[ Started: 2025-02-13 20:44:13 CET ] [ MetaProViz v2.1.4 for BioC-3.21 from https://github.com/saezlab/MetaProViz@development (bf5c928 2025-02-13 11:29:45) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.21" [3] "/home/omnipath/local/R/4.5" "/opt/R-devel/lib/R/library" Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Old packages: 'decoupleR' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/decoupleR_2.13.0.tar.gz' Content type 'application/x-gzip' length 5237132 bytes (5.0 MB) ================================================== downloaded 5.0 MB * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.13.0’ ** 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 (decoupleR) The downloaded source packages are in ‘/tmp/RtmpkPXgsp/downloaded_packages’ Bioconductor version 3.21 (BiocManager 1.30.25), R Under development (unstable) (2025-02-12 r87715) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' OmnipathR (16b42b2d0... -> 0a9253713...) [GitHub] cosmosR (1.15.0 -> 81d1a7fe7...) [GitHub] fgsea (1.33.2 -> da4b3b8ed...) [GitHub] NA (NA -> 97a5846be...) [Git] admisc (NA -> 0.37 ) [CRAN] gridGraphics (NA -> 0.5-1 ) [CRAN] yulab.utils (NA -> 0.2.0 ) [CRAN] ggplotify (NA -> 0.1.2 ) [CRAN] ggfun (NA -> 0.1.8 ) [CRAN] nloptr (NA -> 2.1.1 ) [CRAN] lme4 (NA -> 1.1-36 ) [CRAN] pbkrtest (NA -> 0.5.3 ) [CRAN] car (NA -> 3.1-3 ) [CRAN] rstatix (NA -> 0.7.2 ) [CRAN] mvtnorm (NA -> 1.3-3 ) [CRAN] estimability (NA -> 1.5.1 ) [CRAN] scatterpl... (NA -> 0.3-44 ) [CRAN] multcompView (NA -> 0.1-10 ) [CRAN] leaps (NA -> 3.2 ) [CRAN] flashClust (NA -> 1.01-2 ) [CRAN] emmeans (NA -> 1.10.7 ) [CRAN] ellipse (NA -> 0.5.0 ) [CRAN] GO.db (NA -> 3.20.0 ) [CRAN] treeio (NA -> 1.31.0 ) [CRAN] tidytree (NA -> 0.4.6 ) [CRAN] ape (NA -> 5.8-1 ) [CRAN] qvalue (NA -> 2.39.0 ) [CRAN] ggtree (NA -> 3.15.0 ) [CRAN] GOSemSim (NA -> 2.33.0 ) [CRAN] scatterpie (NA -> 0.2.4 ) [CRAN] ggtangle (NA -> 0.0.6 ) [CRAN] ggnewscale (NA -> 0.5.0 ) [CRAN] DOSE (NA -> 4.1.0 ) [CRAN] aplot (NA -> 0.2.4 ) [CRAN] venn (NA -> 1.12 ) [CRAN] ggpubr (NA -> 0.6.0 ) [CRAN] FactoMineR (NA -> 2.11 ) [CRAN] dendextend (NA -> 1.19.0 ) [CRAN] gson (NA -> 0.1.0 ) [CRAN] enrichplot (NA -> 1.27.4 ) [CRAN] writexl (NA -> 1.5.1 ) [CRAN] reshape (NA -> 0.8.9 ) [CRAN] qcc (NA -> 2.7 ) [CRAN] kableExtra (NA -> 1.4.0 ) [CRAN] inflection (NA -> 1.3.6 ) [CRAN] hash (NA -> 2.2.6.3 ) [CRAN] ggVennDia... (NA -> 1.5.2 ) [CRAN] ggupset (NA -> 0.4.1 ) [CRAN] ggfortify (NA -> 0.4.17 ) [CRAN] factoextra (NA -> 1.0.7 ) [CRAN] EnhancedV... (NA -> 1.25.0 ) [CRAN] clusterPr... (NA -> 4.15.1 ) [CRAN] Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpkPXgsp/file3e8ada5edc9026 Cloning into '/tmp/RtmpkPXgsp/file3e8ada5edc9026'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpkPXgsp/file3e8ada5edc9026/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.63.3.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.3’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-limma/00new/limma/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 (limma) Skipping 1 packages ahead of CRAN: cli Installing 48 packages: admisc, gridGraphics, yulab.utils, ggplotify, ggfun, nloptr, lme4, pbkrtest, car, rstatix, mvtnorm, estimability, scatterplot3d, multcompView, leaps, flashClust, emmeans, ellipse, GO.db, treeio, tidytree, ape, qvalue, ggtree, GOSemSim, scatterpie, ggtangle, ggnewscale, DOSE, aplot, venn, ggpubr, FactoMineR, dendextend, gson, enrichplot, writexl, reshape, qcc, kableExtra, inflection, hash, ggVennDiagram, ggupset, ggfortify, factoextra, EnhancedVolcano, clusterProfiler trying URL 'https://cran.uni-muenster.de/src/contrib/admisc_0.37.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/gridGraphics_0.5-1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/yulab.utils_0.2.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggplotify_0.1.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggfun_0.1.8.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.1.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-36.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/mvtnorm_1.3-3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/estimability_1.5.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/scatterplot3d_0.3-44.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/multcompView_0.1-10.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/leaps_3.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/flashClust_1.01-2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/emmeans_1.10.7.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ellipse_0.5.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/data/annotation/src/contrib/GO.db_3.20.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/treeio_1.31.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/tidytree_0.4.6.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ape_5.8-1.