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This page was generated on 2025-09-03 12:04 -0400 (Wed, 03 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4616
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1476/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.4  (landing page)
Denes Turei
Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: a7f3b9d
git_last_commit_date: 2025-07-16 10:03:35 -0400 (Wed, 16 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for OmnipathR on nebbiolo2

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> #!/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 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0160.0000.016
all_uniprots22.623 1.26138.610
ancestors0.0060.0010.008
annotated_network1.4280.0924.372
annotation_categories91.314 0.06593.001
annotation_resources0.1790.0130.743
annotations0.7070.0661.637
biomart_query1.1680.0853.878
bioplex10.0080.0000.009
bioplex20.0070.0000.008
bioplex30.0070.0000.008
bioplex_all0.0050.0020.008
bioplex_hct116_10.0070.0000.008
bma_motif_es0.8040.0571.605
bma_motif_vs0.2790.0130.876
chalmers_gem0.0090.0000.009
chalmers_gem_id_mapping_table0.0060.0020.008
chalmers_gem_id_type0.0020.0000.002
chalmers_gem_metabolites0.0080.0000.008
chalmers_gem_network0.0070.0000.007
chalmers_gem_raw0.0070.0000.007
chalmers_gem_reactions0.0060.0010.007
common_name0.1600.0010.161
complex_genes0.8390.0402.815
complex_resources0.1360.0040.691
complexes0.2960.0030.921
consensuspathdb_download000
consensuspathdb_raw_table0.0280.0000.028
cosmos_pkn0.0000.0000.001
curated_ligand_receptor_interactions 7.058 0.57717.233
curated_ligrec_stats 42.333 2.727110.619
database_summary1.5260.0853.155
descendants0.0080.0010.009
ensembl_dataset0.0530.0010.055
ensembl_id_mapping_table 2.611 0.18230.608
ensembl_id_type0.0010.0000.002
ensembl_name0.2970.0050.302
ensembl_organisms0.1040.0120.116
ensembl_organisms_raw0.1010.0080.109
ensembl_orthology000
enzsub_graph2.4660.0904.835
enzsub_resources0.1470.0050.908
enzyme_substrate1.1870.0701.849
evex_download0.0080.0010.009
evidences000
extra_attr_values12.140 1.54316.253
extra_attrs7.4981.1788.718
extra_attrs_to_cols13.670 1.42715.122
filter_by_resource 7.761 0.32310.383
filter_extra_attrs22.838 4.45028.105
filter_intercell 6.711 0.57611.723
filter_intercell_network0.0160.0020.018
find_all_paths5.3890.1765.571
from_evidences000
get_db0.0010.0000.001
get_ontology_db0.0090.0000.009
giant_component16.960 0.89524.216
go_annot_download16.109 1.17221.071
go_annot_slim000
go_ontology_download0.0090.0000.009
guide2pharma_download0.0080.0000.008
harmonizome_download0.0080.0010.008
has_extra_attrs12.116 1.45717.896
hmdb_id_mapping_table0.0180.0010.034
hmdb_id_type0.0040.0000.008
hmdb_metabolite_fields0.0020.0000.004
hmdb_protein_fields0.0000.0000.001
hmdb_table0.0170.0020.032
homologene_download0.0140.0020.017
homologene_raw0.1010.0050.168
homologene_uniprot_orthology0.0140.0030.017
hpo_download5.1610.1978.854
htridb_download0.0230.0000.023
id_translation_resources000
id_types0.1190.0020.143
inbiomap_download0.0010.0000.000
inbiomap_raw000
interaction_datasets1.9070.0593.523
interaction_graph1.0160.0152.119
interaction_resources0.2160.0040.751
interaction_types0.2070.0050.212
intercell2.2660.3113.470
intercell_categories1.3860.0991.859
intercell_consensus_filter1.7020.1603.340
intercell_generic_categories0.0870.0010.087
intercell_network0.0090.0010.009
intercell_resources0.1640.0110.757
intercell_summary0.1390.0100.150
is_ontology_id000
is_swissprot0.0680.0040.071
is_trembl0.0700.0010.071
is_uniprot0.0110.0000.011
kegg_api_templates0.0000.0010.001
kegg_conv 2.723 0.21416.209
kegg_databases0.0020.0010.006
kegg_ddi1.3800.0493.680
kegg_find1.3630.0577.312
kegg_info0.0210.0010.026
kegg_link1.1510.0786.649
kegg_list0.9030.0521.887
kegg_open0.0130.0030.015
kegg_operations000
kegg_organism_codes0.0180.0150.033
kegg_organisms0.0310.0040.035
kegg_pathway_annotations000
kegg_pathway_download0.0140.0010.015
kegg_pathway_list0.0130.0010.014
kegg_pathways_download0.0000.0000.001
kegg_picture1.5990.0275.989
kegg_process0.0280.0020.030
kegg_query0.0110.0010.012
kegg_request0.1020.0070.109
kegg_rm_prefix0.8890.0416.015
latin_name0.2630.0050.268
load_db0.0690.0100.078
metalinksdb_sqlite 1.408 0.16611.537
metalinksdb_table0.3800.0240.523
metalinksdb_tables0.0330.0000.032
ncbi_taxid0.4690.0030.472
nichenet_build_model000
nichenet_expression_data0.0160.0020.018
