[ Started: 2025-03-11 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: 'quantreg', 'sparsevctrs', 'wppi' trying URL 'https://cloud.r-project.org/src/contrib/quantreg_6.1.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/sparsevctrs_0.3.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘quantreg’ ... ** this is package ‘quantreg’ version ‘6.1’ ** package ‘quantreg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using Fortran compiler: ‘GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gfortran -fpic -g -O2 -c akj.f -o akj.o gfortran -fpic -g -O2 -c boot.f -o boot.o gfortran -fpic -g -O2 -c bound.f -o bound.o gfortran -fpic -g -O2 -c boundc.f -o boundc.o gfortran -fpic -g -O2 -c brute.f -o brute.o gfortran -fpic -g -O2 -c chlfct.f -o chlfct.o gfortran -fpic -g -O2 -c cholesky.f -o cholesky.o gfortran -fpic -g -O2 -c combos.f -o combos.o gfortran -fpic -g -O2 -c crqf.f -o crqf.o gfortran -fpic -g -O2 -c crqfnb.f -o crqfnb.o gfortran -fpic -g -O2 -c dsel05.f -o dsel05.o gfortran -fpic -g -O2 -c extract.f -o extract.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c frand.c -o frand.o gfortran -fpic -g -O2 -c grexp.f -o grexp.o gfortran -fpic -g -O2 -c idmin.f -o idmin.o gfortran -fpic -g -O2 -c iswap.f -o iswap.o gfortran -fpic -g -O2 -c kuantile.f -o kuantile.o gfortran -fpic -g -O2 -c kuantiles.f -o kuantiles.o gfortran -fpic -g -O2 -c linpack.f -o linpack.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mcmb.c -o mcmb.o gfortran -fpic -g -O2 -c penalty.f -o penalty.o gfortran -fpic -g -O2 -c pfnb.f -o pfnb.o gfortran -fpic -g -O2 -c powell.f -o powell.o gfortran -fpic -g -O2 -c profnb.f -o profnb.o gfortran -fpic -g -O2 -c pwxy.f -o pwxy.o gfortran -fpic -g -O2 -c qfnb.f -o qfnb.o gfortran -fpic -g -O2 -c qselect.f -o qselect.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c quantreg_init.c -o quantreg_init.o gfortran -fpic -g -O2 -c rls.f -o rls.o gfortran -fpic -g -O2 -c rq0.f -o rq0.o gfortran -fpic -g -O2 -c rq1.f -o rq1.o gfortran -fpic -g -O2 -c rqbr.f -o rqbr.o gfortran -fpic -g -O2 -c rqfn.f -o rqfn.o gfortran -fpic -g -O2 -c rqfnb.f -o rqfnb.o gfortran -fpic -g -O2 -c rqfnc.f -o rqfnc.o gfortran -fpic -g -O2 -c rqs.f -o rqs.o gfortran -fpic -g -O2 -c sakj.f -o sakj.o gfortran -fpic -g -O2 -c sparskit2.f -o sparskit2.o gfortran -fpic -g -O2 -c srqfn.f -o srqfn.o gfortran -fpic -g -O2 -c srqfnc.f -o srqfnc.o gfortran -fpic -g -O2 -c srtpai.f -o srtpai.o gcc -shared -L/usr/local/lib -o quantreg.so akj.o boot.o bound.o boundc.o brute.o chlfct.o cholesky.o combos.o crqf.o crqfnb.o dsel05.o extract.o frand.o grexp.o idmin.o iswap.o kuantile.o kuantiles.o linpack.o mcmb.o penalty.o pfnb.o powell.o profnb.o pwxy.o qfnb.o qselect.o quantreg_init.o rls.o rq0.o rq1.o rqbr.o rqfn.o rqfnb.o rqfnc.o rqs.o sakj.o sparskit2.o srqfn.o srqfnc.o srtpai.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath installing to /home/omnipath/local/R/4.5-3.21/00LOCK-quantreg/00new/quantreg/libs ** R ** data ** demo ** 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 (quantreg) * installing *source* package ‘sparsevctrs’ ... ** this is package ‘sparsevctrs’ version ‘0.3.0’ ** package ‘sparsevctrs’ successfully unpacked and MD5 sums checked ** 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 altrep-sparse-double.c -o altrep-sparse-double.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c altrep-sparse-integer.c -o altrep-sparse-integer.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c altrep-sparse-logical.c -o altrep-sparse-logical.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c altrep-sparse-string.c -o altrep-sparse-string.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 sparse-arithmatic.c -o sparse-arithmatic.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sparse-dummy.c -o sparse-dummy.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sparse-extractors.c -o sparse-extractors.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sparse-utils.c -o sparse-utils.o gcc -shared -L/usr/local/lib -o sparsevctrs.so altrep-sparse-double.o altrep-sparse-integer.o altrep-sparse-logical.o altrep-sparse-string.o init.o sparse-arithmatic.o sparse-dummy.o sparse-extractors.o sparse-utils.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-sparsevctrs/00new/sparsevctrs/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 (sparsevctrs) * 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 [2025-03-11 00:05:33] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-11 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:33] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-10 00:08:49 UTC; omnipath [2025-03-11 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-11 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-10 00:08:50 UTC; unix [2025-03-11 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-11 00:05:33] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-11 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=2025-03-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-11 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] [2025-03-11 00:05:33] [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(2025-03-10); 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) [2025-03-11 00:05:33] [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 [2025-03-11 00:05:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Contains 1 files. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-11 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-11 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-11 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-11 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-11 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-11 00:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:33] [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 [2025-03-11 00:05:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-11 00:05:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:36] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-10 00:08:49 UTC; omnipath [2025-03-11 00:05:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-11 00:05:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-10 00:08:50 UTC; unix [2025-03-11 00:05:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-11 00:05:36] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-11 00:05:36] [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=2025-03-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-11 00:05:36] [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] [2025-03-11 00:05:36] [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(2025-03-10); 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) [2025-03-11 00:05:36] [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 [2025-03-11 00:05:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-11 00:05:36] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:36] [TRACE] [OmnipathR] Contains 1 files. [2025-03-11 00:05:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-11 00:05:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-11 00:05:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:36] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-11 00:05:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-11 00:05:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-11 00:05:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-11 00:05:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-11 00:05:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:36] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-11 00:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-11 00:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:39] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-10 00:08:49 UTC; omnipath [2025-03-11 00:05:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-11 00:05:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-10 00:08:50 UTC; unix [2025-03-11 00:05:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-11 00:05:39] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-11 00:05:39] [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=2025-03-11; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-11 00:05:39] [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=8.6.14; 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] [2025-03-11 00:05:39] [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 1.2.4(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(2025-03-10); 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) [2025-03-11 00:05:39] [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 [2025-03-11 00:05:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-11 00:05:39] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:39] [TRACE] [OmnipathR] Contains 1 files. [2025-03-11 00:05:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-11 00:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-11 00:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-11 00:05:39] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-11 00:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-11 00:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-11 00:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-11 00:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-11 00:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-11 00:05:39] [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/RtmpsW3cFj/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: 2025-03-11 00:05:42 CET ]