[ Started: 2024-12-16 12:19:10 CET ]
[ CARNIVAL v2.7.2 for BioC-3.20 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.20"
[3] "/home/omnipath/local/R/4.4"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/ape_5.8-1.tar.gz'
Content type 'application/x-gzip' length 1424541 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c BIONJ.c -o BIONJ.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c NNI.c -o NNI.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c SPR.c -o SPR.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c additive.c -o additive.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c ape.c -o ape.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c bNNI.c -o bNNI.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c bionjs.c -o bionjs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c bipartition.c -o bipartition.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c bitsplits.c -o bitsplits.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c delta_plot.c -o delta_plot.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c dist_dna.c -o dist_dna.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c dist_nodes.c -o dist_nodes.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c ewLasso.c -o ewLasso.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c heap.c -o heap.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c mat_expo.c -o mat_expo.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c me.c -o me.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c me_balanced.c -o me_balanced.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c me_ols.c -o me_ols.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c mvr.c -o mvr.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c mvrs.c -o mvrs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c nj.c -o nj.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c njs.c -o njs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c pic.c -o pic.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c plot_phylo.c -o plot_phylo.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c prop_part.cpp -o prop_part.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c rTrait.c -o rTrait.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c read_dna.c -o read_dna.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3   -c reorder_Rcpp.cpp -o reorder_Rcpp.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c reorder_phylo.c -o reorder_phylo.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c treePop.c -o treePop.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c tree_build.c -o tree_build.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c tree_phylo.c -o tree_phylo.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c triangMtd.c -o triangMtd.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c triangMtds.c -o triangMtds.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include'     -fpic  -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3  -c ultrametric.c -o ultrametric.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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/4.4-3.20/00LOCK-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/RtmpMWXxZ4/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Old packages: 'wppi'
trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/wppi_1.14.0.tar.gz'
Content type 'application/x-gzip' length 663228 bytes (647 KB)
==================================================
downloaded 647 KB

* installing *source* package ‘wppi’ ...
** package ‘wppi’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-12-16 12:19:44] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:44] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-16 12:19:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:44] [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
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:47] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:47] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-16 12:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-16 12:19:49] [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/RtmpMWXxZ4/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 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
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: 2024-12-16 12:19:55 CET ]