[ Started: 2024-10-01 16:08:49 CEST ] [ MetaProViz v2.1.0 for BioC-3.20 from https://github.com/saezlab/MetaProViz@development (348773f 2024-10-01 15:59:50) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" '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: 'decoupleR' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/decoupleR_2.11.0.tar.gz' Content type 'application/x-gzip' length 5037849 bytes (4.8 MB) ================================================== downloaded 4.8 MB * installing *source* package ‘decoupleR’ ... ** package ‘decoupleR’ 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 (decoupleR) The downloaded source packages are in ‘/tmp/RtmpYZLQpy/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' nloptr (NA -> 2.1.1 ) [CRAN] lme4 (NA -> 1.1-35.5) [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] Skipping 1 packages ahead of CRAN: BiocStyle Installing 8 packages: nloptr, lme4, pbkrtest, car, rstatix, ggpubr, FactoMineR, factoextra trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.1.1.tar.gz' Content type 'application/x-gzip' length 2236635 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.5.tar.gz' Content type 'application/x-gzip' length 3300116 bytes (3.1 MB) ================================================== downloaded 3.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/pbkrtest_0.5.3.tar.gz' Content type 'application/x-gzip' length 59013 bytes (57 KB) ================================================== downloaded 57 KB trying URL 'https://cran.uni-muenster.de/src/contrib/car_3.1-3.tar.gz' Content type 'application/x-gzip' length 384407 bytes (375 KB) ================================================== downloaded 375 KB trying URL 'https://cran.uni-muenster.de/src/contrib/rstatix_0.7.2.tar.gz' Content type 'application/x-gzip' length 405256 bytes (395 KB) ================================================== downloaded 395 KB trying URL 'https://cran.uni-muenster.de/src/contrib/ggpubr_0.6.0.tar.gz' Content type 'application/x-gzip' length 1941659 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'https://cran.uni-muenster.de/src/contrib/FactoMineR_2.11.tar.gz' Content type 'application/x-gzip' length 2832656 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://cran.uni-muenster.de/src/contrib/factoextra_1.0.7.tar.gz' Content type 'application/x-gzip' length 1386480 bytes (1.3 MB) ================================================== downloaded 1.3 MB * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... no ------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - 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/4.4-3.20/nloptr’ ERROR: dependency ‘nloptr’ is not available for package ‘lme4’ * removing ‘/home/omnipath/local/R/4.4-3.20/lme4’ ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’ * removing ‘/home/omnipath/local/R/4.4-3.20/pbkrtest’ ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’ * removing ‘/home/omnipath/local/R/4.4-3.20/car’ ERROR: dependency ‘car’ is not available for package ‘rstatix’ * removing ‘/home/omnipath/local/R/4.4-3.20/rstatix’ ERROR: dependency ‘car’ is not available for package ‘FactoMineR’ * removing ‘/home/omnipath/local/R/4.4-3.20/FactoMineR’ ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’ * removing ‘/home/omnipath/local/R/4.4-3.20/ggpubr’ ERROR: dependencies ‘FactoMineR’, ‘ggpubr’ are not available for package ‘factoextra’ * removing ‘/home/omnipath/local/R/4.4-3.20/factoextra’ The downloaded source packages are in ‘/tmp/RtmpYZLQpy/downloaded_packages’ 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: 2024-10-01 16:09:10 CEST ]