| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:03 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.7 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 3.17.7 |
| 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_3.17.7.tar.gz |
| StartedAt: 2025-10-25 02:21:29 -0400 (Sat, 25 Oct 2025) |
| EndedAt: 2025-10-25 02:56:14 -0400 (Sat, 25 Oct 2025) |
| EllapsedTime: 2084.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### 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_3.17.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘3.17.7’
* 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
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-25 02:21:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:21:59] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:21:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-25 02:21:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-25 02:21:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:19:25 UTC; unix
[2025-10-25 02:21:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-25 02:21:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-25 02:21:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-10-25; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-25 02:21:59] [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/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-25 02:21:59] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.7(2025-10-24); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 2.30(2025-09-28); 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 1.5.2(2025-09-08); 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)
[2025-10-25 02:21:59] [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
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-25 02:21:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:21:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-25 02:21:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-25 02:21:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-25 02:21:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:21:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-25 02:21:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:00] [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
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-25 02:22:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:16] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:22:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-25 02:22:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-25 02:22:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:19:25 UTC; unix
[2025-10-25 02:22:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-25 02:22:16] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-25 02:22:16] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-10-25; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-25 02:22:16] [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/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-25 02:22:16] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.7(2025-10-24); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 2.30(2025-09-28); 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 1.5.2(2025-09-08); 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)
[2025-10-25 02:22:16] [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
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-25 02:22:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-25 02:22:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-25 02:22:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-25 02:22:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-25 02:22:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-25 02:22:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:22:17] [TRACE] [OmnipathR] Cache locked: FALSE
.cosmos_pkn: no visible global function definition for
‘metabolite_idsc’
cosmos_ksn: no visible binding for global variable
‘substrate_genesymbol’
cosmos_ksn: no visible binding for global variable ‘residue_type’
cosmos_ksn: no visible binding for global variable ‘residue_offset’
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
cosmos_ksn: no visible binding for global variable ‘mor’
recon3d_genes: no visible binding for global variable ‘notes’
recon3d_genes: no visible binding for global variable ‘annotation’
recon3d_genes: no visible binding for global variable
‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable ‘notes’
recon3d_metabolites: no visible binding for global variable
‘original_bigg_ids’
recon3d_metabolites: no visible binding for global variable
‘annotation’
recon3d_metabolites: no visible global function definition for
‘chalmers_gem_matlab_tibble’
recon3d_metabolites: no visible binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_reactions: no visible binding for global variable ‘notes’
recon3d_reactions: no visible binding for global variable ‘metabolites’
recon3d_reactions: no visible binding for global variable
‘original_bigg_ids’
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:
annotation chalmers_gem_matlab_tibble common_name_ensembl
common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl
latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc
metabolites mor notes original_bigg_ids residue_offset residue_type
substrate_genesymbol
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘recon3d_raw’ ‘recon3d_raw_vmh’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'recon3d.Rd'
‘extra_hmdb’
Undocumented arguments in Rd file 'translate_ids_multi.Rd'
