Meyer, H., Ludwig, L., Mil, C., Linnenbrink, J., Schumacher, F. (2024): The CAST package for training and assessment of spatial prediction models in R. arXiv, https://doi.org/10.48550/arXiv.2404.06978. * Linnenbrink, J., Mil, C., Ludwig, M., and Meyer, H.: kNNDM: k-fold Nearest Neighbour Distance Matching Cross-Validation for map accuracy estimation, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-1308, 2023. * Mil, C., Mateu, J., Pebesma, E., Meyer, H. (2022): Nearest Neighbour Distance Matching Leave-One-Out Cross-Validation for map validation. Methods in Ecology and Evolution 00, 1<80><93> 13. * Meyer, H., Pebesma, E. (2022): Machine learning-based global maps of ecological variables and the challenge of assessing them. Nature Communications. 13. * Meyer, H., Pebesma, E. (2021): Predicting into unknown space? Estimating the area of applicability of spatial prediction models. Methods in Ecology and Evolution. 12, 1620<80><93> 1633. * Meyer, H., Reudenbach, C., Wllauer, S., Nauss, T. (2019): Importance of spatial predictor variable selection in machine learning applications - Moving from data reproduction to spatial prediction. Ecological Modelling. 411, 108815. * Meyer, H., Reudenbach, C., Hengl, T., Katurji, M., Nau<9f>, T. (2018): Improving performance of spatio-temporal machine learning models using forward feature selection and target-oriented validation. Environmental Modelling & Software 101: 1-9. _S_e_e _A_l_s_o: Useful links: * * * Report bugs at trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_bio.zip' Content type 'application/zip' length 49869449 bytes (47.6 MB) ================================================== downloaded 47.6 MB trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_elev.zip' Content type 'application/zip' length 1332437 bytes (1.3 MB) ================================================== downloaded 1.3 MB Error: processing vignette 'cast01-CAST-intro.Rmd' failed with diagnostics: argument "loc" is missing, with no default --- failed re-building 'cast01-CAST-intro.Rmd' --- re-building 'cast02-plotgeodist.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_bio.zip' Content type 'application/zip' length 49869449 bytes (47.6 MB) ================================================== downloaded 47.6 MB --- finished re-building 'cast02-plotgeodist.Rmd' --- re-building 'cast03-CV.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Error: processing vignette 'cast03-CV.Rmd' failed with diagnostics: argument "loc" is missing, with no default --- failed re-building 'cast03-CV.Rmd' --- re-building 'cast04-AOA-tutorial.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") --- finished re-building 'cast04-AOA-tutorial.Rmd' --- re-building 'cast05-parallel.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") --- finished re-building 'cast05-parallel.Rmd' SUMMARY: processing the following files failed: 'cast01-CAST-intro.Rmd' 'cast03-CV.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING See '/tmp/th798/25889513/R-release/151/CAST.Rcheck/00check.log' for details. [1] "2025-12-14 01:05:04 MST" [1] "2025-12-14 01:05:04 MST" Installing package into '/tmp/th798/25889513/R-release/151/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.99' ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.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 mergelist.c -o mergelist.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 shellsort.c -o shellsort.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 frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.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/th798/25889513/R-release/151/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] "2025-12-14 01:05:31 MST" * using log directory '/tmp/th798/25889513/R-release/151/CAST.Rcheck' * using R version 4.5.2 (2025-10-31) * 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 'CAST/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CAST' version '1.0.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: 'mapview' * 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 'CAST' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 ... WARNING Warning in readLines(conn, n = last - first + 1L, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' Warning in readLines(conn, line - oldline, warn = FALSE) : invalid input found on input connection './man/splotdata.Rd' * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(CAST) > > test_check("CAST") Loading required package: ggplot2 Loading required package: lattice note: variables were not weighted either because no weights or model were given, no variable importance could be retrieved from the given model, or the model has a single feature. Check caret::varImp(model) note: No model and no CV folds were given. The DI threshold is therefore based on all training data note: variables were not weighted either because no weights or model were given, no variable importance could be retrieved from the given model, or the model has a single feature. Check caret::varImp(model) note: No model and no CV folds were given. The DI threshold is therefore based on all training data [1] "model using Sepal.Length,Sepal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 8" [1] "model using Sepal.Length,Petal.Length will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 7" [1] "model using Sepal.Length,Petal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 6" [1] "model using Sepal.Width,Petal.Length