[ Started: 2025-04-07 23:40:46 CEST ] [ MetaProViz v2.1.7 for BioC-3.21 from https://github.com/saezlab/MetaProViz@development (64f9eb9 2025-04-02 11:42:46) ] [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: 'basilisk', 'decoupleR' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/basilisk_1.19.3.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/decoupleR_2.13.0.tar.gz' * installing *source* package ‘basilisk’ ... ** this is package ‘basilisk’ version ‘1.19.3’ ** using non-staged installation via StagedInstall field ** 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 * DONE (basilisk) * 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/RtmpAXjNlP/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' cosmosR (1.15.0 -> ef9d5aacc...) [GitHub] NA (NA -> 35cf871ee...) [Git] nloptr (NA -> 2.2.1 ) [CRAN] lme4 (NA -> 1.1-37 ) [CRAN] pbkrtest (NA -> 0.5.3 ) [CRAN] car (NA -> 3.1-3 ) [CRAN] rstatix (NA -> 0.7.2 ) [CRAN] ggpubr (NA -> 0.6.0 ) [CRAN] FactoMineR (NA -> 2.11 ) [CRAN] factoextra (NA -> 1.0.7 ) [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/RtmpAXjNlP/filef580873ae8c73 Cloning into '/tmp/RtmpAXjNlP/filef580873ae8c73'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpAXjNlP/filef580873ae8c73/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_3.63.12.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.12’ ** 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) Installing 8 packages: nloptr, lme4, pbkrtest, car, rstatix, ggpubr, FactoMineR, factoextra trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.2.1.tar.gz' trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-37.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/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/factoextra_1.0.7.tar.gz' * installing *source* package ‘nloptr’ ... ** this is package ‘nloptr’ version ‘2.2.1’ ** 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’ 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’ 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’ 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’ 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’ 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’ 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/RtmpAXjNlP/downloaded_packages’ Downloading GitHub repo saezlab/cosmosR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpAXjNlP/remotesf580816963f9b/saezlab-cosmosR-ef9d5aa/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 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/RtmpAXjNlP/filef5808494b47ee Cloning into '/tmp/RtmpAXjNlP/filef5808494b47ee'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpAXjNlP/filef5808494b47ee/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_3.63.12.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.12’ ** 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: 2025-04-07 23:41:50 CEST ]