[ Started: 2024-03-29 12:27:26 CET ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" also installing the dependency ‘nloptr’ trying URL 'https://cran.uni-muenster.de/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://cran.uni-muenster.de/src/contrib/bslib_0.7.0.tar.gz' Content type 'application/x-gzip' length 5125401 bytes (4.9 MB) ================================================== downloaded 4.9 MB trying URL 'https://cran.uni-muenster.de/src/contrib/future.apply_1.11.2.tar.gz' Content type 'application/x-gzip' length 63881 bytes (62 KB) ================================================== downloaded 62 KB trying URL 'https://cran.uni-muenster.de/src/contrib/gh_1.4.1.tar.gz' Content type 'application/x-gzip' length 46164 bytes (45 KB) ================================================== downloaded 45 KB trying URL 'https://cran.uni-muenster.de/src/contrib/lme4_1.1-35.2.tar.gz' Content type 'application/x-gzip' length 2943611 bytes (2.8 MB) ================================================== downloaded 2.8 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). - sudo brew install 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/4.3-3.18/nloptr’ * installing *source* package ‘bslib’ ... ** package ‘bslib’ 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 ** 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 (bslib) * installing *source* package ‘future.apply’ ... ** package ‘future.apply’ 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 (future.apply) * installing *source* package ‘gh’ ... ** package ‘gh’ 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 (gh) * installing *source* package ‘lme4’ ... ** package ‘lme4’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c external.cpp -o external.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glmFamily.cpp -o glmFamily.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c optimizer.cpp -o optimizer.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c predModule.cpp -o predModule.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.18/RcppEigen/include' -I'/home/omnipath/local/R/4.3-3.18/Matrix/include' -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c respModule.cpp -o respModule.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-lme4/00new/lme4/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 (lme4) The downloaded source packages are in ‘/tmp/Rtmpa5A5aR/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘nloptr’ had non-zero exit status 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29) Old packages: 'iml', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/iml_0.11.2.tar.gz' Content type 'application/x-gzip' length 176756 bytes (172 KB) ================================================== downloaded 172 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/wppi_1.10.0.tar.gz' Content type 'application/x-gzip' length 662114 bytes (646 KB) ================================================== downloaded 646 KB * installing *source* package ‘iml’ ... ** package ‘iml’ 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 (iml) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-03-29 12:28:42] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-29 12:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Contains 1 files. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-29 12:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-29 12:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-29 12:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-29 12:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-29 12:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-29 12:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:42] [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 [2024-03-29 12:28:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-29 12:28:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Contains 1 files. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-29 12:28:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-29 12:28:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-29 12:28:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-29 12:28:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-29 12:28:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-29 12:28:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:44] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-29 12:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-29 12:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:46] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Contains 1 files. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-29 12:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-29 12:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-29 12:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-29 12:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-29 12:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-29 12:28:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-29 12:28:46] [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/Rtmpa5A5aR/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 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29) 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: 2024-03-29 12:28:54 CET ]