‘ramp’ ‘expand’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: recon3d_metabolites
> ### Title: Metabolites from Recon-3D
> ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes
> ### recon3d_compartments
>
> ### ** Examples
>
> recon3d_metabolites()
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on '/home/biocbuild/.cache/OmnipathR/be81cd1c9a119b749e4206f26272806591e8fb4c-1.gz'
Error in chalmers_gem_matlab_tibble(., "mets", "metHMDBID") :
could not find function "chalmers_gem_matlab_tibble"
Calls: recon3d_metabolites ... same_src.data.frame -> is.data.frame -> %>% -> unnest -> unnest
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 79.847 0.071 81.404
omnipath-interactions 46.618 4.580 88.114
curated_ligrec_stats 43.364 3.147 121.017
filter_extra_attrs 39.212 5.902 51.181
nichenet_gr_network_omnipath 25.705 1.047 33.923
giant_component 23.315 0.843 33.929
all_uniprots 22.232 1.252 38.251
nichenet_signaling_network_omnipath 15.620 0.540 21.636
extra_attrs_to_cols 13.857 1.303 15.172
go_annot_download 14.100 0.830 15.429
extra_attr_values 12.827 1.253 16.498
filter_by_resource 12.205 0.338 14.792
filter_intercell 10.835 0.414 17.230
omnipath_for_cosmos 10.327 0.526 32.160
print_interactions 10.083 0.492 15.381
pivot_annotations 9.852 0.629 18.854
extra_attrs 7.977 1.204 9.206
has_extra_attrs 7.846 1.052 9.897
curated_ligand_receptor_interactions 6.918 0.679 17.532
find_all_paths 6.416 0.122 6.872
hpo_download 4.521 0.250 7.008
print_path_vs 2.706 0.409 5.864
ensembl_id_mapping_table 2.537 0.181 26.639
kegg_conv 2.162 0.116 15.948
metalinksdb_sqlite 1.972 0.207 11.537
kegg_picture 2.110 0.039 7.707
kinasephos 1.874 0.098 20.279
kegg_link 1.630 0.067 7.437
kegg_rm_prefix 1.038 0.067 6.187
* 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: 1 ERROR, 2 WARNINGs, 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 ‘3.17.7’ ** 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 [2025-10-24 15:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:38] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-24 15:19:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-24 15:19:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24 [2025-10-24 15:19:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:19:25 UTC; unix [2025-10-24 15:19:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7 [2025-10-24 15:19:38] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-24 15:19:39] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-10-24; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-10-24 15:19:39] [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/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-10-24 15:19:39] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.7(2025-10-24); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 2.30(2025-09-28); 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 1.5.2(2025-09-08); 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) [2025-10-24 15:19:39] [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 [2025-10-24 15:19:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-24 15:19:39] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-24 15:19:39] [TRACE] [OmnipathR] Contains 9 files. [2025-10-24 15:19:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-24 15:19:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-24 15:19:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-24 15:19:39] [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). [2025-10-24 15:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:39] [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). [2025-10-24 15:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-24 15:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:39] [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). [2025-10-24 15:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:39] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-24 15:19:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:41] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-24 15:19:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-24 15:19:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24 [2025-10-24 15:19:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:19:25 UTC; unix [2025-10-24 15:19:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7 [2025-10-24 15:19:41] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-24 15:19:41] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-10-24; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-10-24 15:19:41] [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/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-10-24 15:19:42] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.7(2025-10-24); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 2.30(2025-09-28); 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 1.5.2(2025-09-08); 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) [2025-10-24 15:19:42] [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 [2025-10-24 15:19:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-24 15:19:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-24 15:19:42] [TRACE] [OmnipathR] Contains 1 files. [2025-10-24 15:19:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-24 15:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-24 15:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-24 15:19:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-24 15:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-24 15:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-24 15:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-24 15:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-24 15:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-24 15:19:42] [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 Patched (2025-08-23 r88802) -- "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)
