[ Started: 2025-02-27 01:14:50 CET ] [ MetaProViz v2.1.5 for BioC-3.21 from https://github.com/saezlab/MetaProViz@development (f60c4e9 2025-02-25 17:36:47) ] [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/RtmpxsMSRG/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... -> 7c69da197...) [GitHub] cosmosR (1.15.0 -> 81d1a7fe7...) [GitHub] fgsea (1.33.2 -> da4b3b8ed...) [GitHub] NA (NA -> afdcf4a60...) [Git] 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] 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/RtmpxsMSRG/file125b6e59b29f36 Cloning into '/tmp/RtmpxsMSRG/file125b6e59b29f36'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpxsMSRG/file125b6e59b29f36/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_3.63.5.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.5’ ** 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: tinytex 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' 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/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 ‘2.1.1’ ** 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’ 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/RtmpxsMSRG/downloaded_packages’ Downloading GitHub repo saezlab/OmnipathR@devel Skipping 1 packages ahead of CRAN: tinytex ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpxsMSRG/remotes125b6e4c077a38/saezlab-OmnipathR-7c69da1/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_3.15.11.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.15.11’ ** 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 [2025-02-27 01:15:39] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-27 01:15:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-27 00:15:29 UTC; omnipath [2025-02-27 01:15:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-27 01:15:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-27 00:15:30 UTC; unix [2025-02-27 01:15:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-02-27 01:15:39] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-27 01:15:39] [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=2025-02-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-27 01:15:39] [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] [2025-02-27 01:15:39] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-02-27); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.3(2023-07-06); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.6(2023-12-04); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-02-27 01:15:39] [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 [2025-02-27 01:15:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Contains 1 files. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-27 01:15:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-27 01:15:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-27 01:15:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-27 01:15:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-27 01:15:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-27 01:15:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:40] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-27 01:15:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-27 01:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-27 00:15:29 UTC; omnipath [2025-02-27 01:15:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-02-27 01:15:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-27 00:15:30 UTC; unix [2025-02-27 01:15:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-02-27 01:15:41] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-02-27 01:15:41] [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=2025-02-27; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-02-27 01:15:41] [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] [2025-02-27 01:15:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-02-27); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.3(2023-07-06); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.6(2023-12-04); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-02-27 01:15:41] [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 [2025-02-27 01:15:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-27 01:15:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:41] [TRACE] [OmnipathR] Contains 1 files. [2025-02-27 01:15:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-27 01:15:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-27 01:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-02-27 01:15:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-02-27 01:15:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-27 01:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-27 01:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-27 01:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-27 01:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-27 01:15:41] [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: tinytex ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpxsMSRG/remotes125b6e5d0c4216/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 ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpxsMSRG/remotes125b6e1cb73d1e/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/RtmpxsMSRG/file125b6e1b061b8e Cloning into '/tmp/RtmpxsMSRG/file125b6e1b061b8e'... ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/RtmpxsMSRG/file125b6e1b061b8e/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_3.63.5.tar.gz’ * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.63.5’ ** 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: 2025-02-27 01:16:34 CET ]