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/qvalue_2.39.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/ggtree_3.15.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/GOSemSim_2.33.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/scatterpie_0.2.4.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggtangle_0.0.6.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggnewscale_0.5.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/DOSE_4.1.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/aplot_0.2.4.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/venn_1.12.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/FactoMineR_2.11.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/dendextend_1.19.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/gson_0.1.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/enrichplot_1.27.4.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/writexl_1.5.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/reshape_0.8.9.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/qcc_2.7.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/kableExtra_1.4.0.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/inflection_1.3.6.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/hash_2.2.6.3.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggVennDiagram_1.5.2.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggupset_0.4.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/ggfortify_0.4.17.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/factoextra_1.0.7.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/EnhancedVolcano_1.25.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/clusterProfiler_4.15.1.tar.gz' * installing *source* package ‘admisc’ ... ** this is package ‘admisc’ version ‘0.37’ ** package ‘admisc’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c admisc.c -o admisc.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o gcc -shared -L/usr/local/lib -o admisc.so admisc.o registerDynamicSymbol.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-admisc/00new/admisc/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (admisc) * installing *source* package ‘gridGraphics’ ... ** this is package ‘gridGraphics’ version ‘0.5-1’ ** package ‘gridGraphics’ 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 (gridGraphics) * installing *source* package ‘yulab.utils’ ... ** this is package ‘yulab.utils’ version ‘0.2.0’ ** package ‘yulab.utils’ 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 (yulab.utils) * installing *source* package ‘nloptr’ ... ** this is package ‘nloptr’ version ‘2.1.1’ ** 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). - brew install --cask 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/4.5-3.21/nloptr’ * installing *source* package ‘mvtnorm’ ... ** this is package ‘mvtnorm’ version ‘1.3-3’ ** package ‘mvtnorm’ 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 Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c lpmvnorm.c -o lpmvnorm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ltMatrices.c -o ltMatrices.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c miwa.c -o miwa.o gfortran -fpic -g -O2 -c mvt.f -o mvt.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c mvtnorm-init.c -o mvtnorm-init.o gfortran -fpic -g -O2 -c tvpack.f -o tvpack.o gcc -shared -L/usr/local/lib -o mvtnorm.so C_FORTRAN_interface.o lpmvnorm.o ltMatrices.o miwa.o mvt.o mvtnorm-init.o tvpack.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-mvtnorm/00new/mvtnorm/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 (mvtnorm) * installing *source* package ‘estimability’ ... ** this is package ‘estimability’ version ‘1.5.1’ ** package ‘estimability’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (estimability) * installing *source* package ‘scatterplot3d’ ... ** this is package ‘scatterplot3d’ version ‘0.3-44’ ** package ‘scatterplot3d’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scatterplot3d) * installing *source* package ‘multcompView’ ... ** this is package ‘multcompView’ version ‘0.1-10’ ** package ‘multcompView’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (multcompView) * installing *source* package ‘leaps’ ... ** this is package ‘leaps’ version ‘3.2’ ** package ‘leaps’ 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 Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gfortran -fpic -g -O2 -c leaps.f -o leaps.o gfortran -fpic -g -O2 -c leapshdr.f -o leapshdr.o gcc -shared -L/usr/local/lib -o leaps.so init.o leaps.o leapshdr.o -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-leaps/00new/leaps/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leaps) * installing *source* package ‘flashClust’ ... ** this is package ‘flashClust’ version ‘1.01-2’ ** package ‘flashClust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gfortran -fpic -g -O2 -c hc.f -o hc.o gfortran -fpic -g -O2 -c hcass2.f -o hcass2.o gcc -shared -L/usr/local/lib -o flashClust.so hc.o hcass2.o -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-flashClust/00new/flashClust/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flashClust) * installing *source* package ‘ellipse’ ... ** this is package ‘ellipse’ version ‘0.5.0’ ** package ‘ellipse’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ellipse) * installing *source* package ‘GO.db’ ... ** this is package ‘GO.db’ version ‘3.20.0’ ** 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 (GO.db) * installing *source* package ‘ape’ ... ** this is package ‘ape’ version ‘5.8-1’ ** 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"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c BIONJ.c -o BIONJ.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c NNI.c -o NNI.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SPR.c -o SPR.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c additive.c -o additive.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ape.c -o ape.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bNNI.c -o bNNI.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bionjs.c -o bionjs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bipartition.c -o bipartition.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bitsplits.c -o bitsplits.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delta_plot.c -o delta_plot.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c dist_dna.c -o dist_dna.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c dist_nodes.c -o dist_nodes.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ewLasso.c -o ewLasso.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c heap.c -o heap.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mat_expo.c -o mat_expo.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c me.c -o me.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c me_balanced.c -o me_balanced.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c me_ols.c -o me_ols.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mvr.c -o mvr.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mvrs.c -o mvrs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c nj.c -o nj.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c njs.c -o njs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c pic.c -o pic.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c plot_phylo.c -o plot_phylo.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c prop_part.cpp -o prop_part.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c rTrait.c -o rTrait.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c read_dna.c -o read_dna.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c reorder_Rcpp.cpp -o reorder_Rcpp.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c reorder_phylo.c -o reorder_phylo.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c treePop.c -o treePop.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tree_build.c -o tree_build.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tree_phylo.c -o tree_phylo.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c triangMtd.c -o triangMtd.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c triangMtds.c -o triangMtds.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ultrametric.c -o ultrametric.o g++ -std=gnu++17 -shared -L/usr/local/lib -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 -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-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 ‘qvalue’ ... ** this is package ‘qvalue’ version ‘2.39.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qvalue) * installing *source* package ‘ggnewscale’ ... ** this is package ‘ggnewscale’ version ‘0.5.0’ ** package ‘ggnewscale’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggnewscale) * installing *source* package ‘dendextend’ ... ** this is package ‘dendextend’ version ‘1.19.0’ ** package ‘dendextend’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dendextend) * installing *source* package ‘gson’ ... ** this is package ‘gson’ version ‘0.1.0’ ** package ‘gson’ 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 (gson) * installing *source* package ‘writexl’ ... ** this is package ‘writexl’ version ‘1.5.1’ ** package ‘writexl’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c write_xlsx.c -o write_xlsx.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/app.c -o libxlsxwriter/app.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/format.c -o libxlsxwriter/format.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/theme.c -o libxlsxwriter/theme.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/chart.c -o libxlsxwriter/chart.