Denes Turei
| Snapshot Date: 2026-01-12 13:45 -0500 (Mon, 12 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 27b34f4 |
| git_last_commit_date: 2025-12-10 09:01:42 -0500 (Wed, 10 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-15 11:59 -0500 (Thu, 15 Jan 2026).
| 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" | 4886 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4672 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.18.3 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.18.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.18.3.tar.gz |
| StartedAt: 2026-01-13 12:29:14 -0000 (Tue, 13 Jan 2026) |
| EndedAt: 2026-01-13 12:41:00 -0000 (Tue, 13 Jan 2026) |
| EllapsedTime: 706.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.18.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.18.3’
* 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
[2026-01-13 12:30:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:30:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-01-13 12:30:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-01-12
[2026-01-13 12:30:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-01-12 21:12:20 UTC; unix
[2026-01-13 12:30:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2026-01-13 12:30:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-01-13 12:30:15] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-01-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-01-13 12:30:16] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2026-01-13 12:30:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.18.3(2026-01-12); 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 1.1.0(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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2026-01-13 12:30:16] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Contains 1 files.
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-01-13 12:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-01-13 12:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-01-13 12:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-01-13 12:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:16] [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
[2026-01-13 12:30:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:30:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:30:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-01-13 12:30:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-01-12
[2026-01-13 12:30:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-01-12 21:12:20 UTC; unix
[2026-01-13 12:30:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2026-01-13 12:30:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-01-13 12:30:43] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-01-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-01-13 12:30:43] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2026-01-13 12:30:43] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.18.3(2026-01-12); 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 1.1.0(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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2026-01-13 12:30:43] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Contains 1 files.
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-01-13 12:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-01-13 12:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-01-13 12:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-01-13 12:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:30:43] [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")
[2026-01-13 12:38:38] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2026-01-13 12:38:38] [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>
[2026-01-13 12:38:38] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-01-13 12:38:38] [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`.
[2026-01-13 12:38:38] [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`
[2026-01-13 12:38:39] [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`.
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:38:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:38:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:39] [INFO] [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-01-13 12:38:39] [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`
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-01-13 12:38:39] [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`
[2026-01-13 12:38:39] [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`.
[2026-01-13 12:38:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-01-13 12:38:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Sending HTTP request.
[2026-01-13 12:38:39] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-01-13 12:38:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Downloaded 1014 bytes in 0.335729s from www.ensembl.org (2.9 Kb/s); Redirect: 0s, DNS look up: 0.008159s, Connection: 0.170386s, Pretransfer: 0.17046s, First byte at: 0.335635s
[2026-01-13 12:38:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: E08A:3A459:14802B:14F55F:69655D80; Server: GitHub.com; X-Cache-Hits: 2; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: 543595c662ed42cba75df6f51c392a817b2ef382; Content-Encoding: gzip; Date: Tue, 13 Jan 2026 12:44:53 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630051-LCY; Pragma: no-cache; X-Timer: S1768308293.302800,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 358; Content-Length: 1014
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=E08A:3A459:14802B:14F55F:69655D80,Server=GitHub.com,X-Cache-Hits=2,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=543595c662ed42cba75df6f51c392a817b2ef382,Content-Encoding=gzip,Date=Tue, 13 Jan 2026 12:44:53 GMT,Expires=0,X-Served-By=cache-lcy-egml8630051-LCY,Pragma=no-cache,X-Timer=S1768308293.302800,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=358,Content-Length=1014]
[2026-01-13 12:38:39] [TRACE] [OmnipathR] Calling reader callback on response.
