Build/check report for BioC 3.22 - CHECK results for OmnipathR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4891
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*

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: 3.18.4

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_3.18.4.tar.gz

StartedAt: 2026-02-26 02:42:34 -0500 (Thu, 26 Feb 2026)

EndedAt: 2026-02-26 03:18:43 -0500 (Thu, 26 Feb 2026)

EllapsedTime: 2169.4 seconds

RetCode: 1

Status: ERROR

CheckDir: OmnipathR.Rcheck

Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.18.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘3.18.4’
* 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
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-25
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-25 20:09:55 UTC; unix
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 02:43:04] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 02:43:04] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 02:43:04] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 02:43:04] [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
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 02:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 02:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:05] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-25
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-25 20:09:55 UTC; unix
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 02:43:21] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 02:43:21] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 02:43:21] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 02:43:21] [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
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 02:43:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:43:22] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
patch_httr2_keep_handle: no visible binding for global variable
  ‘handle’
patch_httr2_keep_handle: no visible global function definition for
  ‘ORIGINAL’
Undefined global functions or variables:
  ORIGINAL enzyme_genesymbol handle
* 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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="ensembl_peptide_id"/>
    </Dataset>
</Query>
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-02-26 02:50:21] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:21] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-02-26 02:50:21] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 02:50:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.175009s from www.ensembl.org (5.7 Kb/s); Redirect: 0s, DNS look up: 0.008348s, Connection: 0.009139s, Pretransfer: 0.009206s, First byte at: 0.174849s
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 3118:11FA79:1AE112:1BCA44:697C5971; Server: GitHub.com; X-Cache-Hits: 13; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; X-Fastly-Request-ID: 3136d0908e0f4b98dc6b2f94632dd7d7d339b285; Content-Encoding: gzip; Date: Thu, 26 Feb 2026 07:50:22 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630071-LCY; Pragma: no-cache; X-Timer: S1772092222.141758,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Content-Length: 1014; Content-Type: text/html; charset=utf-8; Age: 439; Via: 1.1 varnish, 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=3118:11FA79:1AE112:1BCA44:697C5971,Server=GitHub.com,X-Cache-Hits=13,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,X-Fastly-Request-ID=3136d0908e0f4b98dc6b2f94632dd7d7d339b285,Content-Encoding=gzip,Date=Thu, 26 Feb 2026 07:50:22 GMT,Expires=0,X-Served-By=cache-lcy-egml8630071-LCY,Pragma=no-cache,X-Timer=S1772092222.141758,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Content-Length=1014,Content-Type=text/html; charset=utf-8,Age=439,Via=1.1 varnish, 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004),Connection=keep-alive]
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-02-26 02:50:22] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:50:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:22] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2026-02-26 02:50:22] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <html>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <head>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <style>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] html,
[2026-02-26 02:50:22] [WARN]    [OmnipathR] body {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] padding: 0;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] margin: 0;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] height: 100%;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] body {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] display: grid;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] font-size: 90%;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] h1 {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] font-size: 1.5rem;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] h2 {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] font-size: 1.2rem;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] h3 {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] font-size: 1.1rem;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] header {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] grid-row: header;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] padding: 5px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] height: 60px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] background-color: #333366;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] header img {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] width: 185px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] height: 45px
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] main {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] grid-row: main;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] padding: 20px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] .mirrors {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] margin-top: 20px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] padding: 10px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] footer {
[2026-02-26 02:50:22] [WARN]    [OmnipathR] grid-row: footer;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] padding: 0 20px;
[2026-02-26 02:50:22] [WARN]    [OmnipathR] }
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </style>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </head>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <body>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <header>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </header>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <main>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <p>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2026-02-26 02:50:22] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2026-02-26 02:50:22] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </p>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <div class="mirrors">
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <ul>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </ul>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2026-02-26 02:50:22] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2026-02-26 02:50:22] [WARN]    [OmnipathR] data centre.
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </div>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </main>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <footer>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </footer>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </body>
[2026-02-26 02:50:22] [WARN]    [OmnipathR] </html>
[2026-02-26 02:50:22] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
    ▆
 1. ├─OmnipathR::ensembl_id_mapping_table("ensp")
 2. │ └─... %>% trim_and_distinct
 3. ├─OmnipathR:::trim_and_distinct(.)
 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 5. ├─dplyr::distinct(.)
 6. ├─dplyr::mutate(., across(everything(), str_trim))
 7. ├─rlang::set_names(., c("From", "To"))
 8. └─rlang::abort(message = message)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                91.360  0.105  94.662
curated_ligrec_stats                 46.646  4.847 156.373
all_uniprots                         24.248  2.045  38.730
curated_ligand_receptor_interactions  7.560  1.228  37.387
annotated_network                     1.675  0.233  18.630
annotations                           0.776  0.092  14.866
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 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 ‘3.18.4’
** 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
[2026-02-25 15:10:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-25 15:10:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:08] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-25 15:10:08] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-25 15:10:08] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-25
[2026-02-25 15:10:08] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-25 20:09:55 UTC; unix
[2026-02-25 15:10:08] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-25 15:10:08] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-25 15:10:09] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2026-02-25; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-25 15:10:09] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-25 15:10:09] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-25 15:10:09] [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
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Contains 9 files.
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-25 15:10:09] [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).
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:09] [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).
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:09] [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).
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:09] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2026-02-25 15:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-25 15:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-25
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-25 20:09:55 UTC; unix
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-25 15:10:11] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2026-02-25; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-25 15:10:12] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-25 15:10:12] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-25 15:10:12] [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
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-25 15:10:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-25 15:10:12] [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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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)
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-25
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-25 20:09:55 UTC; unix
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 02:50:25] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 02:50:25] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 02:50:25] [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 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 02:50:25] [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
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Contains 39 files.
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 02:50:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-26 02:50:26] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 90.565   7.521 170.309

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

name	user	system	elapsed
OmnipathR	0.000	0.000	0.001
all_uniprot_acs	0.017	0.000	0.017
all_uniprots	24.248	2.045	38.730
ancestors	0.008	0.001	0.009
annotated_network	1.675	0.233	18.630
annotation_categories	91.360	0.105	94.662
annotation_resources	0.139	0.050	0.998
annotations	0.776	0.092	14.866
biomart_query	1.125	0.166	3.804
bioplex1	0.008	0.000	0.008
bioplex2	0.008	0.000	0.008
bioplex3	0.008	0.000	0.008
bioplex_all	0.008	0.000	0.008
bioplex_hct116_1	0.007	0.000	0.007
bma_motif_es	0.760	0.106	2.913
bma_motif_vs	0.322	0.020	1.197
chalmers_gem	0.01	0.00	0.01
chalmers_gem_id_mapping_table	0.008	0.000	0.008
chalmers_gem_id_type	0.001	0.000	0.000
chalmers_gem_metabolites	0.009	0.000	0.009
chalmers_gem_network	0.009	0.000	0.009
chalmers_gem_raw	0.009	0.000	0.009
chalmers_gem_reactions	0.006	0.004	0.010
common_name	0.159	0.007	0.165
complex_genes	0.910	0.129	3.787
complex_resources	0.198	0.032	1.017
complexes	0.340	0.016	1.172
consensuspathdb_download	0	0	0
consensuspathdb_raw_table	0.008	0.000	0.009
cosmos_pkn	0	0	0
curated_ligand_receptor_interactions	7.560	1.228	37.387
curated_ligrec_stats	46.646	4.847	156.373
database_summary	1.817	0.125	4.818
descendants	0.008	0.001	0.010
ensembl_dataset	0.051	0.000	0.051