[ Started: 2024-04-29 15:29:19 CEST ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" also installing the dependency ‘nloptr’ trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/ape_5.8.tar.gz' Content type 'application/x-gzip' length 1579438 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cran.uni-muenster.de/src/contrib/bookdown_0.39.tar.gz' Content type 'application/x-gzip' length 858950 bytes (838 KB) ================================================== downloaded 838 KB trying URL 'https://cran.uni-muenster.de/src/contrib/brio_1.1.5.tar.gz' Content type 'application/x-gzip' length 13172 bytes (12 KB) ================================================== downloaded 12 KB trying URL 'https://cran.uni-muenster.de/src/contrib/fs_1.6.4.tar.gz' Content type 'application/x-gzip' length 1201506 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/ggplot2_3.5.1.tar.gz' Content type 'application/x-gzip' length 3604371 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://cran.uni-muenster.de/src/contrib/gtable_0.3.5.tar.gz' Content type 'application/x-gzip' length 130227 bytes (127 KB) ================================================== downloaded 127 KB trying URL 'https://cran.uni-muenster.de/src/contrib/iml_0.11.3.tar.gz' Content type 'application/x-gzip' length 176861 bytes (172 KB) ================================================== downloaded 172 KB trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.3.tar.gz' Content type 'application/x-gzip' length 2942302 bytes (2.8 MB) ================================================== downloaded 2.8 MB trying URL 'https://cran.uni-muenster.de/src/contrib/matrixStats_1.3.0.tar.gz' Content type 'application/x-gzip' length 213441 bytes (208 KB) ================================================== downloaded 208 KB trying URL 'https://cran.uni-muenster.de/src/contrib/openssl_2.1.2.tar.gz' Content type 'application/x-gzip' length 1211054 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://cran.uni-muenster.de/src/contrib/pkgdown_2.0.9.tar.gz' Content type 'application/x-gzip' length 855137 bytes (835 KB) ================================================== downloaded 835 KB trying URL 'https://cran.uni-muenster.de/src/contrib/prediction_0.3.17.tar.gz' Content type 'application/x-gzip' length 74982 bytes (73 KB) ================================================== downloaded 73 KB trying URL 'https://cran.uni-muenster.de/src/contrib/RcppArmadillo_0.12.8.2.1.tar.gz' Content type 'application/x-gzip' length 1405114 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cran.uni-muenster.de/src/contrib/reticulate_1.36.1.tar.gz' Content type 'application/x-gzip' length 1637384 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'https://cran.uni-muenster.de/src/contrib/segmented_2.0-4.tar.gz' Content type 'application/x-gzip' length 287660 bytes (280 KB) ================================================== downloaded 280 KB trying URL 'https://cran.uni-muenster.de/src/contrib/testthat_3.2.1.1.tar.gz' Content type 'application/x-gzip' length 739761 bytes (722 KB) ================================================== downloaded 722 KB trying URL 'https://cran.uni-muenster.de/src/contrib/uwot_0.2.2.tar.gz' Content type 'application/x-gzip' length 602996 bytes (588 KB) ================================================== downloaded 588 KB trying URL 'https://cran.uni-muenster.de/src/contrib/xopen_1.0.1.tar.gz' Content type 'application/x-gzip' length 11855 bytes (11 KB) ================================================== downloaded 11 KB * installing *source* package ‘ape’ ... ** package ‘ape’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c BIONJ.c -o BIONJ.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c NNI.c -o NNI.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SPR.c -o SPR.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c additive.c -o additive.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ape.c -o ape.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bNNI.c -o bNNI.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bionjs.c -o bionjs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bipartition.c -o bipartition.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bitsplits.c -o bitsplits.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delta_plot.c -o delta_plot.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dist_dna.c -o dist_dna.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dist_nodes.c -o dist_nodes.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ewLasso.c -o ewLasso.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c heap.c -o heap.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mat_expo.c -o mat_expo.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c me.c -o me.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c me_balanced.c -o me_balanced.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c me_ols.c -o me_ols.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mvr.c -o mvr.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mvrs.c -o mvrs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c -o nj.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c njs.c -o njs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pic.c -o pic.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plot_phylo.c -o plot_phylo.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c prop_part.cpp -o prop_part.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rTrait.c -o rTrait.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_dna.c -o read_dna.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reorder_Rcpp.cpp -o reorder_Rcpp.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reorder_phylo.c -o reorder_phylo.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treePop.c -o treePop.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tree_build.c -o tree_build.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tree_phylo.c -o tree_phylo.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c triangMtd.c -o triangMtd.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c triangMtds.c -o triangMtds.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ultrametric.c -o ultrametric.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-ape/00new/ape/libs ** 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 ** 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 (ape) * installing *source* package ‘bookdown’ ... ** package ‘bookdown’ 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 (bookdown) * installing *source* package ‘brio’ ... ** package ‘brio’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c brio.c -o brio.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c file_line_endings.c -o file_line_endings.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_file.c -o read_file.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_file_raw.c -o read_file_raw.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_lines.c -o read_lines.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write_file.c -o write_file.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write_file_raw.c -o write_file_raw.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write_lines.c -o write_lines.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o brio.so brio.o file_line_endings.o init.o read_file.o read_file_raw.o read_lines.o write_file.o write_file_raw.o write_lines.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-brio/00new/brio/libs ** 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 ** 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 (brio) * installing *source* package ‘fs’ ... ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dir.cc -o dir.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c error.cc -o error.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c file.cc -o file.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fs.cc -o fs.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getmode.cc -o getmode.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c id.cc -o id.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cc -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c link.cc -o link.