nichenet_gr_network0.0450.0010.047
nichenet_gr_network_evex0.0130.0030.016
nichenet_gr_network_harmonizome0.0150.0020.017
nichenet_gr_network_htridb0.0130.0020.015
nichenet_gr_network_omnipath27.437 1.05849.086
nichenet_gr_network_pathwaycommons0.0070.0010.009
nichenet_gr_network_regnetwork0.0080.0000.008
nichenet_gr_network_remap0.0080.0000.007
nichenet_gr_network_trrust0.0070.0000.007
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0210.0010.022
nichenet_lr_network_guide2pharma0.0080.0000.008
nichenet_lr_network_omnipath0.0200.0020.022
nichenet_lr_network_ramilowski0.0070.0000.007
nichenet_main0.0010.0000.000
nichenet_networks0.0330.0030.036
nichenet_optimization000
nichenet_remove_orphan_ligands0.0200.0020.022
nichenet_results_dir000
nichenet_signaling_network0.0230.0020.024
nichenet_signaling_network_cpdb0.0060.0020.008
nichenet_signaling_network_evex0.0070.0010.008
nichenet_signaling_network_harmonizome0.0080.0000.008
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath21.379 0.81144.514
nichenet_signaling_network_pathwaycommons0.9200.0231.032
nichenet_signaling_network_vinayagam0.0100.0010.011
nichenet_test000
nichenet_workarounds000
obo_parser0.2160.0160.313
oma_code0.3190.0070.325
oma_organisms0.1540.0070.162
oma_pairwise0.0230.0050.028
oma_pairwise_genesymbols0.0170.0020.019
oma_pairwise_translated0.0160.0010.017
omnipath-interactions 51.686 4.294103.435
omnipath_cache_autoclean000
omnipath_cache_clean0.0140.0020.016
omnipath_cache_clean_db0.1550.0220.177
omnipath_cache_download_ready0.7920.0820.901
omnipath_cache_filter_versions0.0900.0080.102
omnipath_cache_get0.0740.0100.083
omnipath_cache_key0.0010.0000.002
omnipath_cache_latest_or_new0.0620.0040.067
omnipath_cache_load0.7460.0323.064
omnipath_cache_move_in0.1360.0070.147
omnipath_cache_remove0.0790.0010.084
omnipath_cache_save0.1650.0190.322
omnipath_cache_search0.0010.0000.000
omnipath_cache_set_ext0.0660.0070.077
omnipath_cache_update_status0.1510.0040.155
omnipath_cache_wipe000
omnipath_config_path0.0000.0000.001
omnipath_for_cosmos11.151 0.42243.201
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0030.0000.003
omnipath_msg0.0110.0010.023
omnipath_query6.4440.2048.269
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0430.0000.044
omnipath_set_console_loglevel0.0060.0000.006
omnipath_set_logfile_loglevel0.0040.0010.006
omnipath_set_loglevel0.0030.0000.003
omnipath_show_db0.0980.0090.108
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.000
ontology_name_id0.0000.0010.002
organism_for0.2910.0040.295
pathwaycommons_download0.0010.0000.001
pivot_annotations12.893 0.98323.238
preppi_download0.0010.0000.001
preppi_filter0.0020.0000.001
print_bma_motif_es1.0580.1612.374
print_bma_motif_vs0.3350.0080.971
print_interactions 7.417 0.38612.503
print_path_es1.4560.1003.055
print_path_vs4.2580.2468.423
pubmed_open5.1170.1555.266
query_info1.4910.0232.267
ramilowski_download0.0010.0000.002
ramp_id_mapping_table0.0010.0000.002
ramp_id_type0.0070.0000.007
ramp_sqlite0.0000.0010.002
ramp_table0.0010.0000.005
ramp_tables0.0000.0010.001
regnetwork_directions0.0020.0000.006
regnetwork_download0.0010.0000.005
relations_list_to_table0.2180.0100.310
relations_table_to_graph000
relations_table_to_list0.1420.0070.186
remap_dorothea_download0.0010.0000.001
remap_filtered000
remap_tf_target_download000
resource_info0.9920.0311.253
resources0.1220.0050.742
resources_colname1.5790.0694.614
resources_in6.8600.3719.312
show_network000
signed_ptms7.2140.2488.937
simplify_intercell_network0.0010.0010.002
static_table 5.690 0.41411.555
static_tables0.0990.0150.124
stitch_actions0.0010.0000.001
stitch_links0.0010.0000.000
stitch_network0.0010.0000.000
stitch_remove_prefixes0.0060.0010.006
swap_relations0.0750.0030.111
swissprots_only0.1290.0040.133
tfcensus_download0.5270.0430.776
translate_ids 1.059 0.04012.141
translate_ids_multi 8.231 0.31041.994
trembls_only0.1290.0010.130
trrust_download0.0000.0000.001
uniprot_full_id_mapping_table 0.950 0.04713.395
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0000.0010.001
uniprot_id_type0.0030.0000.002
uniprot_idmapping_id_types0.4870.0161.052
uniprot_organisms17.621 1.11721.451
unique_intercell_network0.0000.0010.001
unnest_evidences000
uploadlists_id_type0.0010.0000.002
vinayagam_download000
walk_ontology_tree0.0010.0000.002
with_extra_attrs11.707 1.30115.487
with_references0.9050.0782.514
zenodo_download0.0000.0010.001