[ Started: 2025-06-18 02:16:38 CEST ]
[ 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"     
trying URL 'https://cran.uni-muenster.de/src/contrib/data.table_1.17.6.tar.gz'
Content type 'application/x-gzip' length 5840031 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

* installing *source* package ‘data.table’ ...
** this is package ‘data.table’ version ‘1.17.6’
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
gcc 13.3.0
zlib 1.3 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** 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   -fopenmp  -fpic  -g -O2  -c assign.c -o assign.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c between.c -o between.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c bmerge.c -o bmerge.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c chmatch.c -o chmatch.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c cj.c -o cj.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c coalesce.c -o coalesce.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c dogroups.c -o dogroups.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fastmean.c -o fastmean.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fcast.c -o fcast.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fifelse.c -o fifelse.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fmelt.c -o fmelt.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c forder.c -o forder.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c frank.c -o frank.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fread.c -o fread.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c freadR.c -o freadR.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c froll.c -o froll.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c frollR.c -o frollR.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c frolladaptive.c -o frolladaptive.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fsort.c -o fsort.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fwrite.c -o fwrite.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c fwriteR.c -o fwriteR.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c gsumm.c -o gsumm.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c idatetime.c -o idatetime.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c ijoin.c -o ijoin.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c inrange.c -o inrange.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c nafill.c -o nafill.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c negate.c -o negate.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c nqrecreateindices.c -o nqrecreateindices.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c openmp-utils.c -o openmp-utils.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c programming.c -o programming.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c quickselect.c -o quickselect.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c rbindlist.c -o rbindlist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c reorder.c -o reorder.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c shift.c -o shift.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c snprintf.c -o snprintf.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c subset.c -o subset.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c transpose.c -o transpose.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c types.c -o types.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c uniqlist.c -o uniqlist.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c utils.c -o utils.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c vecseq.c -o vecseq.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include   -fopenmp  -fpic  -g -O2  -c wrappers.c -o wrappers.o
gcc -shared -L/usr/local/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz
PKG_CFLAGS = -fopenmp
PKG_LIBS = -fopenmp -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /home/omnipath/local/R/4.5-3.21/00LOCK-data.table/00new/data.table/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 (data.table)

The downloaded source packages are in
	‘/tmp/RtmpxQki8l/downloaded_packages’
Bioconductor version 3.21 (BiocManager 1.30.26), R Under development (unstable)
  (2025-02-12 r87715)
Old packages: 'RUnit', 'tensor', 'wppi'
trying URL 'https://cloud.r-project.org/src/contrib/RUnit_0.4.33.1.tar.gz'
trying URL 'https://cloud.r-project.org/src/contrib/tensor_1.5.1.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.16.0.tar.gz'
* installing *source* package ‘RUnit’ ...
** this is package ‘RUnit’ version ‘0.4.33.1’
** package ‘RUnit’ successfully unpacked and MD5 sums checked
** 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 (RUnit)
* installing *source* package ‘tensor’ ...
** this is package ‘tensor’ version ‘1.5.1’
** package ‘tensor’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** 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 (tensor)
* installing *source* package ‘wppi’ ...
** this is package ‘wppi’ version ‘1.16.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-17 01:31:59 UTC; unix
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-06-18 02:17:11] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-06-18 02:17:11] [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=2025-06-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
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[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
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[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Contains 1 files.
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
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[2025-06-18 02:17:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
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[2025-06-18 02:17:11] [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
[2025-06-18 02:17:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-18 02:17:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:14] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-06-18 02:17:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-06-18 02:17:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-17 01:31:59 UTC; unix
[2025-06-18 02:17:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-06-18 02:17:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-06-18 02:17:14] [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=2025-06-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-06-18 02:17:14] [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]
[2025-06-18 02:17:15] [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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.3.0(2025-06-06); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-18 02:17:15] [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
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Contains 1 files.
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:15] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-06-18 02:17:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-06-18 02:17:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-17 01:31:59 UTC; unix
[2025-06-18 02:17:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-06-18 02:17:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-06-18 02:17:17] [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=2025-06-18; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-06-18 02:17:17] [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]
[2025-06-18 02:17:17] [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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.3.0(2025-06-06); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); 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 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-04-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-18 02:17:17] [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
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Contains 1 files.
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-18 02:17:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-06-18 02:17:17] [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/RtmpxQki8l/downloaded_packages’
Bioconductor version 3.21 (BiocManager 1.30.26), 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: 2025-06-18 02:17:20 CEST ]