Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-03 12:04 -0400 (Wed, 03 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1476/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.17.4 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: OmnipathR |
Version: 3.17.4 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.17.4.tar.gz |
StartedAt: 2025-09-03 02:26:50 -0400 (Wed, 03 Sep 2025) |
EndedAt: 2025-09-03 03:03:39 -0400 (Wed, 03 Sep 2025) |
EllapsedTime: 2208.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OmnipathR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.17.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.17.4’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 35 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... 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 ... OK * 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 [2025-09-03 02:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-03 02:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:27:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-03 02:27:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-02 [2025-09-03 02:27:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-02 19:14:48 UTC; unix [2025-09-03 02:27:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-03 02:27:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-03 02:27:20] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-09-03 02:27:20] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; lapack_version=3.12.0] [2025-09-03 02:27:20] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.17.4(2025-09-02); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-03 02:27:20] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-09-03 02:27:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-03 02:27:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:27:20] [TRACE] [OmnipathR] Contains 1 files. [2025-09-03 02:27:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-03 02:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-03 02:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:27:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-09-03 02:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-03 02:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-03 02:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-03 02:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-03 02:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:20] [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 [2025-09-03 02:27:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-03 02:27:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:27:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-03 02:27:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-02 [2025-09-03 02:27:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-02 19:14:48 UTC; unix [2025-09-03 02:27:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-03 02:27:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-03 02:27:37] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-09-03 02:27:37] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; lapack_version=3.12.0] [2025-09-03 02:27:37] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.17.4(2025-09-02); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-03 02:27:37] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-09-03 02:27:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-03 02:27:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:27:37] [TRACE] [OmnipathR] Contains 1 files. [2025-09-03 02:27:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-03 02:27:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-03 02:27:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:27:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-09-03 02:27:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-03 02:27:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-03 02:27:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-03 02:27:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-03 02:27:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:27:37] [TRACE] [OmnipathR] Cache locked: FALSE taxon_names_table: no visible binding for global variable ‘latin_name_uniprot’ taxon_names_table: no visible binding for global variable ‘latin_name_ensembl’ taxon_names_table: no visible binding for global variable ‘latin_name_oma’ taxon_names_table: no visible binding for global variable ‘common_name_ensembl’ taxon_names_table: no visible binding for global variable ‘common_name_uniprot’ Undefined global functions or variables: common_name_ensembl common_name_uniprot latin_name_ensembl latin_name_oma latin_name_uniprot * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 91.314 0.065 93.001 