[ Started: 2025-02-25 00:05:10 CET ]
[ CARNIVAL v2.7.2 for BioC-3.21 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[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: 'ggnewscale', 'iml', 'R.utils', 'reticulate', 'uwot', 'wppi'
trying URL 'https://cloud.r-project.org/src/contrib/ggnewscale_0.5.1.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/iml_0.11.4.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/R.utils_2.13.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/reticulate_1.41.0.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/uwot_0.2.3.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz'
* installing *source* package ‘ggnewscale’ ...
** this is package ‘ggnewscale’ version ‘0.5.1’
** package ‘ggnewscale’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** 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 (ggnewscale)
* installing *source* package ‘iml’ ...
** this is package ‘iml’ version ‘0.11.4’
** 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 ‘R.utils’ ...
** this is package ‘R.utils’ version ‘2.13.0’
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function warnings to warnings.default, which was defined in environment R.utils.
Warning in setGenericS3.default("use") :
  Renamed the preexisting function use to use.default, which was defined in environment R.utils.
Warning in setMethodS3.default("use", "default", function(pkg = "R.utils",  :
  Method already existed and was overwritten: use.default
** help
*** installing help indices
** 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 (R.utils)
* installing *source* package ‘reticulate’ ...
** this is package ‘reticulate’ version ‘1.41.0’
** package ‘reticulate’ successfully unpacked and MD5 sums checked
** 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/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/usr/local/include    -fpic  -g -O2   -c event_loop.cpp -o event_loop.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/usr/local/include    -fpic  -g -O2   -c libpython.cpp -o libpython.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/usr/local/include    -fpic  -g -O2   -c output.cpp -o output.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/usr/local/include    -fpic  -g -O2   -c pending_py_calls_notifier.cpp -o pending_py_calls_notifier.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/usr/local/include    -fpic  -g -O2   -c python.cpp -o python.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/usr/local/include    -fpic  -g -O2   -c readline.cpp -o readline.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/usr/local/include    -fpic  -g -O2   -c signals.cpp -o signals.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o pending_py_calls_notifier.o python.o readline.o signals.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-reticulate/00new/reticulate/libs
** 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
** 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 (reticulate)
* installing *source* package ‘uwot’ ...
** this is package ‘uwot’ version ‘0.2.3’
** package ‘uwot’ successfully unpacked and MD5 sums checked
** 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../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c connected_components.cpp -o connected_components.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c nn_parallel.cpp -o nn_parallel.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c perplexity.cpp -o perplexity.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c r_uwot.cpp -o r_uwot.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c smooth_knn.cpp -o smooth_knn.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c supervised.cpp -o supervised.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c thread.cpp -o thread.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.5-3.21/dqrng/include' -I'/home/omnipath/local/R/4.5-3.21/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.21/RcppAnnoy/include' -I'/home/omnipath/local/R/4.5-3.21/RcppProgress/include' -I/usr/local/include   -DRCPP_NO_RTTI -fpic  -g -O2   -c transform.cpp -o transform.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o uwot.so RcppExports.o connected_components.o nn_parallel.o perplexity.o r_uwot.o smooth_knn.o supervised.o thread.o transform.o
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-uwot/00new/uwot/libs
** 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
** 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 (uwot)
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.15.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-24 00:19:31 UTC; omnipath
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-24 00:19:32 UTC; unix
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-25 00:06:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-25 00:06:49] [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=2025-02-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-25 00:06:49] [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]
[2025-02-25 00:06:49] [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
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-25 00:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:49] [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
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-24 00:19:31 UTC; omnipath
[2025-02-25 00:06:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-25 00:06:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-24 00:19:32 UTC; unix
[2025-02-25 00:06:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-25 00:06:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-25 00:06:52] [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=2025-02-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-25 00:06:52] [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]
[2025-02-25 00:06:52] [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
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-25 00:06:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-25 00:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-25 00:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:53] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:55] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-24 00:19:31 UTC; omnipath
[2025-02-25 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-25 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-24 00:19:32 UTC; unix
[2025-02-25 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-25 00:06:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-25 00:06:55] [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=2025-02-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-25 00:06:55] [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]
[2025-02-25 00:06:55] [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
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-25 00:06:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-25 00:06:55] [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/RtmpXXbaVm/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' 

[ Finished: 2025-02-25 00:06:58 CET ]