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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 1484/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.16.2  (landing page)
Denes Turei
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_21
git_last_commit: e923fc4
git_last_commit_date: 2025-08-30 05:55:56 -0400 (Sat, 30 Aug 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for OmnipathR on nebbiolo1

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: 3.16.2
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.16.2.tar.gz
StartedAt: 2025-10-16 01:49:26 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 02:19:52 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 1826.2 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.16.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘3.16.2’
* 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
[2025-10-16 01:49:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-16 01:49:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:49:55] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 01:49:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-16 01:49:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-15
[2025-10-16 01:49:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-15 19:08:19 UTC; unix
[2025-10-16 01:49:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-16 01:49:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-16 01:49:56] [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=2025-10-16; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-16 01:49:56] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-16 01:49:56] [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 2.2.0(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 3.16.2(2025-10-15); 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 1.3.3(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 2.30(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)
[2025-10-16 01:49:56] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:49:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-16 01:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:49:56] [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
[2025-10-16 01:50:13] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-16 01:50:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:50:13] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 01:50:13] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-16 01:50:13] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-15
[2025-10-16 01:50:13] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-15 19:08:19 UTC; unix
[2025-10-16 01:50:13] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-16 01:50:13] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-16 01:50:13] [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=2025-10-16; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-16 01:50:13] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-16 01:50:14] [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 2.2.0(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 3.16.2(2025-10-15); 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 1.3.3(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 2.30(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)
[2025-10-16 01:50:14] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:50:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 01:50:14] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                89.692  0.070  91.134
omnipath-interactions                54.589  4.431 112.887
curated_ligrec_stats                 38.454  2.664 105.156
filter_extra_attrs                   24.446  4.730  29.906
nichenet_gr_network_omnipath         25.814  1.528  34.326
giant_component                      23.771  1.340  36.551
go_annot_download                    19.992  1.225  25.075
nichenet_signaling_network_omnipath  16.108  1.103  22.189
with_extra_attrs                     15.217  1.925  21.792
has_extra_attrs                      14.627  1.721  17.404
translate_ids_multi                  14.066  0.844  33.987
extra_attrs_to_cols                  12.859  1.274  14.154
omnipath_for_cosmos                  12.133  0.929  34.340
extra_attr_values                    11.178  1.369  14.824
pivot_annotations                     9.245  0.601  18.429
filter_by_resource                    7.578  0.262  10.206
extra_attrs                           6.584  1.107   7.721
curated_ligand_receptor_interactions  6.456  0.760  16.070
static_table                          6.726  0.349   7.923
filter_intercell                      5.887  0.417  10.254
print_interactions                    5.908  0.256  10.211
find_all_paths                        5.148  0.094   5.240
signed_ptms                           4.508  0.237   5.328
kegg_conv                             2.718  0.307  14.836
ensembl_id_mapping_table              2.279  0.161  19.296
uniprot_full_id_mapping_table         2.289  0.144  14.509
kegg_picture                          1.846  0.070   6.842
all_uniprots                          1.437  0.143  13.320
metalinksdb_sqlite                    1.246  0.277  11.515
kegg_link                             1.226  0.128   7.372
translate_ids                         1.074  0.051  11.193
kegg_rm_prefix                        0.680  0.052   5.186
* 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-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.


Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.16.2’
** 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
[2025-10-15 15:08:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 15:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-15 15:08:33] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-15 15:08:33] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-15
[2025-10-15 15:08:33] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-15 19:08:19 UTC; unix
[2025-10-15 15:08:33] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-15 15:08:33] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-15 15:08:33] [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=2025-10-15; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-15 15:08:33] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-15 15:08:34] [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 2.2.0(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 3.16.2(2025-10-15); 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 1.3.3(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 2.30(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)
[2025-10-15 15:08:34] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Contains 8 files.
