[ Started: 2025-03-13 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: 'edgeR', 'GenomeInfoDbData', 'wppi'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/edgeR_4.5.9.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/data/annotation/src/contrib/GenomeInfoDbData_1.2.14.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz'
* installing *source* package ‘edgeR’ ...
** this is package ‘edgeR’ version ‘4.5.9’
** 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 R_exports.c -o R_exports.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c add_prior_count.c -o add_prior_count.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c clowess.c -o clowess.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c compute_apl.c -o compute_apl.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c compute_cpm.c -o compute_cpm.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c compute_nbdev.c -o compute_nbdev.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c exact_test_by_dev.c -o exact_test_by_dev.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c fmm_spline.c -o fmm_spline.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c glm.c -o glm.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c good_turing.c -o good_turing.o
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 interpolator.c -o interpolator.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c loess_by_col.c -o loess_by_col.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c object.c -o object.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ql_glm.c -o ql_glm.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ql_weights.c -o ql_weights.o
gcc -shared -L/usr/local/lib -o edgeR.so R_exports.o R_process_hairpin_reads.o add_prior_count.o clowess.o compute_apl.o compute_cpm.o compute_nbdev.o exact_test_by_dev.o fmm_spline.o glm.o good_turing.o init.o interpolator.o loess_by_col.o object.o ql_glm.o ql_weights.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-edgeR/00new/edgeR/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 (edgeR)
* installing *source* package ‘GenomeInfoDbData’ ...
** this is package ‘GenomeInfoDbData’ version ‘1.2.14’
** using staged installation
** data
** inst
** 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 (GenomeInfoDbData)
* 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
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 00:05:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-12 00:10:35 UTC; omnipath
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-12 00:10:36 UTC; unix
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 00:05:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-13 00:05:28] [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=2025-03-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 00:05:28] [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]
[2025-03-13 00:05:28] [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 1.2.4(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 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-12); 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 1.4.5(2025-03-07); 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); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 00:05:28] [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
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 00:05:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:28] [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
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:31] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:31] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-12 00:10:35 UTC; omnipath
[2025-03-13 00:05:31] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-13 00:05:31] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-12 00:10:36 UTC; unix
[2025-03-13 00:05:31] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 00:05:31] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-13 00:05:31] [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=2025-03-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 00:05:31] [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]
[2025-03-13 00:05:31] [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 1.2.4(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 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-12); 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 1.4.5(2025-03-07); 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); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 00:05:31] [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
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:31] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-13 00:05:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 00:05:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:33] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-12 00:10:35 UTC; omnipath
[2025-03-13 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-13 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-12 00:10:36 UTC; unix
[2025-03-13 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 00:05:33] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-13 00:05:33] [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=2025-03-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 00:05:33] [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]
[2025-03-13 00:05:34] [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 1.2.4(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 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-12); 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 1.4.5(2025-03-07); 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); wppi 1.15.0(2024-10-29); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 00:05:34] [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
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 00:05:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 00:05:34] [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/RtmpgsJH0E/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: 2025-03-13 00:05:36 CET ]