[ Started: 2025-02-21 01:14:06 CET ]
[ MetaProViz v2.1.4 for BioC-3.21 from https://github.com/saezlab/MetaProViz@development (670ba16 2025-02-20 16:20:03) ]
[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/RtmpEd1ina/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]
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/RtmpEd1ina/file2ca2eb1dbf91c6
Cloning into '/tmp/RtmpEd1ina/file2ca2eb1dbf91c6'...
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpEd1ina/file2ca2eb1dbf91c6/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)
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: <https://cmake.org/>
-------------------------------------------------------
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/RtmpEd1ina/downloaded_packages’
Downloading GitHub repo saezlab/OmnipathR@devel
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpEd1ina/remotes2ca2eb67fa5f73/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
[2025-02-21 01:14:56] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-21 01:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 00:14:46 UTC; omnipath
[2025-02-21 01:14:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-21 01:14:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 00:14:47 UTC; unix
[2025-02-21 01:14:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-21 01:14:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-21 01:14:56] [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=2025-02-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-21 01:14:56] [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]
[2025-02-21 01:14:56] [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
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-21 01:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-21 01:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-21 01:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-21 01:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-21 01:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:56] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-21 01:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:58] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-02-21 00:14:46 UTC; omnipath
[2025-02-21 01:14:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-21 01:14:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-21 00:14:47 UTC; unix
[2025-02-21 01:14:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-21 01:14:58] [INFO] [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-21 01:14:58] [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=2025-02-21; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-21 01:14:58] [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]
[2025-02-21 01:14:58] [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
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-21 01:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-21 01:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-21 01:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-21 01:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-21 01:14:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-21 01:14:58] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
Downloading GitHub repo saezlab/cosmosR@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpEd1ina/remotes2ca2eb6de9fba5/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/RtmpEd1ina/remotes2ca2eb19006f3c/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/RtmpEd1ina/file2ca2eb2c431fc3
Cloning into '/tmp/RtmpEd1ina/file2ca2eb2c431fc3'...
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/tmp/RtmpEd1ina/file2ca2eb2c431fc3/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: 2025-02-21 01:15:51 CET ]