omnipath-interactions 51.686 4.294 103.435 curated_ligrec_stats 42.333 2.727 110.619 nichenet_gr_network_omnipath 27.437 1.058 49.086 filter_extra_attrs 22.838 4.450 28.105 all_uniprots 22.623 1.261 38.610 nichenet_signaling_network_omnipath 21.379 0.811 44.514 uniprot_organisms 17.621 1.117 21.451 giant_component 16.960 0.895 24.216 go_annot_download 16.109 1.172 21.071 extra_attrs_to_cols 13.670 1.427 15.122 pivot_annotations 12.893 0.983 23.238 extra_attr_values 12.140 1.543 16.253 has_extra_attrs 12.116 1.457 17.896 with_extra_attrs 11.707 1.301 15.487 omnipath_for_cosmos 11.151 0.422 43.201 extra_attrs 7.498 1.178 8.718 translate_ids_multi 8.231 0.310 41.994 filter_by_resource 7.761 0.323 10.383 print_interactions 7.417 0.386 12.503 curated_ligand_receptor_interactions 7.058 0.577 17.233 signed_ptms 7.214 0.248 8.937 filter_intercell 6.711 0.576 11.723 resources_in 6.860 0.371 9.312 omnipath_query 6.444 0.204 8.269 static_table 5.690 0.414 11.555 find_all_paths 5.389 0.176 5.571 hpo_download 5.161 0.197 8.854 pubmed_open 5.117 0.155 5.266 print_path_vs 4.258 0.246 8.423 kegg_conv 2.723 0.214 16.209 ensembl_id_mapping_table 2.611 0.182 30.608 kegg_picture 1.599 0.027 5.989 metalinksdb_sqlite 1.408 0.166 11.537 kegg_find 1.363 0.057 7.312 kegg_link 1.151 0.078 6.649 translate_ids 1.059 0.040 12.141 uniprot_full_id_mapping_table 0.950 0.047 13.395 kegg_rm_prefix 0.889 0.041 6.015 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.17.4’ ** using staged installation ** 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 [2025-09-02 15:15:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-02 15:15:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-02 15:15:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-02 15:15:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-02 [2025-09-02 15:15:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-02 19:14:48 UTC; unix [2025-09-02 15:15:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-02 15:15:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-02 15:15:02] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-09-02 15:15:03] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; lapack_version=3.12.0] [2025-09-02 15:15:03] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.17.4(2025-09-02); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-02 15:15:03] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-09-02 15:15:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-02 15:15:03] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-02 15:15:03] [TRACE] [OmnipathR] Contains 7 files. [2025-09-02 15:15:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-02 15:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-02 15:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-02 15:15:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-09-02 15:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-02 15:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-02 15:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-02 15:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-02 15:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:03] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-09-02 15:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-02 15:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-02 15:15:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-02 15:15:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-02 [2025-09-02 15:15:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-02 19:14:48 UTC; unix [2025-09-02 15:15:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-02 15:15:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-02 15:15:05] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-09-02 15:15:05] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; lapack_version=3.12.0] [2025-09-02 15:15:05] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.17.4(2025-09-02); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-02 15:15:05] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-09-02 15:15:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-02 15:15:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-02 15:15:05] [TRACE] [OmnipathR] Contains 1 files. [2025-09-02 15:15:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-02 15:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-02 15:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-02 15:15:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-09-02 15:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-02 15:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-02 15:15:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-02 15:15:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-02 15:15:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-02 15:15:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #!/usr/bin/env Rscript > > # > # This file is part of the `OmnipathR` R package > # > # Copyright > # 2018-2024 > # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University > # > # File author(s): Alberto Valdeolivas > # Dénes Türei (turei.denes@gmail.com) > # Attila Gábor > # > # Distributed under the MIT (Expat) License. > # See accompanying file `LICENSE` or find a copy at > # https://directory.fsf.org/wiki/License:Expat > # > # Website: https://r.omnipathdb.org/ > # Git repo: https://github.com/saezlab/OmnipathR > # > > > library(testthat) > library(OmnipathR) [2025-09-03 02:45:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-03 02:45:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:45:25] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:45:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-03 02:45:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-02 [2025-09-03 02:45:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-02 19:14:48 UTC; unix [2025-09-03 02:45:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-03 02:45:25] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-03 02:45:26] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-09-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-09-03 02:45:26] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; lapack_version=3.12.0] [2025-09-03 02:45:26] [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); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 3.17.4(2025-09-02); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); 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 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); 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); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-03 02:45:26] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-09-03 02:45:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-03 02:45:26] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:45:26] [TRACE] [OmnipathR] Contains 22 files. [2025-09-03 02:45:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-03 02:45:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-03 02:45:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:45:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-03 02:45:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-09-03 02:45:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-03 02:45:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:45:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-03 02:45:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:45:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-03 02:45:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:45:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-03 02:45:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-03 02:45:26] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 44.566 2.922 77.713
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.016 | 0.000 | 0.016 | |
all_uniprots | 22.623 | 1.261 | 38.610 | |
ancestors | 0.006 | 0.001 | 0.008 | |
annotated_network | 1.428 | 0.092 | 4.372 | |
annotation_categories | 91.314 | 0.065 | 93.001 | |
annotation_resources | 0.179 | 0.013 | 0.743 | |
annotations | 0.707 | 0.066 | 1.637 | |
biomart_query | 1.168 | 0.085 | 3.878 | |
bioplex1 | 0.008 | 0.000 | 0.009 | |
bioplex2 | 0.007 | 0.000 | 0.008 | |
bioplex3 | 0.007 | 0.000 | 0.008 | |
bioplex_all | 0.005 | 0.002 | 0.008 | |
bioplex_hct116_1 | 0.007 | 0.000 | 0.008 | |
bma_motif_es | 0.804 | 0.057 | 1.605 | |
bma_motif_vs | 0.279 | 0.013 | 0.876 | |
chalmers_gem | 0.009 | 0.000 | 0.009 | |
chalmers_gem_id_mapping_table | 0.006 | 0.002 | 0.008 | |
chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
chalmers_gem_metabolites | 0.008 | 0.000 | 0.008 | |
chalmers_gem_network | 0.007 | 0.000 | 0.007 | |
chalmers_gem_raw | 0.007 | 0.000 | 0.007 | |
chalmers_gem_reactions | 0.006 | 0.001 | 0.007 | |
common_name | 0.160 | 0.001 | 0.161 | |
complex_genes | 0.839 | 0.040 | 2.815 | |
complex_resources | 0.136 | 0.004 | 0.691 | |
complexes | 0.296 | 0.003 | 0.921 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.028 | 0.000 | 0.028 | |
cosmos_pkn | 0.000 | 0.000 | 0.001 | |
curated_ligand_receptor_interactions | 7.058 | 0.577 | 17.233 | |
curated_ligrec_stats | 42.333 | 2.727 | 110.619 | |
database_summary | 1.526 | 0.085 | 3.155 | |
descendants | 0.008 | 0.001 | 0.009 | |
ensembl_dataset | 0.053 | 0.001 | 0.055 | |
ensembl_id_mapping_table | 2.611 | 0.182 | 30.608 | |
ensembl_id_type | 0.001 | 0.000 | 0.002 | |
ensembl_name | 0.297 | 0.005 | 0.302 | |
ensembl_organisms | 0.104 | 0.012 | 0.116 | |