[2026-01-13 12:38:40] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-01-13 12:38:40] [INFO] [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2026-01-13 12:38:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:38:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:40] [INFO] [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2026-01-13 12:38:40] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-01-13 12:38:40] [WARN] [OmnipathR] <html>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <head>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <title>Service unavailable</title>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <meta name="robots" content="noindex">
[2026-01-13 12:38:40] [WARN] [OmnipathR] <base href="//status.ensembl.org">
[2026-01-13 12:38:40] [WARN] [OmnipathR] <style>
[2026-01-13 12:38:40] [WARN] [OmnipathR] html,
[2026-01-13 12:38:40] [WARN] [OmnipathR] body {
[2026-01-13 12:38:40] [WARN] [OmnipathR] padding: 0;
[2026-01-13 12:38:40] [WARN] [OmnipathR] margin: 0;
[2026-01-13 12:38:40] [WARN] [OmnipathR] height: 100%;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] body {
[2026-01-13 12:38:40] [WARN] [OmnipathR] display: grid;
[2026-01-13 12:38:40] [WARN] [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2026-01-13 12:38:40] [WARN] [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2026-01-13 12:38:40] [WARN] [OmnipathR] font-size: 90%;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] h1 {
[2026-01-13 12:38:40] [WARN] [OmnipathR] font-size: 1.5rem;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] h2 {
[2026-01-13 12:38:40] [WARN] [OmnipathR] font-size: 1.2rem;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] h3 {
[2026-01-13 12:38:40] [WARN] [OmnipathR] font-size: 1.1rem;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] header {
[2026-01-13 12:38:40] [WARN] [OmnipathR] grid-row: header;
[2026-01-13 12:38:40] [WARN] [OmnipathR] padding: 5px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] height: 60px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] background-color: #333366;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] header img {
[2026-01-13 12:38:40] [WARN] [OmnipathR] width: 185px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] height: 45px
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] main {
[2026-01-13 12:38:40] [WARN] [OmnipathR] grid-row: main;
[2026-01-13 12:38:40] [WARN] [OmnipathR] padding: 20px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] .mirrors {
[2026-01-13 12:38:40] [WARN] [OmnipathR] border: solid 1px #ccc;
[2026-01-13 12:38:40] [WARN] [OmnipathR] margin-top: 20px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] padding: 10px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] footer {
[2026-01-13 12:38:40] [WARN] [OmnipathR] grid-row: footer;
[2026-01-13 12:38:40] [WARN] [OmnipathR] padding: 0 20px;
[2026-01-13 12:38:40] [WARN] [OmnipathR] }
[2026-01-13 12:38:40] [WARN] [OmnipathR] </style>
[2026-01-13 12:38:40] [WARN] [OmnipathR] </head>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <body>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <header>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2026-01-13 12:38:40] [WARN] [OmnipathR] </header>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <main>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <h1>Server Status</h1>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <p>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2026-01-13 12:38:40] [WARN] [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2026-01-13 12:38:40] [WARN] [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2026-01-13 12:38:40] [WARN] [OmnipathR] </p>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <div class="mirrors">
[2026-01-13 12:38:40] [WARN] [OmnipathR] <h3>Ensembl mirrors</h3>
[2026-01-13 12:38:40] [WARN] [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2026-01-13 12:38:40] [WARN] [OmnipathR] <ul>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2026-01-13 12:38:40] [WARN] [OmnipathR] </ul>
[2026-01-13 12:38:40] [WARN] [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2026-01-13 12:38:40] [WARN] [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2026-01-13 12:38:40] [WARN] [OmnipathR] data centre.
