[ Started: 2026-10-25 17:48:26 CET ] [ OmnipathR v4.1.1 for BioC-3.24 from https://github.com/saezlab/OmnipathR@devel (9ce957c 2026-10-20 12:23:32) ] [ R version 4.6.1 Patched (2026-10-12 r90666) -- "Happy Hop" at /opt/R-4.6-patched/bin ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck’ * using R version 4.6.1 Patched (2026-10-12 r90666) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * current time: 2026-10-25 16:48:27 UTC * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘4.1.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 7.6Mb sub-directories of 1Mb or more: doc 6.1Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2026-10-25 17:48:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-25 17:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:48:59] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-10-25 17:48:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-10-25 16:47:02 UTC; omnipath [2026-10-25 17:48:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-10-25 17:48:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-10-25 16:48:30 UTC; unix [2026-10-25 17:48:59] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.1 [2026-10-25 17:48:59] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-10-25 17:49:00] [INFO] [OmnipathR] Session info: [version=R version 4.6.1 Patched (2026-10-12 r90666); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-10-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-10-25 17:49:00] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-4.6-patched/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-10-25 17:49:00] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.6(2026-09-01); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 8.1.0(2026-10-14); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.9(2026-09-01); httr2 1.3.0(2026-07-13); igraph 2.3.4(2026-09-30); jsonlite 2.0.0(2025-03-27); knitr 1.52(2026-09-06); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.3(2026-08-24); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.1(2026-10-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.2(2026-07-05); readr 2.2.0(2026-02-19); readxl 1.6.0(2026-10-17); rlang 1.3.0(2026-07-05); rmarkdown 2.32(2026-09-01); RSQLite 3.53.3(2026-06-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.4(2026-06-04); stringi 1.8.9(2026-08-04); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.3(2026-06-19); xfun 0.62(2026-10-16); XML 3.99-0.25(2026-09-27); xml2 1.6.0(2026-06-22); yaml 2.3.12(2025-12-10); zip 3.0.2(2026-08-04) [2026-10-25 17:49:00] [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 [2026-10-25 17:49:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-10-25 17:49:00] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-10-25 17:49:00] [TRACE] [OmnipathR] Contains 1 files. [2026-10-25 17:49:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-10-25 17:49:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-25 17:49:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-10-25 17:49:00] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-10-25 17:49:00] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-10-25 17:49:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:00] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-10-25 17:49:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:00] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-10-25 17:49:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:00] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-10-25 17:49:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:00] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2026-10-25 17:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-25 17:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:11] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-10-25 17:49:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-10-25 16:47:02 UTC; omnipath [2026-10-25 17:49:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-10-25 17:49:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-10-25 16:48:30 UTC; unix [2026-10-25 17:49:11] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.1 [2026-10-25 17:49:11] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-10-25 17:49:11] [INFO] [OmnipathR] Session info: [version=R version 4.6.1 Patched (2026-10-12 r90666); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-10-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-10-25 17:49:11] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-4.6-patched/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-10-25 17:49:11] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.6(2026-09-01); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 8.1.0(2026-10-14); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.9(2026-09-01); httr2 1.3.0(2026-07-13); igraph 2.3.4(2026-09-30); jsonlite 2.0.0(2025-03-27); knitr 1.52(2026-09-06); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.3(2026-08-24); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.1(2026-10-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.2(2026-07-05); readr 2.2.0(2026-02-19); readxl 1.6.0(2026-10-17); rlang 1.3.0(2026-07-05); rmarkdown 2.32(2026-09-01); RSQLite 3.53.3(2026-06-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.4(2026-06-04); stringi 1.8.9(2026-08-04); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.3(2026-06-19); xfun 0.62(2026-10-16); XML 3.99-0.25(2026-09-27); xml2 1.6.0(2026-06-22); yaml 2.3.12(2025-12-10); zip 3.0.2(2026-08-04) [2026-10-25 17:49:11] [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 [2026-10-25 17:49:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-10-25 17:49:11] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-10-25 17:49:11] [TRACE] [OmnipathR] Contains 1 files. [2026-10-25 17:49:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-10-25 17:49:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-25 17:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-10-25 17:49:11] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-10-25 17:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-10-25 17:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-10-25 17:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-10-25 17:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:11] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-10-25 17:49:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-25 17:49:11] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 74.731 0.046 74.903 curated_ligrec_stats 32.782 3.684 39.311 omnipath-interactions 26.731 2.316 31.476 filter_extra_attrs 20.008 3.417 23.784 all_uniprots 18.580 0.886 59.597 nichenet_gr_network_omnipath 14.523 0.704 15.901 nichenet_signaling_network_omnipath 13.263 0.541 14.503 extra_attr_values 10.033 0.995 11.400 extra_attrs_to_cols 9.803 0.935 11.125 pivot_annotations 8.726 0.955 10.279 with_extra_attrs 8.240 0.758 9.249 go_annot_download 8.331 0.565 8.457 giant_component 7.198 0.385 8.015 omnipath_for_cosmos 6.467 0.439 69.251 filter_by_resource 6.226 0.221 7.095 has_extra_attrs 5.303 0.784 6.130 extra_attrs 5.155 0.700 5.930 print_interactions 5.110 0.354 5.889 curated_ligand_receptor_interactions 4.945 0.422 5.977 translate_ids_multi 5.160 0.139 5.457 filter_intercell 4.507 0.328 5.368 ensembl_id_mapping_table 2.077 0.250 59.497 kegg_conv 1.543 0.150 10.897 translate_ids 0.908 0.096 29.921 kinasephos 0.868 0.118 13.420 uniprot_full_id_mapping_table 0.860 0.098 38.109 biomart_query 0.832 0.092 26.001 kegg_link 0.624 0.040 5.449 kegg_find 0.530 0.044 21.280 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.24/2026-10-25_1734/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-10-25 18:15:11 CET ]