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/hash_table.c -o libxlsxwriter/hash_table.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/utility.c -o libxlsxwriter/utility.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/content_types.c -o libxlsxwriter/content_types.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/packager.c -o libxlsxwriter/packager.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/workbook.c -o libxlsxwriter/workbook.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/core.c -o libxlsxwriter/core.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/relationships.c -o libxlsxwriter/relationships.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/worksheet.c -o libxlsxwriter/worksheet.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/custom.c -o libxlsxwriter/custom.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/shared_strings.c -o libxlsxwriter/shared_strings.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/xmlwriter.c -o libxlsxwriter/xmlwriter.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/drawing.c -o libxlsxwriter/drawing.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/styles.c -o libxlsxwriter/styles.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c tmpfileplus/tmpfileplus.c -o tmpfileplus/tmpfileplus.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/chartsheet.c -o libxlsxwriter/chartsheet.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c minizip/ioapi.c -o minizip/ioapi.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c minizip/zip.c -o minizip/zip.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/metadata.c -o libxlsxwriter/metadata.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/comment.c -o libxlsxwriter/comment.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/vml.c -o libxlsxwriter/vml.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c md5/md5.c -o md5/md5.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -Iinclude -DUSE_R_LANG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c libxlsxwriter/table.c -o libxlsxwriter/table.o ar rcs libxlsxwriter/libstatxlsxwriter.a libxlsxwriter/app.o libxlsxwriter/format.o libxlsxwriter/theme.o libxlsxwriter/chart.o libxlsxwriter/hash_table.o libxlsxwriter/utility.o libxlsxwriter/content_types.o libxlsxwriter/packager.o libxlsxwriter/workbook.o libxlsxwriter/core.o libxlsxwriter/relationships.o libxlsxwriter/worksheet.o libxlsxwriter/custom.o libxlsxwriter/shared_strings.o libxlsxwriter/xmlwriter.o libxlsxwriter/drawing.o libxlsxwriter/styles.o tmpfileplus/tmpfileplus.o libxlsxwriter/chartsheet.o minizip/ioapi.o minizip/zip.o libxlsxwriter/metadata.o libxlsxwriter/comment.o libxlsxwriter/vml.o md5/md5.o libxlsxwriter/table.o gcc -shared -L/usr/local/lib -o writexl.so write_xlsx.o -Llibxlsxwriter -lstatxlsxwriter -lz installing to /home/omnipath/local/R/4.5-3.21/00LOCK-writexl/00new/writexl/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (writexl) * installing *source* package ‘reshape’ ... ** this is package ‘reshape’ version ‘0.8.9’ ** package ‘reshape’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (reshape) * installing *source* package ‘qcc’ ... ** this is package ‘qcc’ version ‘2.7’ ** package ‘qcc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qcc) * installing *source* package ‘kableExtra’ ... ** this is package ‘kableExtra’ version ‘1.4.0’ ** package ‘kableExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kableExtra) * installing *source* package ‘inflection’ ... ** this is package ‘inflection’ version ‘1.3.6’ ** package ‘inflection’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (inflection) * installing *source* package ‘hash’ ... ** this is package ‘hash’ version ‘2.2.6.3’ ** package ‘hash’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (hash) * installing *source* package ‘ggupset’ ... ** this is package ‘ggupset’ version ‘0.4.1’ ** package ‘ggupset’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (ggupset) * installing *source* package ‘ggfortify’ ... ** this is package ‘ggfortify’ version ‘0.4.17’ ** package ‘ggfortify’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggfortify) * installing *source* package ‘EnhancedVolcano’ ... ** this is package ‘EnhancedVolcano’ version ‘1.25.0’ ** 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 (EnhancedVolcano) * installing *source* package ‘ggplotify’ ... ** this is package ‘ggplotify’ version ‘0.1.2’ ** package ‘ggplotify’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggplotify) * installing *source* package ‘ggfun’ ... ** this is package ‘ggfun’ version ‘0.1.8’ ** package ‘ggfun’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggfun) ERROR: dependency ‘nloptr’ is not available for package ‘lme4’ Perhaps try a variation of: install.packages('nloptr') * removing ‘/home/omnipath/local/R/4.5-3.21/lme4’ * installing *source* package ‘emmeans’ ... ** this is package ‘emmeans’ version ‘1.10.7’ ** package ‘emmeans’ 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 (emmeans) * installing *source* package ‘tidytree’ ... ** this is package ‘tidytree’ version ‘0.4.6’ ** package ‘tidytree’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tidytree) * installing *source* package ‘GOSemSim’ ... ** this is package ‘GOSemSim’ version ‘2.33.