[2026-01-13 12:38:40] [WARN] [OmnipathR] </div>
[2026-01-13 12:38:40] [WARN] [OmnipathR] </main>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <footer>
[2026-01-13 12:38:40] [WARN] [OmnipathR] <p>© 2025 EMBL-EBI</p>
[2026-01-13 12:38:40] [WARN] [OmnipathR] </footer>
[2026-01-13 12:38:40] [WARN] [OmnipathR] </body>
[2026-01-13 12:38:40] [WARN] [OmnipathR] </html>
[2026-01-13 12:38:40] [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 107.576 0.000 123.371
curated_ligrec_stats 44.069 2.915 170.764
all_uniprots 34.496 2.483 62.180
curated_ligand_receptor_interactions 7.754 0.554 26.319
annotated_network 1.486 0.062 6.177
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.18.3’ ** 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 [2026-01-12 21:12:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-01-12 21:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:40] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-01-12 21:12:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-01-12 21:12:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-01-12 [2026-01-12 21:12:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-01-12 21:12:20 UTC; unix [2026-01-12 21:12:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3 [2026-01-12 21:12:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2026-01-12 21:12:41] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-01-12; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-01-12 21:12:41] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2026-01-12 21:12:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.18.3(2026-01-12); 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 1.1.0(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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2026-01-12 21:12:41] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-01-12 21:12:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-01-12 21:12:41] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-01-12 21:12:41] [TRACE] [OmnipathR] Contains 7 files. [2026-01-12 21:12:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-01-12 21:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-01-12 21:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-01-12 21:12:41] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-01-12 21:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-01-12 21:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-01-12 21:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-01-12 21:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-01-12 21:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:41] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-01-12 21:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-01-12 21:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:44] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-01-12 21:12:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-01-12 21:12:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-01-12 [2026-01-12 21:12:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-01-12 21:12:20 UTC; unix [2026-01-12 21:12:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3 [2026-01-12 21:12:44] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2026-01-12 21:12:44] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-01-12; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-01-12 21:12:44] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2026-01-12 21:12:45] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.18.3(2026-01-12); 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 1.1.0(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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2026-01-12 21:12:45] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-01-12 21:12:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-01-12 21:12:45] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-01-12 21:12:45] [TRACE] [OmnipathR] Contains 1 files. [2026-01-12 21:12:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-01-12 21:12:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-01-12 21:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-01-12 21:12:45] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-01-12 21:12:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-01-12 21:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-01-12 21:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-01-12 21:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-01-12 21:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-01-12 21:12:45] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2026-01-13 12:38:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:38:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:45] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:38:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-01-13 12:38:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-01-12
[2026-01-13 12:38:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-01-12 21:12:20 UTC; unix
[2026-01-13 12:38:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2026-01-13 12:38:45] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-01-13 12:38:46] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-01-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-01-13 12:38:46] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2026-01-13 12:38:46] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.18.3(2026-01-12); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2026-01-13 12:38:46] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Contains 39 files.
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-01-13 12:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-01-13 12:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-01-13 12:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-01-13 12:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-01-13 12:38:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-01-13 12:38:47] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
58.564 3.616 122.833
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.021 | 0.008 | 0.029 | |
| all_uniprots | 34.496 | 2.483 | 62.180 | |
| ancestors | 0.008 | 0.004 | 0.012 | |
| annotated_network | 1.486 | 0.062 | 6.177 | |
| annotation_categories | 107.576 | 0.000 | 123.371 | |
| annotation_resources | 0.092 | 0.000 | 0.982 | |
| annotations | 0.747 | 0.008 | 2.879 | |
| biomart_query | 0.695 | 0.030 | 2.279 | |
| bioplex1 | 0.013 | 0.000 | 0.013 | |
| bioplex2 | 0.012 | 0.000 | 0.013 | |
| bioplex3 | 0.013 | 0.000 | 0.013 | |
| bioplex_all | 0.013 | 0.000 | 0.013 | |
| bioplex_hct116_1 | 0.012 | 0.000 | 0.013 | |
| bma_motif_es | 0.737 | 0.013 | 2.596 | |
| bma_motif_vs | 0.275 | 0.017 | 1.441 | |
| chalmers_gem | 0.015 | 0.000 | 0.027 | |
| chalmers_gem_id_mapping_table | 0.011 | 0.004 | 0.035 | |
| chalmers_gem_id_type | 0.003 | 0.000 | 0.006 | |
| chalmers_gem_metabolites | 0.014 | 0.000 | 0.030 | |
| chalmers_gem_network | 0.013 | 0.000 | 0.026 | |
| chalmers_gem_raw | 0.013 | 0.000 | 0.028 | |
| chalmers_gem_reactions | 0.013 | 0.001 | 0.031 | |
| common_name | 0.181 | 0.000 | 0.388 | |
| complex_genes | 0.757 | 0.037 | 3.040 | |
| complex_resources | 0.081 | 0.001 | 0.954 | |
| complexes | 0.213 | 0.017 | 1.379 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.009 | 0.004 | 0.024 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.754 | 0.554 | 26.319 | |
| curated_ligrec_stats | 44.069 | 2.915 | 170.764 | |
| database_summary | 2.116 | 0.132 | 3.768 | |
| descendants | 0.013 | 0.000 | 0.013 | |
| ensembl_dataset | 0.057 | 0.000 | 0.057 | |