[2025-10-25 02:37:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-25 02:37:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:37:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:37:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-25 02:37:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-25 02:37:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:19:25 UTC; unix
[2025-10-25 02:37:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-25 02:37:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-25 02:37:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-10-25; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-25 02:37:53] [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/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-25 02:37:53] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); 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 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.7(2025-10-24); 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 1.1.0(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 2.30(2025-09-28); 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 1.5.2(2025-09-08); 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)
[2025-10-25 02:37:53] [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
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Contains 12 files.
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-25 02:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:37:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-25 02:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-25 02:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-25 02:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:37:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-25 02:37:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-25 02:37:53] [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
50.292 3.413 89.381
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.000 | 0.000 | |
| all_uniprot_acs | 0.011 | 0.007 | 0.018 | |
| all_uniprots | 22.232 | 1.252 | 38.251 | |
| ancestors | 0.007 | 0.002 | 0.009 | |
| annotated_network | 1.422 | 0.084 | 4.502 | |
| annotation_categories | 79.847 | 0.071 | 81.404 | |
| annotation_resources | 0.157 | 0.015 | 0.883 | |
| annotations | 0.753 | 0.060 | 1.718 | |
| biomart_query | 1.172 | 0.056 | 4.085 | |
| bioplex1 | 0.007 | 0.001 | 0.008 | |
| bioplex2 | 0.007 | 0.001 | 0.008 | |
| bioplex3 | 0.007 | 0.001 | 0.008 | |
| bioplex_all | 0.007 | 0.001 | 0.008 | |
| bioplex_hct116_1 | 0.008 | 0.000 | 0.008 | |
| bma_motif_es | 0.765 | 0.062 | 1.722 | |
| bma_motif_vs | 0.333 | 0.013 | 1.006 | |
| chalmers_gem | 0.009 | 0.001 | 0.010 | |
| chalmers_gem_id_mapping_table | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_network | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_raw | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_reactions | 0.027 | 0.000 | 0.028 | |
| common_name | 0.126 | 0.000 | 0.126 | |
| complex_genes | 0.809 | 0.044 | 2.692 | |
| complex_resources | 0.174 | 0.013 | 0.927 | |
| complexes | 0.206 | 0.014 | 0.894 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.027 | 0.000 | 0.027 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.918 | 0.679 | 17.532 | |
| curated_ligrec_stats | 43.364 | 3.147 | 121.017 | |
| database_summary | 1.675 | 0.079 | 3.218 | |
| descendants | 0.009 | 0.000 | 0.009 | |
| ensembl_dataset | 0.049 | 0.000 | 0.048 | |
| ensembl_id_mapping_table | 2.537 | 0.181 | 26.639 | |
| ensembl_id_type | 0.001 | 0.001 | 0.002 | |
| ensembl_name | 0.319 | 0.003 | 0.322 | |
| ensembl_organisms | 0.109 | 0.003 | 0.112 | |
| ensembl_organisms_raw | 0.100 | 0.007 | 0.107 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.380 | 0.097 | 4.520 | |
| enzsub_resources | 0.144 | 0.009 | 0.894 | |
| enzyme_substrate | 1.075 | 0.033 | 1.826 | |
| evex_download | 0.009 | 0.000 | 0.008 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 12.827 | 1.253 | 16.498 | |
| extra_attrs | 7.977 | 1.204 | 9.206 | |
| extra_attrs_to_cols | 13.857 | 1.303 | 15.172 | |
| filter_by_resource | 12.205 | 0.338 | 14.792 | |
| filter_extra_attrs | 39.212 | 5.902 | 51.181 | |
| filter_intercell | 10.835 | 0.414 | 17.230 | |
| filter_intercell_network | 0.016 | 0.002 | 0.019 | |
| find_all_paths | 6.416 | 0.122 | 6.872 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.019 | 0.000 | 0.026 | |
| giant_component | 23.315 | 0.843 | 33.929 | |
| go_annot_download | 14.100 | 0.830 | 15.429 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.008 | 0.000 | 0.008 | |
| guide2pharma_download | 0.007 | 0.001 | 0.008 | |
| harmonizome_download | 0.006 | 0.001 | 0.008 | |
| has_extra_attrs | 7.846 | 1.052 | 9.897 | |
| hmdb_id_mapping_table | 0.016 | 0.001 | 0.029 | |
| hmdb_id_type | 0.004 | 0.000 | 0.008 | |
| hmdb_metabolite_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.020 | 0.001 | 0.040 | |
| homologene_download | 0.017 | 0.001 | 0.038 | |
| homologene_raw | 0.105 | 0.004 | 0.215 | |
| homologene_uniprot_orthology | 0.168 | 0.001 | 0.309 | |
| hpo_download | 4.521 | 0.250 | 7.008 | |
| htridb_download | 0.017 | 0.002 | 0.019 | |
| id_translation_resources | 0.001 | 0.000 | 0.000 | |
| id_types | 0.082 | 0.013 | 0.095 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 1.721 | 0.108 | 2.989 | |