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ICmethod.cpp -o ICmethod.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -shared -L/usr/local/lib -o GOSemSim.so ICmethod.o RcppExports.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-GOSemSim/00new/GOSemSim/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 (GOSemSim) * installing *source* package ‘venn’ ... ** this is package ‘venn’ version ‘1.12’ ** package ‘venn’ 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 (venn) ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’ Perhaps try a variation of: install.packages('lme4') * removing ‘/home/omnipath/local/R/4.5-3.21/pbkrtest’ * installing *source* package ‘treeio’ ... ** this is package ‘treeio’ version ‘1.31.0’ ** 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 (treeio) * installing *source* package ‘scatterpie’ ... ** this is package ‘scatterpie’ version ‘0.2.4’ ** package ‘scatterpie’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scatterpie) * installing *source* package ‘ggtangle’ ... ** this is package ‘ggtangle’ version ‘0.0.6’ ** package ‘ggtangle’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggtangle) * installing *source* package ‘DOSE’ ... ** this is package ‘DOSE’ version ‘4.1.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DOSE) * installing *source* package ‘aplot’ ... ** this is package ‘aplot’ version ‘0.2.4’ ** package ‘aplot’ 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 (aplot) ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’ Perhaps try a variation of: install.packages(c('pbkrtest', 'lme4')) * removing ‘/home/omnipath/local/R/4.5-3.21/car’ * installing *source* package ‘ggtree’ ... ** this is package ‘ggtree’ version ‘3.15.0’ ** 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 (ggtree) * installing *source* package ‘ggVennDiagram’ ... ** this is package ‘ggVennDiagram’ version ‘1.5.2’ ** package ‘ggVennDiagram’ 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 (ggVennDiagram) ERROR: dependency ‘car’ is not available for package ‘rstatix’ Perhaps try a variation of: install.packages('car') * removing ‘/home/omnipath/local/R/4.5-3.21/rstatix’ ERROR: dependency ‘car’ is not available for package ‘FactoMineR’ Perhaps try a variation of: install.packages('car') * removing ‘/home/omnipath/local/R/4.5-3.21/FactoMineR’ * installing *source* package ‘enrichplot’ ... ** this is package ‘enrichplot’ version ‘1.27.4’ ** 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 (enrichplot) ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’ Perhaps try a variation of: install.packages('rstatix') * removing ‘/home/omnipath/local/R/4.5-3.21/ggpubr’ * installing *source* package ‘clusterProfiler’ ... ** this is package ‘clusterProfiler’ version ‘4.15.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (clusterProfiler) ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’ Perhaps try a variation of: install.packages(c('FactoMineR', 'ggpubr')) * removing ‘/home/omnipath/local/R/4.5-3.21/factoextra’ The downloaded source packages are in ‘/tmp/RtmpkPXgsp/downloaded_packages’ Downloading GitHub repo saezlab/OmnipathR@devel Skipping 1 packages ahead of CRAN: cli ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpkPXgsp/remotes3e8ada5c219310/saezlab-OmnipathR-0a92537/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘OmnipathR/.github’ * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.15.9.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.15.9’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-02-13 20:48:25] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-13 20:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-13 19:48:15 UTC; omnipath [2025-02-13 20:48:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-13 20:48:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-13 19:48:15 UTC; unix [2025-02-13 20:48:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-13 20:48:25] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-13 20:48:25] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-13 20:48:25] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-02-13 20:48:25] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-02-13 20:48:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Contains 1 files. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-13 20:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-13 20:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-13 20:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-13 20:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-13 20:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-13 20:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:25] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-13 20:48:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-13 20:48:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-13 19:48:15 UTC; omnipath [2025-02-13 20:48:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-13 20:48:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-13 19:48:15 UTC; unix [2025-02-13 20:48:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9 [2025-02-13 20:48:26] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-13 20:48:26] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-13 20:48:26] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-02-13 20:48:26] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-02-13 20:48:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-13 20:48:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:27] [TRACE] [OmnipathR] Contains 1 files. [2025-02-13 20:48:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-13 20:48:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-13 20:48:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-13 20:48:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-13 20:48:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-13 20:48:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-13 20:48:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-13 20:48:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-13 20:48:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-13 20:48:27] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) Downloading GitHub repo saezlab/cosmosR@HEAD Skipping 1 packages ahead of CRAN: cli ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpkPXgsp/remotes3e8ada42cf77c2/saezlab-cosmosR-81d1a7f/DESCRIPTION’ ... OK * preparing ‘cosmosR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘cosmosR_1.9.1.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘cosmosR/vignettes/net_compr_MOON_files/figure-markdown_strict/extract_subnetwork_from_scored_MOON_network_1.png’ * installing *source* package ‘cosmosR’ ... ** this is package ‘cosmosR’ version ‘1.9.1’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cosmosR) Downloading GitHub repo ctlab/fgsea@HEAD Skipping 1 packages ahead of CRAN: cli ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpkPXgsp/remotes3e8ada5c0ba17a/alserglab-fgsea-da4b3b8/DESCRIPTION’ ... OK * preparing ‘fgsea’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘fgsea_1.33.1.tar.gz’ * installing *source* package ‘fgsea’ ... ** this is package ‘fgsea’ version ‘1.33.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c ScoreRuler.cpp -o ScoreRuler.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c fastGSEA.cpp -o fastGSEA.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c fgseaMultilevel.cpp -o fgseaMultilevel.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c geseca.cpp -o geseca.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/BH/include' -I/usr/local/include -fpic -g -O2 -c util.cpp -o util.o g++ -std=gnu++17 -shared -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-fgsea/00new/fgsea/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 (fgsea) Downloading git repo https://git.bioconductor.org/packages/limma.git '/usr/bin/git' clone --depth 1 --no-hardlinks https://git.bioconductor.org/packages/limma.git /tmp/RtmpkPXgsp/file3e8ada265e09a3 Cloning into '/tmp/RtmpkPXgsp/file3e8ada265e09a3'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpkPXgsp/file3e8ada265e09a3/DESCRIPTION’ ... OK * preparing ‘limma’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘limma_3.63.3.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.3’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c normexp.c -o normexp.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-limma/00new/limma/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 (limma) Warning messages: 1: In i.p(...) : installation of package ‘nloptr’ had non-zero exit status 2: In i.p(...) : installation of package ‘lme4’ had non-zero exit status 3: In i.p(...) : installation of package ‘pbkrtest’ had non-zero exit status 4: In i.p(...) : installation of package ‘car’ had non-zero exit status 5: In i.p(...) : installation of package ‘rstatix’ had non-zero exit status 6: In i.p(...) : installation of package ‘FactoMineR’ had non-zero exit status 7: In i.p(...) : installation of package ‘ggpubr’ had non-zero exit status 8: In i.p(...) : installation of package ‘factoextra’ had non-zero exit status [ Finished: 2025-02-13 20:49:20 CET ]