will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 5" [1] "model using Sepal.Width,Petal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 4" [1] "model using Petal.Length,Petal.Width will be trained now..." note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 . [1] "maximum number of models that still need to be trained: 3" [1] "vars selected: Petal.Length,Petal.Width with Accuracy 0.953" [1] "model using additional variable Sepal.Length will be trained now..." note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . [1] "maximum number of models that still need to be trained: 2" [1] "model using additional variable Sepal.Width will be trained now..." note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . [1] "maximum number of models that still need to be trained: 1" [1] "vars selected: Petal.Length,Petal.Width,Sepal.Width with Accuracy 0.954" [1] "model using additional variable Sepal.Length will be trained now..." [1] "maximum number of models that still need to be trained: 0" [1] "vars selected: Petal.Length,Petal.Width,Sepal.Width with Accuracy 0.954" Spherical geometry (s2) switched off Spherical geometry (s2) switched on Spherical geometry (s2) switched off Spherical geometry (s2) switched on features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched off Spherical geometry (s2) switched on features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched off features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched on features are extracted from the modeldomain samplesize for new data shouldn't be larger than number of pixels. Samplesize was reduced to 100 Spherical geometry (s2) switched off variable(s) 'fct' is (are) treated as categorical variables time variable that has been selected: Date time variable that has been selected: Date time variable that has been selected: Date note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . note: only 2 unique complexity parameters in default grid. Truncating the grid to 2 . Spherical geometry (s2) switched on although coordinates are longitude/latitude, st_sample assumes that they are planar although coordinates are longitude/latitude, st_sample assumes that they are planar 1000 prediction points are sampled from the modeldomain Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points Gij <= Gj; a random CV assignment is returned variable(s) 'fct' is (are) treated as categorical variables some prediction points contain NAs, which will be removed Gij <= Gj; a random CV assignment is returned 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points variable(s) 'fct' is (are) treated as categorical variables 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points variable(s) 'fct' is (are) treated as categorical variables 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points 1000 prediction points are sampled from the modeldomain predictor values are extracted for prediction points 1000 prediction points are sampled from the modeldomain 1000 prediction points are sampled from the modeldomain 1000 prediction points are sampled from the modeldomain 1000 prediction points are sampled from the modeldomain [ FAIL 3 | WARN 199 | SKIP 10 | PASS 110 ] == Skipped tests (10) ========================================================== * On CRAN (10): 'test-errorProfiles.R:3:3', 'test-errorProfiles.R:36:3', 'test-errorProfiles.R:67:3', 'test-fss.R:3:3', 'test-fss.R:27:3', 'test-fss.R:47:3', 'test-fss.R:70:3', 'test-fss.R:120:5', 'test-fss.R:135:5', 'test-fss.R:152:5' == Failed tests ================================================================ -- Failure ('test-geodist.R:250:3'): geodist works with categorical variables in feature space -- `mean_prediction2sample` (`actual`) not equal to 0.1625 (`expected`). `actual`: 0.1626 `expected`: 0.1625 -- Error ('test-knndm.R:261:3'): kNNDM works in feature space with clustered training points -- Error in `wk_handle.wk_wkb(wkb, s2_geography_writer(oriented = oriented, check = check, tessellate_tol = if (planar) { tessellate_tol_m/s2_earth_radius_meters() } else { Inf }))`: Loop 9 is not valid: Edge 568 crosses edge 571 Backtrace: x 1. \-CAST::knndm(...) at test-knndm.R:261:3 2. +-sf::st_union(...) 3. \-sf:::st_union.sf(...) 4. +-sf::st_union(st_geometry(x), ..., by_feature = by_feature, is_coverage = is_coverage) 5. \-sf:::st_union.sfc(...) 6. +-sf::st_as_sfc(s2::s2_union_agg(x, ...), crs = st_crs(x)) 7. \-s2::s2_union_agg(x, ...) 8. +-s2:::new_s2_geography(...) 9. | \-base::structure(x, class = c("s2_geography", "wk_vctr")) 10. +-s2:::cpp_s2_union_agg(...) 11. \-s2::s2_union(x, options = options) 12. +-s2::as_s2_geography(x) 13. \-sf:::as_s2_geography.sfc(x) 14. \-sf:::st_as_s2.sfc(x, ..., oriented = oriented) 15. +-s2::as_s2_geography(st_as_binary(x), ..., oriented = oriented) 16. \-s2:::as_s2_geography.WKB(st_as_binary(x), ..., oriented = oriented) 17. \-s2::s2_geog_from_wkb(x, oriented = oriented, check = check) 18. +-wk::wk_handle(...) 19. \-wk:::wk_handle.wk_wkb(...) -- Error ('test-knndm.R:339:3'): kNNDM works in feature space with Mahalanobis distance -- Error in `wk_handle.wk_wkb(wkb, s2_geography_writer(oriented = oriented, check = check, tessellate_tol = if (planar) { tessellate_tol_m/s2_earth_radius_meters() } else { Inf }))`: Loop 9 is not valid: Edge 568 crosses edge 571 Backtrace: x 1. \-CAST::knndm(...) at test-knndm.R:339:3 2. +-sf::st_union(...) 3. \-sf:::st_union.sf(...) 