[ Started: 2026-03-26 20:24:13 CET ]
[ CARNIVAL v2.5.1 for BioC-3.23 from https://github.com/saezlab/CARNIVAL@dev (81a0120 2022-03-17 09:59:10) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.6-3.23"
[3] "/home/omnipath/local/R/4.6"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
  (2026-03-23 r89685)
Old packages: 'assorthead', 'biocViews', 'clue', 'rmarkdown', 'wppi'
trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/assorthead_1.5.14.tar.gz'
trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/biocViews_1.79.4.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/clue_0.3-68.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.31.tar.gz'
trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/wppi_1.19.0.tar.gz'
* installing *source* package ‘assorthead’ ...
** this is package ‘assorthead’ version ‘1.5.14’
** 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 (assorthead)
* installing *source* package ‘biocViews’ ...
** this is package ‘biocViews’ version ‘1.79.4’
** using staged installation
** R
** data
** 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 (biocViews)
* installing *source* package ‘clue’ ...
** this is package ‘clue’ version ‘0.3-68’
** package ‘clue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c assignment.c -o assignment.o
gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c clue.c -o clue.o
gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c lsap.c -o lsap.o
gcc -std=gnu2x -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c trees.c -o trees.o
gcc -std=gnu2x -shared -L/usr/local/lib -o clue.so assignment.o clue.o init.o lsap.o trees.o
installing to /home/omnipath/local/R/4.6-3.23/00LOCK-clue/00new/clue/libs
** R
** data
** 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 (clue)
* installing *source* package ‘rmarkdown’ ...
** this is package ‘rmarkdown’ version ‘2.31’
** package ‘rmarkdown’ 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 (rmarkdown)
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.19.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-26 20:24:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:41:40 UTC; omnipath
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:41:42 UTC; unix
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.11
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-26 20:24:39] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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]
[2026-03-26 20:24:39] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-26 20:24:39] [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
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-26 20:24:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:40] [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
[2026-03-26 20:24:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-26 20:24:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:42] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:41:40 UTC; omnipath
[2026-03-26 20:24:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-26 20:24:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:41:42 UTC; unix
[2026-03-26 20:24:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.11
[2026-03-26 20:24:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-26 20:24:43] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-26 20:24:43] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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]
[2026-03-26 20:24:43] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-26 20:24:43] [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
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:43] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:41:40 UTC; omnipath
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:41:42 UTC; unix
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.11
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-26 20:24:45] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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]
[2026-03-26 20:24:45] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.11(2026-03-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); wppi 1.19.0(2025-11-18); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-26 20:24:45] [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
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-26 20:24:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-26 20:24:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-26 20:24:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-26 20:24:46] [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/Rtmp4SKNjt/downloaded_packages’
Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
  (2026-03-23 r89685)
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: rmarkdown
[ Finished: 2026-03-26 20:24:49 CET ]