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:34] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-15 15:08:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-15 15:08:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-15
[2025-10-15 15:08:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-15 19:08:19 UTC; unix
[2025-10-15 15:08:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-15 15:08:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-15 15:08:36] [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=2025-10-15; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-15 15:08:36] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-15 15:08:36] [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 2.2.0(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 3.16.2(2025-10-15); 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 1.3.3(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 2.30(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)
[2025-10-15 15:08:36] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-15 15:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-15 15:08:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-15 15:08:37] [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.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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)
[2025-10-16 02:05:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-16 02:05:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 02:05:45] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 02:05:45] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-16 02:05:45] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-15
[2025-10-16 02:05:45] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-15 19:08:19 UTC; unix
[2025-10-16 02:05:45] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-16 02:05:45] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-16 02:05:46] [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=2025-10-16; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-16 02:05:46] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-16 02:05:46] [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 2.2.0(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 3.16.2(2025-10-15); 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)
[2025-10-16 02:05:46] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Contains 21 files.
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 02:05:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-16 02:05:46] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 18.324   1.641  47.926 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.0170.0020.019
all_uniprots 1.437 0.14313.320
ancestors0.0070.0010.008
annotated_network1.3070.0884.273
annotation_categories89.692 0.07091.134
annotation_resources0.1330.0120.742
annotations0.5980.0381.366
biomart_query1.0530.0753.808
bioplex10.0090.0000.009
bioplex20.0080.0000.008
bioplex30.0080.0000.007
bioplex_all0.0090.0000.008
bioplex_hct116_10.0070.0000.008
bma_motif_es0.6270.0661.636
bma_motif_vs0.2700.0040.896
chalmers_gem0.0070.0020.009
chalmers_gem_id_mapping_table0.0070.0010.008
chalmers_gem_id_type0.0020.0000.002
chalmers_gem_metabolites0.0070.0010.008
chalmers_gem_network0.0070.0010.008
chalmers_gem_raw0.0060.0020.008
chalmers_gem_reactions0.0070.0010.008
common_name0.0280.0010.029
complex_genes0.7380.0232.394
complex_resources0.1690.0070.724
complexes0.2870.0150.884
consensuspathdb_download0.0010.0000.001
consensuspathdb_raw_table0.0090.0000.009
cosmos_pkn000
curated_ligand_receptor_interactions 6.456 0.76016.070
curated_ligrec_stats 38.454 2.664105.156
