[ Started: 2023-02-17 01:00:54 CET ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10 r83330) Old packages: 'ape' trying URL 'https://cloud.r-project.org/src/contrib/ape_5.7.tar.gz' Content type 'application/x-gzip' length 1577932 bytes (1.5 MB) ================================================== downloaded 1.5 MB * installing *source* package ‘ape’ ... ** package ‘ape’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c NNI.c -o NNI.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c plot_phylo.c -o plot_phylo.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_dna.c -o read_dna.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ultrametric.c -o ultrametric.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -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/4.2-3.16/00LOCK-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) The downloaded source packages are in ‘/tmp/RtmpTpNSDB/downloaded_packages’ [ Finished: 2023-02-17 01:01:29 CET ]