| interaction_graph | 0.949 | 0.043 | 1.948 | |
| interaction_resources | 0.222 | 0.039 | 1.153 | |
| interaction_types | 0.176 | 0.022 | 0.264 | |
| intercell | 2.141 | 0.182 | 4.811 | |
| intercell_categories | 1.677 | 0.064 | 3.326 | |
| intercell_consensus_filter | 2.524 | 0.296 | 4.957 | |
| intercell_generic_categories | 0.127 | 0.012 | 0.139 | |
| intercell_network | 0.012 | 0.004 | 0.017 | |
| intercell_resources | 0.151 | 0.022 | 0.909 | |
| intercell_summary | 0.112 | 0.009 | 0.120 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.091 | 0.002 | 0.093 | |
| is_trembl | 0.083 | 0.008 | 0.091 | |
| is_uniprot | 0.013 | 0.001 | 0.015 | |
| kegg_api_templates | 0.001 | 0.000 | 0.002 | |
| kegg_conv | 2.162 | 0.116 | 15.948 | |
| kegg_databases | 0.001 | 0.000 | 0.001 | |
| kegg_ddi | 1.094 | 0.048 | 3.273 | |
| kegg_find | 1.241 | 0.052 | 4.691 | |
| kegg_info | 0.025 | 0.000 | 0.052 | |
| kegg_link | 1.630 | 0.067 | 7.437 | |
| kegg_list | 1.442 | 0.067 | 3.277 | |
| kegg_open | 0.017 | 0.003 | 0.020 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.021 | 0.012 | 0.032 | |
| kegg_organisms | 0.051 | 0.004 | 0.080 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.024 | 0.001 | 0.049 | |
| kegg_pathway_list | 0.022 | 0.000 | 0.043 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 2.110 | 0.039 | 7.707 | |
| kegg_process | 0.029 | 0.001 | 0.030 | |
| kegg_query | 0.013 | 0.000 | 0.013 | |
| kegg_request | 0.101 | 0.004 | 0.105 | |
| kegg_rm_prefix | 1.038 | 0.067 | 6.187 | |
| kinasephos | 1.874 | 0.098 | 20.279 | |
| latin_name | 0.474 | 0.009 | 0.502 | |
| load_db | 0.141 | 0.007 | 0.147 | |
| metalinksdb_sqlite | 1.972 | 0.207 | 11.537 | |
| metalinksdb_table | 0.473 | 0.028 | 0.685 | |
| metalinksdb_tables | 0.047 | 0.000 | 0.047 | |
| ncbi_taxid | 0.535 | 0.009 | 0.548 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.021 | 0.001 | 0.022 | |
| nichenet_gr_network | 0.048 | 0.005 | 0.052 | |
| nichenet_gr_network_evex | 0.017 | 0.000 | 0.017 | |
| nichenet_gr_network_harmonizome | 0.016 | 0.002 | 0.018 | |
| nichenet_gr_network_htridb | 0.017 | 0.001 | 0.018 | |
| nichenet_gr_network_omnipath | 25.705 | 1.047 | 33.923 | |
| nichenet_gr_network_pathwaycommons | 0.023 | 0.000 | 0.048 | |
| nichenet_gr_network_regnetwork | 0.021 | 0.002 | 0.043 | |
| nichenet_gr_network_remap | 0.019 | 0.004 | 0.033 | |
| nichenet_gr_network_trrust | 0.019 | 0.001 | 0.020 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.059 | 0.006 | 0.130 | |
| nichenet_lr_network_guide2pharma | 0.017 | 0.003 | 0.041 | |
| nichenet_lr_network_omnipath | 0.060 | 0.006 | 0.104 | |
| nichenet_lr_network_ramilowski | 0.014 | 0.003 | 0.017 | |
| nichenet_main | 0.001 | 0.000 | 0.000 | |
| nichenet_networks | 0.085 | 0.011 | 0.145 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.066 | 0.003 | 0.139 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.065 | 0.010 | 0.135 | |
| nichenet_signaling_network_cpdb | 0.015 | 0.004 | 0.019 | |
| nichenet_signaling_network_evex | 0.019 | 0.002 | 0.042 | |
| nichenet_signaling_network_harmonizome | 0.022 | 0.003 | 0.050 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 15.620 | 0.540 | 21.636 | |
| nichenet_signaling_network_pathwaycommons | 0.010 | 0.002 | 0.011 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.002 | 0.009 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.152 | 0.027 | 0.238 | |
| oma_code | 0.144 | 0.006 | 0.150 | |
| oma_organisms | 0.068 | 0.007 | 0.075 | |
| oma_pairwise | 0.007 | 0.003 | 0.010 | |
| oma_pairwise_genesymbols | 0.009 | 0.001 | 0.009 | |
| oma_pairwise_translated | 0.009 | 0.000 | 0.009 | |
| omnipath-interactions | 46.618 | 4.580 | 88.114 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.007 | 0.001 | 0.009 | |
| omnipath_cache_clean_db | 0.081 | 0.016 | 0.097 | |
| omnipath_cache_download_ready | 0.489 | 0.073 | 0.624 | |
| omnipath_cache_filter_versions | 0.077 | 0.005 | 0.086 | |
| omnipath_cache_get | 0.063 | 0.008 | 0.070 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.050 | 0.001 | 0.052 | |
| omnipath_cache_load | 0.851 | 0.075 | 3.212 | |
| omnipath_cache_move_in | 0.148 | 0.018 | 0.170 | |
| omnipath_cache_remove | 0.082 | 0.014 | 0.101 | |
| omnipath_cache_save | 0.159 | 0.018 | 0.305 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.065 | 0.008 | 0.078 | |
| omnipath_cache_update_status | 0.102 | 0.007 | 0.109 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 10.327 | 0.526 | 32.160 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.000 | 0.002 | |
| omnipath_msg | 0.005 | 0.000 | 0.005 | |
| omnipath_query | 3.490 | 0.093 | 3.599 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.022 | 0.003 | 0.025 | |
| omnipath_set_console_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_show_db | 0.061 | 0.004 | 0.065 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.000 | 0.000 | |
| organism_for | 0.188 | 0.004 | 0.191 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 9.852 | 0.629 | 18.854 | |
| preppi_download | 0.000 | 0.000 | 0.001 | |
| preppi_filter | 0.000 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.637 | 0.047 | 1.839 | |
| print_bma_motif_vs | 0.301 | 0.015 | 1.030 | |
| print_interactions | 10.083 | 0.492 | 15.381 | |
| print_path_es | 2.618 | 0.325 | 4.546 | |
| print_path_vs | 2.706 | 0.409 | 5.864 | |
| pubmed_open | 4.308 | 0.276 | 4.603 | |
| query_info | 0.744 | 0.016 | 0.973 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0.002 | 0.001 | 0.002 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.000 | 0.001 | 0.000 | |
| ramp_tables | 0 | 0 | 0 | |