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c path.cc -o path.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.cc -o utils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c unix/getmode.cc -o unix/getmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bsd/setmode.c -o bsd/setmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bsd/strmode.c -o bsd/strmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bsd/reallocarray.c -o bsd/reallocarray.o (cd libuv-1.44.2 \ && CC="gcc" CPPFLAGS="" CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro" ./configure --quiet) make --directory=libuv-1.44.2 \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/RtmpOEkMbY/R.INSTALL11badf9e3ac3/fs/src/libuv-1.44.2' 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/libuv_la-strtok.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/RtmpOEkMbY/R.INSTALL11badf9e3ac3/fs/src/libuv-1.44.2' g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv-1.44.2/.libs/libuv.a -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-fs/00new/fs/libs ** 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 ** 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 (fs) * installing *source* package ‘gtable’ ... ** package ‘gtable’ 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 (gtable) * installing *source* package ‘matrixStats’ ... ** package ‘matrixStats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c 000.init.c -o 000.init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c allocMatrix2.c -o allocMatrix2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c anyMissing.c -o anyMissing.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c binCounts.c -o binCounts.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c binMeans.c -o binMeans.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c colCounts.c -o colCounts.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c colOrderStats.c -o colOrderStats.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c colRanges.c -o colRanges.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c diff2.c -o diff2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c indexByRow.c -o indexByRow.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c logSumExp.c -o logSumExp.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mean2.c -o mean2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c naming.c -o naming.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c productExpSumLog.c -o productExpSumLog.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c psortKM.c -o psortKM.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowCounts.c -o rowCounts.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowCummaxs.c -o rowCummaxs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowCummins.c -o rowCummins.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowCumprods.c -o rowCumprods.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowCumsums.c -o rowCumsums.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowDiffs.c -o rowDiffs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowLogSumExp.c -o rowLogSumExp.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowMads.c -o rowMads.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowMeans2.c -o rowMeans2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowMedians.c -o rowMedians.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowOrderStats.c -o rowOrderStats.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowRanges.c -o rowRanges.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowRanksWithTies.c -o rowRanksWithTies.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowSums2.c -o rowSums2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowVars.c -o rowVars.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c signTabulate.c -o signTabulate.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sum2.c -o sum2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c validateIndices.c -o validateIndices.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c weightedMean.c -o weightedMean.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c weightedMedian.c -o weightedMedian.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c x_OP_y.c -o x_OP_y.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o matrixStats.so 000.init.o allocMatrix2.o anyMissing.o binCounts.o binMeans.o colCounts.o colOrderStats.o colRanges.o diff2.o indexByRow.o logSumExp.o mean2.o naming.o productExpSumLog.o psortKM.o rowCounts.o rowCummaxs.o rowCummins.o rowCumprods.o rowCumsums.o rowDiffs.o rowLogSumExp.o rowMads.o rowMeans2.o rowMedians.o rowOrderStats.o rowRanges.o rowRanksWithTies.o rowSums2.o rowVars.o signTabulate.o sum2.o validateIndices.o weightedMean.o weightedMedian.o x_OP_y.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-matrixStats/00new/matrixStats/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 (matrixStats) * installing *source* package ‘openssl’ ... ** package ‘openssl’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS= Using PKG_LIBS=-l:libssl.so.3 -l:libcrypto.so.3 ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o openssl.so bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c aes.c -o aes.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base64.c -o base64.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bignum.c -o bignum.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cert.c -o cert.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compatibility.c -o compatibility.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c diffie.c -o diffie.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c envelope.c -o envelope.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c error.c -o error.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hash.c -o hash.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c info.c -o info.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c keygen.c -o keygen.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c keys.c -o keys.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c onload.c -o onload.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c openssh.c -o openssh.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c password.c -o password.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pbkdf.c -o pbkdf.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pem.c -o pem.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pkcs12.c -o pkcs12.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pkcs7.c -o pkcs7.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rand.c -o rand.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rsa.c -o rsa.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c signing.c -o signing.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ssl.c -o ssl.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stream.c -o stream.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c write.c -o write.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c x25519.c -o x25519.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o gcc -I"/usr/share/R/include" -DNDEBUG -DOPENSSL_SUPPRESS_DEPRECATED -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bcrypt/blowfish.c -o bcrypt/blowfish.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt_pbkdf.o bcrypt/blowfish.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o openssl.so aes.o base64.o bignum.o cert.o compatibility.o diffie.o envelope.o error.o hash.o info.o keygen.o keys.o onload.o openssh.o password.o pbkdf.o pem.o pkcs12.o pkcs7.o rand.o rsa.o signing.o ssl.o stream.o write.o x25519.o -Lbcrypt -lstatbcrypt -l:libssl.so.3 -l:libcrypto.so.3 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-openssl/00new/openssl/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 (openssl) * installing *source* package ‘prediction’ ... ** package ‘prediction’ 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 ** 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 (prediction) * installing *source* package ‘RcppArmadillo’ ... ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked ** using staged installation 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 g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking whether we have a suitable tempdir... /tmp checking whether R CMD SHLIB can already compile programs using OpenMP... yes checking LAPACK_LIBS... system LAPACK found configure: creating ./config.status config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppArmadillo.cpp -o RcppArmadillo.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastLm.cpp -o fastLm.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo) * installing *source* package ‘reticulate’ ... ** package ‘reticulate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c event_loop.cpp -o event_loop.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c libpython.cpp -o libpython.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c output.cpp -o output.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c python.cpp -o python.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c readline.cpp -o readline.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c signals.cpp -o signals.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-reticulate/00new/reticulate/libs ** 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 ** 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 (reticulate) * installing *source* package ‘segmented’ ... ** package ‘segmented’ 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 ** 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 (segmented) * installing *source* package ‘uwot’ ... ** package ‘uwot’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c connected_components.cpp -o connected_components.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nn_parallel.cpp -o nn_parallel.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c perplexity.cpp -o perplexity.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c r_uwot.cpp -o r_uwot.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c smooth_knn.cpp -o smooth_knn.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c supervised.cpp -o supervised.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c thread.cpp -o thread.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.18/dqrng/include' -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppAnnoy/include' -I'/home/omnipath/local/R/4.3-3.18/RcppProgress/include' -DRCPP_NO_RTTI -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c transform.cpp -o transform.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o uwot.so RcppExports.o connected_components.o nn_parallel.o perplexity.o r_uwot.o smooth_knn.o supervised.o thread.o transform.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-uwot/00new/uwot/libs ** 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 ** 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 (uwot) * installing *source* package ‘xopen’ ... ** package ‘xopen’ 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 (xopen) * installing *source* package ‘ggplot2’ ... ** package ‘ggplot2’ 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 (ggplot2) * installing *source* package ‘pkgdown’ ... ** package ‘pkgdown’ 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 (pkgdown) * installing *source* package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c reassign.c -o reassign.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-catch.cpp -o test-catch.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-example.cpp -o test-example.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-testthat/00new/testthat/libs ** 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 ** 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 (testthat) * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation 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 g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... no ------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - sudo brew install cmake (MacOS; inside a terminal with Homebrew) - sudo port install cmake (MacOS; inside a terminal with MacPorts) Alternatively install CMake from: ------------------------------------------------------- ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/omnipath/local/R/4.3-3.18/nloptr’ * installing *source* package ‘iml’ ... ** package ‘iml’ 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 (iml) * installing *source* package ‘lme4’ ... ** package ‘lme4’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c external.cpp -o external.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glmFamily.cpp -o glmFamily.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optimizer.cpp -o optimizer.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c predModule.cpp -o predModule.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c respModule.cpp -o respModule.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-lme4/00new/lme4/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 (lme4) The downloaded source packages are in ‘/tmp/RtmpIOeiFI/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘nloptr’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29) Old packages: 'AnnotationHub', 'GSVA', 'wppi' trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationHub_3.10.1.tar.gz' Content type 'application/x-gzip' length 994797 bytes (971 KB) ================================================== downloaded 971 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GSVA_1.50.5.tar.gz' Content type 'application/x-gzip' length 2266106 bytes (2.2 MB) ================================================== downloaded 2.2 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/wppi_1.10.0.tar.gz' Content type 'application/x-gzip' length 662114 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘AnnotationHub’ ... ** 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 (AnnotationHub) * installing *source* package ‘GSVA’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c kernel_estimation.c -o kernel_estimation.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ks_test.c -o ks_test.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c register_cmethods.c -o register_cmethods.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-GSVA/00new/GSVA/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 (GSVA) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-04-29 15:34:55] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:55] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Contains 1 files. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-29 15:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-29 15:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-29 15:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-29 15:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-29 15:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:55] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-04-29 15:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:58] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Contains 1 files. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-29 15:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-29 15:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-29 15:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-29 15:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-29 15:34:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:34:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-04-29 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:35:00] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Contains 1 files. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-29 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:35:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-04-29 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-29 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-29 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-29 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-29 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-29 15:35:00] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) The downloaded source packages are in ‘/tmp/RtmpIOeiFI/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: BiocStyle [ Finished: 2024-04-29 15:35:07 CEST ]