database_summary1.5930.0662.863
descendants0.0120.0030.015
ensembl_dataset0.0150.0020.017
ensembl_id_mapping_table 2.279 0.16119.296
ensembl_id_type0.0020.0000.002
ensembl_name0.0590.0050.064
ensembl_organisms0.1290.0170.145
ensembl_organisms_raw0.1040.0080.112
ensembl_orthology0.0000.0010.001
enzsub_graph2.0030.1384.200
enzsub_resources0.1430.0020.734
enzyme_substrate1.0300.0211.637
evex_download0.0080.0010.009
evidences000
extra_attr_values11.178 1.36914.824
extra_attrs6.5841.1077.721
extra_attrs_to_cols12.859 1.27414.154
filter_by_resource 7.578 0.26210.206
filter_extra_attrs24.446 4.73029.906
filter_intercell 5.887 0.41710.254
filter_intercell_network0.0180.0020.020
find_all_paths5.1480.0945.240
from_evidences0.0000.0010.000
get_db000
get_ontology_db0.010.000.01
giant_component23.771 1.34036.551
go_annot_download19.992 1.22525.075
go_annot_slim0.0010.0000.001
go_ontology_download0.0220.0010.046
guide2pharma_download0.0240.0010.049
harmonizome_download0.0240.0030.051
has_extra_attrs14.627 1.72117.404
hmdb_id_mapping_table0.0070.0020.009
hmdb_id_type0.0020.0000.002
hmdb_metabolite_fields0.0010.0000.001
hmdb_protein_fields0.0010.0000.001
hmdb_table0.0090.0000.009
homologene_download0.0070.0010.009
homologene_raw0.0190.0020.021
homologene_uniprot_orthology0.0090.0010.009
hpo_download3.2670.1963.956
htridb_download0.0120.0000.013
id_translation_resources0.0000.0010.000
id_types0.0590.0000.059
inbiomap_download000
inbiomap_raw000
interaction_datasets0.6820.0291.023
interaction_graph0.4530.0131.279
interaction_resources0.0920.0050.774
interaction_types0.0650.0010.066
intercell0.8890.0541.743
intercell_categories0.6770.0440.897
intercell_consensus_filter1.9410.3444.969
intercell_generic_categories0.1160.0230.276
intercell_network0.0290.0020.066
intercell_resources0.1880.0131.031
intercell_summary0.1050.0270.258
is_ontology_id0.0010.0000.000
is_swissprot0.0650.0030.134
is_trembl0.0680.0030.141
is_uniprot0.0230.0010.049
kegg_api_templates0.0010.0060.017
kegg_conv 2.718 0.30714.836
kegg_databases0.0000.0010.001
kegg_ddi1.4780.0823.256
kegg_find1.7270.1263.958
kegg_info0.0420.0100.052
kegg_link1.2260.1287.372
kegg_list0.5870.0441.546
kegg_open0.0120.0030.015
kegg_operations000
kegg_organism_codes0.0260.1140.140
kegg_organisms0.0260.0100.036
kegg_pathway_annotations0.0010.0000.000
kegg_pathway_download0.0150.0010.016
kegg_pathway_list0.0150.0000.015
kegg_pathways_download0.0010.0000.000
kegg_picture1.8460.0706.842
kegg_process0.0190.0020.021
kegg_query0.0080.0010.009
kegg_request0.0600.0020.062
kegg_rm_prefix0.6800.0525.186
latin_name0.0640.0010.065
load_db0.0700.0110.081
metalinksdb_sqlite 1.246 0.27711.515
metalinksdb_table0.4240.0530.495
metalinksdb_tables0.0380.0030.041
ncbi_taxid0.1370.0100.148
nichenet_build_model0.0000.0010.001
nichenet_expression_data0.0170.0020.019
nichenet_gr_network0.0430.0080.051
nichenet_gr_network_evex0.0140.0030.018
nichenet_gr_network_harmonizome0.0180.0010.019
nichenet_gr_network_htridb0.0150.0020.017
nichenet_gr_network_omnipath25.814 1.52834.326
nichenet_gr_network_pathwaycommons0.0070.0020.010
nichenet_gr_network_regnetwork0.0080.0000.009
nichenet_gr_network_remap0.0070.0020.008
nichenet_gr_network_trrust0.0050.0040.009
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0200.0060.027
nichenet_lr_network_guide2pharma0.0460.0000.047
nichenet_lr_network_omnipath0.0240.0030.026
nichenet_lr_network_ramilowski0.0080.0000.008
nichenet_main0.0000.0010.000
nichenet_networks0.0370.0030.041
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0200.0040.025
nichenet_results_dir000
nichenet_signaling_network0.0270.0000.027
nichenet_signaling_network_cpdb0.0090.0000.008
