[ Started: 2025-03-06 00:05:09 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', 'GO.db', 'locfit', 'spatstat.univar', 'wppi' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/edgeR_4.5.6.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/data/annotation/src/contrib/GO.db_3.21.0.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/locfit_1.5-9.12.tar.gz' trying URL 'https://cloud.r-project.org/src/contrib/spatstat.univar_3.1-2.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/wppi_1.15.0.tar.gz' * installing *source* package ‘GO.db’ ... ** this is package ‘GO.db’ version ‘3.21.0’ ** using staged installation ** R ** inst ** 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 (GO.db) * installing *source* package ‘locfit’ ... ** this is package ‘locfit’ version ‘1.5-9.12’ ** package ‘locfit’ 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 -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c S_enter.c -o S_enter.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c band.c -o band.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dbinom.c -o dbinom.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dens_haz.c -o dens_haz.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dens_int.c -o dens_int.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dens_odi.c -o dens_odi.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c density.c -o density.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ev_atree.c -o ev_atree.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ev_interp.c -o ev_interp.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ev_kdtre.c -o ev_kdtre.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ev_main.c -o ev_main.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ev_sphere.c -o ev_sphere.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ev_trian.c -o ev_trian.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c family.c -o family.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fitted.c -o fitted.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c frend.c -o frend.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_adap.c -o lf_adap.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_dercor.c -o lf_dercor.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_fitfun.c -o lf_fitfun.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_nbhd.c -o lf_nbhd.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_robust.c -o lf_robust.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_vari.c -o lf_vari.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lf_wdiag.c -o lf_wdiag.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c lfstr.c -o lfstr.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c locfit.c -o locfit.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_chol.c -o m_chol.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_eigen.c -o m_eigen.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_icirc.c -o m_icirc.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_imont.c -o m_imont.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_isimp.c -o m_isimp.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_isphr.c -o m_isphr.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_jacob.c -o m_jacob.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_max.c -o m_max.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_qr.c -o m_qr.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_solve.c -o m_solve.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_svd.c -o m_svd.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c m_vector.c -o m_vector.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c math.c -o math.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c minmax.c -o minmax.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pcomp.c -o pcomp.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c preplot.c -o preplot.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c prob.c -o prob.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c procv.c -o procv.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scb.c -o scb.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scb_cons.c -o scb_cons.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scb_crit.c -o scb_crit.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scb_iface.c -o scb_iface.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c simul.c -o simul.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c smisc.c -o smisc.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c startlf.c -o startlf.o gcc -std=gnu17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c weight.c -o weight.o gcc -std=gnu17 -shared -L/usr/local/lib -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-locfit/00new/locfit/libs ** R ** data ** 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 ** 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 (locfit) * installing *source* package ‘spatstat.univar’ ... ** this is package ‘spatstat.univar’ version ‘3.1-2’ ** package ‘spatstat.univar’ 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 access.c -o access.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c adaptive.c -o adaptive.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c colonel.c -o colonel.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hotrod.c -o hotrod.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 kernels.c -o kernels.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tabnum.c -o tabnum.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c taylorboot.c -o taylorboot.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c whist.c -o whist.o gcc -shared -L/usr/local/lib -o spatstat.univar.so access.o adaptive.o colonel.o hotrod.o init.o kernels.o tabnum.o taylorboot.o whist.o installing to /home/omnipath/local/R/4.5-3.21/00LOCK-spatstat.univar/00new/spatstat.univar/libs ** R ** inst ** 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 ** 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 (spatstat.univar) * 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 [2025-03-06 00:05:41] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-06 00:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-05 00:10:46 UTC; omnipath [2025-03-06 00:05:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-06 00:05:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-05 00:10:47 UTC; unix [2025-03-06 00:05:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-06 00:05:41] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-06 00:05:41] [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=2025-03-06; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-06 00:05:41] [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] [2025-03-06 00:05:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); 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 1.1.0(2025-01-18); 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(2025-03-05); 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 1.4.4(2025-02-27); 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) [2025-03-06 00:05:41] [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 [2025-03-06 00:05:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Contains 1 files. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-06 00:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-06 00:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-06 00:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-06 00:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-06 00:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-06 00:05:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:41] [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 [2025-03-06 00:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-06 00:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-05 00:10:46 UTC; omnipath [2025-03-06 00:05:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-06 00:05:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-05 00:10:47 UTC; unix [2025-03-06 00:05:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-06 00:05:44] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-06 00:05:44] [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=2025-03-06; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-06 00:05:44] [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] [2025-03-06 00:05:44] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); 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 1.1.0(2025-01-18); 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(2025-03-05); 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 1.4.4(2025-02-27); 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) [2025-03-06 00:05:44] [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 [2025-03-06 00:05:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-06 00:05:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:44] [TRACE] [OmnipathR] Contains 1 files. [2025-03-06 00:05:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-06 00:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-06 00:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:44] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-06 00:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-06 00:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-06 00:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-06 00:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-06 00:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:45] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-06 00:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-06 00:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:47] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-05 00:10:46 UTC; omnipath [2025-03-06 00:05:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-06 00:05:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-05 00:10:47 UTC; unix [2025-03-06 00:05:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-06 00:05:47] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-06 00:05:47] [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=2025-03-06; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-06 00:05:47] [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] [2025-03-06 00:05:47] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); 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 1.1.0(2025-01-18); 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(2025-03-05); 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 1.4.4(2025-02-27); 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) [2025-03-06 00:05:47] [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 [2025-03-06 00:05:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-06 00:05:47] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:47] [TRACE] [OmnipathR] Contains 1 files. [2025-03-06 00:05:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-06 00:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-06 00:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-06 00:05:47] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-06 00:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-06 00:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-06 00:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-06 00:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-06 00:05:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-06 00:05:47] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘edgeR’ ... ** this is package ‘edgeR’ version ‘4.5.6’ ** 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) The downloaded source packages are in ‘/tmp/RtmpzCgjUF/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: 2025-03-06 00:05:59 CET ]