[ Started: 2025-04-17 23:40:13 CEST ]
[ mistyR v1.10.0 for BioC-3.21 from https://github.com/saezlab/mistyR@master (8bb8ba9 2024-03-25 14:10:38) ]

[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: 'cosmosR', 'fgsea', 'OmnipathR'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/cosmosR_1.16.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/fgsea_1.34.0.tar.gz'
trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/OmnipathR_3.16.0.tar.gz'
* installing *source* package ‘cosmosR’ ...
** this is package ‘cosmosR’ version ‘1.16.0’
** 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)
* installing *source* package ‘fgsea’ ...
** this is package ‘fgsea’ version ‘1.34.0’
** 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)
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.16.0’
** 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
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 23:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 21:40:49 UTC; unix
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-17 23:40:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-17 23:40:59] [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=2025-04-17; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-04-17 23:40:59] [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]
[2025-04-17 23:40:59] [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 6.2.2(2025-03-24); 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 0.1.3(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 1.1.2(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); 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); 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 1.27.0(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 1.1.6(2025-04-11); 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 1.8.7(2025-03-27); 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 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); 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 2.3.2(2025-02-01)
[2025-04-17 23:40:59] [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
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:40:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:40:59] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:41:00] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:41:00] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-16 22:40:50 UTC; biocbuild
[2025-04-17 23:41:00] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-04-17 23:41:00] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 21:40:49 UTC; unix
[2025-04-17 23:41:00] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-17 23:41:00] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-17 23:41:00] [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=2025-04-17; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-04-17 23:41:00] [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]
[2025-04-17 23:41:00] [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 6.2.2(2025-03-24); 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 0.1.3(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 1.1.2(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); 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); 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 1.27.0(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 1.1.6(2025-04-11); 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 1.8.7(2025-03-27); 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 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); 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 2.3.2(2025-02-01)
[2025-04-17 23:41:00] [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
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:41:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-17 23:41:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:41:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-17 23:41:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-17 23:41:01] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

The downloaded source packages are in
	‘/tmp/RtmpD7AQfQ/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' 

Skipping 1 packages ahead of CRAN: recipes
[ Finished: 2025-04-17 23:41:03 CEST ]