ensembl_organisms_raw | 0.101 | 0.008 | 0.109 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 2.466 | 0.090 | 4.835 | |
enzsub_resources | 0.147 | 0.005 | 0.908 | |
enzyme_substrate | 1.187 | 0.070 | 1.849 | |
evex_download | 0.008 | 0.001 | 0.009 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 12.140 | 1.543 | 16.253 | |
extra_attrs | 7.498 | 1.178 | 8.718 | |
extra_attrs_to_cols | 13.670 | 1.427 | 15.122 | |
filter_by_resource | 7.761 | 0.323 | 10.383 | |
filter_extra_attrs | 22.838 | 4.450 | 28.105 | |
filter_intercell | 6.711 | 0.576 | 11.723 | |
filter_intercell_network | 0.016 | 0.002 | 0.018 | |
find_all_paths | 5.389 | 0.176 | 5.571 | |
from_evidences | 0 | 0 | 0 | |
get_db | 0.001 | 0.000 | 0.001 | |
get_ontology_db | 0.009 | 0.000 | 0.009 | |
giant_component | 16.960 | 0.895 | 24.216 | |
go_annot_download | 16.109 | 1.172 | 21.071 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.009 | 0.000 | 0.009 | |
guide2pharma_download | 0.008 | 0.000 | 0.008 | |
harmonizome_download | 0.008 | 0.001 | 0.008 | |
has_extra_attrs | 12.116 | 1.457 | 17.896 | |
hmdb_id_mapping_table | 0.018 | 0.001 | 0.034 | |
hmdb_id_type | 0.004 | 0.000 | 0.008 | |
hmdb_metabolite_fields | 0.002 | 0.000 | 0.004 | |
hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
hmdb_table | 0.017 | 0.002 | 0.032 | |
homologene_download | 0.014 | 0.002 | 0.017 | |
homologene_raw | 0.101 | 0.005 | 0.168 | |
homologene_uniprot_orthology | 0.014 | 0.003 | 0.017 | |
hpo_download | 5.161 | 0.197 | 8.854 | |
htridb_download | 0.023 | 0.000 | 0.023 | |
id_translation_resources | 0 | 0 | 0 | |
id_types | 0.119 | 0.002 | 0.143 | |
inbiomap_download | 0.001 | 0.000 | 0.000 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 1.907 | 0.059 | 3.523 | |
interaction_graph | 1.016 | 0.015 | 2.119 | |
interaction_resources | 0.216 | 0.004 | 0.751 | |
interaction_types | 0.207 | 0.005 | 0.212 | |
intercell | 2.266 | 0.311 | 3.470 | |
intercell_categories | 1.386 | 0.099 | 1.859 | |
intercell_consensus_filter | 1.702 | 0.160 | 3.340 | |
intercell_generic_categories | 0.087 | 0.001 | 0.087 | |
intercell_network | 0.009 | 0.001 | 0.009 | |
intercell_resources | 0.164 | 0.011 | 0.757 | |
intercell_summary | 0.139 | 0.010 | 0.150 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.068 | 0.004 | 0.071 | |
is_trembl | 0.070 | 0.001 | 0.071 | |
is_uniprot | 0.011 | 0.000 | 0.011 | |
kegg_api_templates | 0.000 | 0.001 | 0.001 | |
kegg_conv | 2.723 | 0.214 | 16.209 | |
kegg_databases | 0.002 | 0.001 | 0.006 | |
kegg_ddi | 1.380 | 0.049 | 3.680 | |
kegg_find | 1.363 | 0.057 | 7.312 | |
kegg_info | 0.021 | 0.001 | 0.026 | |
kegg_link | 1.151 | 0.078 | 6.649 | |
kegg_list | 0.903 | 0.052 | 1.887 | |
kegg_open | 0.013 | 0.003 | 0.015 | |
kegg_operations | 0 | 0 | 0 | |
kegg_organism_codes | 0.018 | 0.015 | 0.033 | |
kegg_organisms | 0.031 | 0.004 | 0.035 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.014 | 0.001 | 0.015 | |
kegg_pathway_list | 0.013 | 0.001 | 0.014 | |
kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
kegg_picture | 1.599 | 0.027 | 5.989 | |
kegg_process | 0.028 | 0.002 | 0.030 | |
kegg_query | 0.011 | 0.001 | 0.012 | |
kegg_request | 0.102 | 0.007 | 0.109 | |
kegg_rm_prefix | 0.889 | 0.041 | 6.015 | |
latin_name | 0.263 | 0.005 | 0.268 | |
load_db | 0.069 | 0.010 | 0.078 | |
metalinksdb_sqlite | 1.408 | 0.166 | 11.537 | |
metalinksdb_table | 0.380 | 0.024 | 0.523 | |
metalinksdb_tables | 0.033 | 0.000 | 0.032 | |
ncbi_taxid | 0.469 | 0.003 | 0.472 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.016 | 0.002 | 0.018 | |
nichenet_gr_network | 0.045 | 0.001 | 0.047 | |
nichenet_gr_network_evex | 0.013 | 0.003 | 0.016 | |
nichenet_gr_network_harmonizome | 0.015 | 0.002 | 0.017 | |
nichenet_gr_network_htridb | 0.013 | 0.002 | 0.015 | |
nichenet_gr_network_omnipath | 27.437 | 1.058 | 49.086 | |
nichenet_gr_network_pathwaycommons | 0.007 | 0.001 | 0.009 | |
nichenet_gr_network_regnetwork | 0.008 | 0.000 | 0.008 | |
nichenet_gr_network_remap | 0.008 | 0.000 | 0.007 | |
nichenet_gr_network_trrust | 0.007 | 0.000 | 0.007 | |
nichenet_ligand_activities | 0 | 0 | 0 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.021 | 0.001 | 0.022 | |
nichenet_lr_network_guide2pharma | 0.008 | 0.000 | 0.008 | |
nichenet_lr_network_omnipath | 0.020 | 0.002 | 0.022 | |
nichenet_lr_network_ramilowski | 0.007 | 0.000 | 0.007 | |
nichenet_main | 0.001 | 0.000 | 0.000 | |
nichenet_networks | 0.033 | 0.003 | 0.036 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.020 | 0.002 | 0.022 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.023 | 0.002 | 0.024 | |
nichenet_signaling_network_cpdb | 0.006 | 0.002 | 0.008 | |
nichenet_signaling_network_evex | 0.007 | 0.001 | 0.008 | |
nichenet_signaling_network_harmonizome | 0.008 | 0.000 | 0.008 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 21.379 | 0.811 | 44.514 | |