4. +-sf::st_union(st_geometry(x), ..., by_feature = by_feature, is_coverage = is_coverage) 5. \-sf:::st_union.sfc(...) 6. +-sf::st_as_sfc(s2::s2_union_agg(x, ...), crs = st_crs(x)) 7. \-s2::s2_union_agg(x, ...) 8. +-s2:::new_s2_geography(...) 9. | \-base::structure(x, class = c("s2_geography", "wk_vctr")) 10. +-s2:::cpp_s2_union_agg(...) 11. \-s2::s2_union(x, options = options) 12. +-s2::as_s2_geography(x) 13. \-sf:::as_s2_geography.sfc(x) 14. \-sf:::st_as_s2.sfc(x, ..., oriented = oriented) 15. +-s2::as_s2_geography(st_as_binary(x), ..., oriented = oriented) 16. \-s2:::as_s2_geography.WKB(st_as_binary(x), ..., oriented = oriented) 17. \-s2::s2_geog_from_wkb(x, oriented = oriented, check = check) 18. +-wk::wk_handle(...) 19. \-wk:::wk_handle.wk_wkb(...) [ FAIL 3 | WARN 199 | SKIP 10 | PASS 110 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building 'cast01-CAST-intro.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") CAST package:CAST R Documentation '_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s _D_e_s_c_r_i_p_t_i_o_n: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. CAST includes functions to improve spatial-temporal modelling tasks using 'caret'. It includes the newly suggested 'Nearest neighbor distance matching' cross-validation to estimate the performance of spatial prediction models and allows for spatial variable selection to selects suitable predictor variables in view to their contribution to the spatial model performance. CAST further includes functionality to estimate the (spatial) area of applicability of prediction models by analysing the similarity between new data and training data. Methods are described in Meyer et al. (2018); Meyer et al. (2019); Meyer and Pebesma (2021); Mil et al. (2022); Meyer and Pebesma (2022); Linnenbrink et al. (2023). The package is described in detail in Meyer et al. (2024). _D_e_t_a_i_l_s: 'caret' Applications for Spatio-Temporal models _A_u_t_h_o_r(_s): Hanna Meyer, Carles Mil, Marvin Ludwig, Jan Linnenbrink, Fabian Schumacher _R_e_f_e_r_e_n_c_e_s: * Meyer, H., Ludwig, L., Mil, C., Linnenbrink, J., Schumacher, F. (2024): The CAST package for training and assessment of spatial prediction models in R. arXiv, https://doi.org/10.48550/arXiv.2404.06978. * Linnenbrink, J., Mil, C., Ludwig, M., and Meyer, H.: kNNDM: k-fold Nearest Neighbour Distance Matching Cross-Validation for map accuracy estimation, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2023-1308, 2023. * Mil, C., Mateu, J., Pebesma, E., Meyer, H. (2022): Nearest Neighbour Distance Matching Leave-One-Out Cross-Validation for map validation. Methods in Ecology and Evolution 00, 1<80><93> 13. * Meyer, H., Pebesma, E. (2022): Machine learning-based global maps of ecological variables and the challenge of assessing them. Nature Communications. 13. * Meyer, H., Pebesma, E. (2021): Predicting into unknown space? Estimating the area of applicability of spatial prediction models. Methods in Ecology and Evolution. 12, 1620<80><93> 1633. * Meyer, H., Reudenbach, C., Wllauer, S., Nauss, T. (2019): Importance of spatial predictor variable selection in machine learning applications - Moving from data reproduction to spatial prediction. Ecological Modelling. 411, 108815. * Meyer, H., Reudenbach, C., Hengl, T., Katurji, M., Nau<9f>, T. (2018): Improving performance of spatio-temporal machine learning models using forward feature selection and target-oriented validation. Environmental Modelling & Software 101: 1-9. _S_e_e _A_l_s_o: Useful links: * * * Report bugs at trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_bio.zip' Content type 'application/zip' length 49869449 bytes (47.6 MB) ================================================== downloaded 47.6 MB trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_elev.zip' Content type 'application/zip' length 1332437 bytes (1.3 MB) ================================================== downloaded 1.3 MB Error: processing vignette 'cast01-CAST-intro.Rmd' failed with diagnostics: argument "loc" is missing, with no default --- failed re-building 'cast01-CAST-intro.Rmd' --- re-building 'cast02-plotgeodist.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") trying URL 'https://geodata.ucdavis.edu/climate/worldclim/2_1/base/wc2.1_10m_bio.zip' Content type 'application/zip' length 49869449 bytes (47.6 MB) ================================================== downloaded 47.6 MB --- finished re-building 'cast02-plotgeodist.Rmd' --- re-building 'cast03-CV.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Error: processing vignette 'cast03-CV.Rmd' failed with diagnostics: argument "loc" is missing, with no default --- failed re-building 'cast03-CV.Rmd' --- re-building 'cast04-AOA-tutorial.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") --- finished re-building 'cast04-AOA-tutorial.Rmd' --- re-building 'cast05-parallel.Rmd' using rmarkdown Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") Warning in attr(x, "match.length") : 'xfun::attr()' is deprecated. Use 'xfun::attr2()' instead. See help("Deprecated") --- finished re-building 'cast05-parallel.Rmd' SUMMARY: processing the following files failed: 'cast01-CAST-intro.Rmd' 'cast03-CV.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING See '/tmp/th798/25889513/R-release/151/CAST.Rcheck/00check.log' for details. [1] "2025-12-14 01:14:18 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + unlink(dt.git, recursive=TRUE, force=TRUE) + 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) + } >