nichenet_signaling_network_evex0.0070.0020.008
nichenet_signaling_network_harmonizome0.0060.0020.008
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath16.108 1.10322.189
nichenet_signaling_network_pathwaycommons0.1490.0050.188
nichenet_signaling_network_vinayagam0.0270.0000.037
nichenet_test0.0010.0000.000
nichenet_workarounds000
obo_parser0.2220.0150.416
oma_code0.0810.0030.163
oma_organisms0.1760.0310.410
oma_pairwise0.0250.0030.053
oma_pairwise_genesymbols0.0240.0040.054
oma_pairwise_translated0.0270.0040.061
omnipath-interactions 54.589 4.431112.887
omnipath_cache_autoclean0.0000.0000.001
omnipath_cache_clean0.0180.0010.019
omnipath_cache_clean_db0.1930.0200.283
omnipath_cache_download_ready1.0600.1371.944
omnipath_cache_filter_versions0.2270.0340.562
omnipath_cache_get0.2080.0340.518
omnipath_cache_key0.0050.0000.020
omnipath_cache_latest_or_new0.2810.0330.732
omnipath_cache_load1.1040.0733.942
omnipath_cache_move_in0.3330.0440.573
omnipath_cache_remove0.2060.0230.391
omnipath_cache_save0.3370.0410.672
omnipath_cache_search0.0020.0000.002
omnipath_cache_set_ext0.2060.0180.451
omnipath_cache_update_status0.2790.0640.443
omnipath_cache_wipe000
omnipath_config_path0.0030.0000.006
omnipath_for_cosmos12.133 0.92934.340
omnipath_load_config000
omnipath_log0.0000.0000.001
omnipath_logfile0.0020.0000.002
omnipath_msg0.0030.0020.005
omnipath_query3.1760.1863.362
omnipath_reset_config000
omnipath_save_config0.0010.0000.001
omnipath_set_cachedir0.0200.0020.022
omnipath_set_console_loglevel0.0030.0000.004
omnipath_set_logfile_loglevel0.0030.0000.004
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.0560.0020.059
omnipath_unlock_cache_db000
only_from0.0010.0000.001
ontology_ensure_id0.0000.0010.001
ontology_ensure_name0.0000.0010.001
ontology_name_id0.0000.0010.001
organism_for0.0420.0000.042
pathwaycommons_download0.0010.0000.001
pivot_annotations 9.245 0.60118.429
preppi_download0.0000.0000.001
preppi_filter0.0000.0010.001
print_bma_motif_es0.6470.0761.520
print_bma_motif_vs0.2090.0160.844
print_interactions 5.908 0.25610.211
print_path_es0.8280.0622.397
print_path_vs2.2220.1764.964
pubmed_open3.4870.0993.583
query_info0.3350.0060.517
ramilowski_download000
ramp_id_mapping_table0.0010.0010.000
ramp_id_type0.0020.0000.002
ramp_sqlite0.0000.0010.000
ramp_table000
ramp_tables000
regnetwork_directions000
regnetwork_download0.0010.0010.001
relations_list_to_table0.0720.0080.178
relations_table_to_graph000
relations_table_to_list0.0620.0090.084
remap_dorothea_download0.0010.0000.001
remap_filtered0.0000.0000.001
remap_tf_target_download0.0000.0000.001
resource_info0.3870.0610.631
resources0.0820.0120.794
resources_colname1.1570.0503.900
resources_in3.3840.2173.604
show_network0.0000.0000.001
signed_ptms4.5080.2375.328
simplify_intercell_network0.0000.0000.001
static_table6.7260.3497.923
static_tables0.1050.0050.114
stitch_actions0.0000.0020.002
stitch_links0.0010.0000.001
stitch_network0.0020.0000.001
stitch_remove_prefixes0.0110.0030.014
swap_relations0.1440.0140.173
swissprots_only0.0750.0020.077
tfcensus_download1.0360.0341.214
translate_ids 1.074 0.05111.193
translate_ids_multi14.066 0.84433.987
trembls_only0.1080.0090.118
trrust_download0.0020.0000.003
uniprot_full_id_mapping_table 2.289 0.14414.509
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0010.0000.002
uniprot_id_type0.0050.0000.004
uniprot_idmapping_id_types0.7280.0241.566
unique_intercell_network0.0010.0000.002
unnest_evidences0.0010.0000.001
uploadlists_id_type0.0040.0000.004
vinayagam_download0.0010.0000.001
walk_ontology_tree0.0020.0000.002
with_extra_attrs15.217 1.92521.792
with_references1.4820.0943.860
zenodo_download0.0010.0010.001