nichenet_signaling_network_pathwaycommons | 0.920 | 0.023 | 1.032 | |
nichenet_signaling_network_vinayagam | 0.010 | 0.001 | 0.011 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.216 | 0.016 | 0.313 | |
oma_code | 0.319 | 0.007 | 0.325 | |
oma_organisms | 0.154 | 0.007 | 0.162 | |
oma_pairwise | 0.023 | 0.005 | 0.028 | |
oma_pairwise_genesymbols | 0.017 | 0.002 | 0.019 | |
oma_pairwise_translated | 0.016 | 0.001 | 0.017 | |
omnipath-interactions | 51.686 | 4.294 | 103.435 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.014 | 0.002 | 0.016 | |
omnipath_cache_clean_db | 0.155 | 0.022 | 0.177 | |
omnipath_cache_download_ready | 0.792 | 0.082 | 0.901 | |
omnipath_cache_filter_versions | 0.090 | 0.008 | 0.102 | |
omnipath_cache_get | 0.074 | 0.010 | 0.083 | |
omnipath_cache_key | 0.001 | 0.000 | 0.002 | |
omnipath_cache_latest_or_new | 0.062 | 0.004 | 0.067 | |
omnipath_cache_load | 0.746 | 0.032 | 3.064 | |
omnipath_cache_move_in | 0.136 | 0.007 | 0.147 | |
omnipath_cache_remove | 0.079 | 0.001 | 0.084 | |
omnipath_cache_save | 0.165 | 0.019 | 0.322 | |
omnipath_cache_search | 0.001 | 0.000 | 0.000 | |
omnipath_cache_set_ext | 0.066 | 0.007 | 0.077 | |
omnipath_cache_update_status | 0.151 | 0.004 | 0.155 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_config_path | 0.000 | 0.000 | 0.001 | |
omnipath_for_cosmos | 11.151 | 0.422 | 43.201 | |
omnipath_load_config | 0 | 0 | 0 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.003 | 0.000 | 0.003 | |
omnipath_msg | 0.011 | 0.001 | 0.023 | |
omnipath_query | 6.444 | 0.204 | 8.269 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.043 | 0.000 | 0.044 | |
omnipath_set_console_loglevel | 0.006 | 0.000 | 0.006 | |
omnipath_set_logfile_loglevel | 0.004 | 0.001 | 0.006 | |
omnipath_set_loglevel | 0.003 | 0.000 | 0.003 | |
omnipath_show_db | 0.098 | 0.009 | 0.108 | |
omnipath_unlock_cache_db | 0 | 0 | 0 | |
only_from | 0 | 0 | 0 | |
ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
ontology_ensure_name | 0.001 | 0.000 | 0.000 | |
ontology_name_id | 0.000 | 0.001 | 0.002 | |
organism_for | 0.291 | 0.004 | 0.295 | |
pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
pivot_annotations | 12.893 | 0.983 | 23.238 | |
preppi_download | 0.001 | 0.000 | 0.001 | |
preppi_filter | 0.002 | 0.000 | 0.001 | |
print_bma_motif_es | 1.058 | 0.161 | 2.374 | |
print_bma_motif_vs | 0.335 | 0.008 | 0.971 | |
print_interactions | 7.417 | 0.386 | 12.503 | |
print_path_es | 1.456 | 0.100 | 3.055 | |
print_path_vs | 4.258 | 0.246 | 8.423 | |
pubmed_open | 5.117 | 0.155 | 5.266 | |
query_info | 1.491 | 0.023 | 2.267 | |
ramilowski_download | 0.001 | 0.000 | 0.002 | |
ramp_id_mapping_table | 0.001 | 0.000 | 0.002 | |
ramp_id_type | 0.007 | 0.000 | 0.007 | |
ramp_sqlite | 0.000 | 0.001 | 0.002 | |
ramp_table | 0.001 | 0.000 | 0.005 | |
ramp_tables | 0.000 | 0.001 | 0.001 | |
regnetwork_directions | 0.002 | 0.000 | 0.006 | |
regnetwork_download | 0.001 | 0.000 | 0.005 | |
relations_list_to_table | 0.218 | 0.010 | 0.310 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.142 | 0.007 | 0.186 | |
remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
remap_filtered | 0 | 0 | 0 | |
remap_tf_target_download | 0 | 0 | 0 | |
resource_info | 0.992 | 0.031 | 1.253 | |
resources | 0.122 | 0.005 | 0.742 | |
resources_colname | 1.579 | 0.069 | 4.614 | |
resources_in | 6.860 | 0.371 | 9.312 | |
show_network | 0 | 0 | 0 | |
signed_ptms | 7.214 | 0.248 | 8.937 | |
simplify_intercell_network | 0.001 | 0.001 | 0.002 | |
static_table | 5.690 | 0.414 | 11.555 | |
static_tables | 0.099 | 0.015 | 0.124 | |
stitch_actions | 0.001 | 0.000 | 0.001 | |
stitch_links | 0.001 | 0.000 | 0.000 | |
stitch_network | 0.001 | 0.000 | 0.000 | |
stitch_remove_prefixes | 0.006 | 0.001 | 0.006 | |
swap_relations | 0.075 | 0.003 | 0.111 | |
swissprots_only | 0.129 | 0.004 | 0.133 | |
tfcensus_download | 0.527 | 0.043 | 0.776 | |
translate_ids | 1.059 | 0.040 | 12.141 | |
translate_ids_multi | 8.231 | 0.310 | 41.994 | |
trembls_only | 0.129 | 0.001 | 0.130 | |
trrust_download | 0.000 | 0.000 | 0.001 | |
uniprot_full_id_mapping_table | 0.950 | 0.047 | 13.395 | |
uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
uniprot_id_mapping_table | 0.000 | 0.001 | 0.001 | |
uniprot_id_type | 0.003 | 0.000 | 0.002 | |
uniprot_idmapping_id_types | 0.487 | 0.016 | 1.052 | |
uniprot_organisms | 17.621 | 1.117 | 21.451 | |
unique_intercell_network | 0.000 | 0.001 | 0.001 | |
unnest_evidences | 0 | 0 | 0 | |
uploadlists_id_type | 0.001 | 0.000 | 0.002 | |
vinayagam_download | 0 | 0 | 0 | |
walk_ontology_tree | 0.001 | 0.000 | 0.002 | |
with_extra_attrs | 11.707 | 1.301 | 15.487 | |
with_references | 0.905 | 0.078 | 2.514 | |
zenodo_download | 0.000 | 0.001 | 0.001 | |