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This page was generated on 2026-04-27 11:33 -0400 (Mon, 27 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4822
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 1504/2365HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.99.0  (landing page)
Denes Turei
Snapshot Date: 2026-04-26 13:45 -0400 (Sun, 26 Apr 2026)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 886a999
git_last_commit_date: 2026-04-20 21:32:47 -0400 (Mon, 20 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    ERROR  
See other builds for OmnipathR in R Universe.

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: 3.99.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings OmnipathR_3.99.0.tar.gz
StartedAt: 2026-04-27 02:16:54 -0400 (Mon, 27 Apr 2026)
EndedAt: 2026-04-27 02:52:57 -0400 (Mon, 27 Apr 2026)
EllapsedTime: 2162.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings OmnipathR_3.99.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/OmnipathR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 06:16:55 UTC
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.99.0’
* 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
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-26
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-26 19:09:52 UTC; unix
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-27 02:17:26] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-27 02:17:26] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-26); 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 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.3(2026-04-20); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-27 02:17:26] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Contains 1 files.
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-27 02:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-27 02:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-27 02:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:27] [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
[2026-04-27 02:17:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:17:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-26
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-26 19:09:52 UTC; unix
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-04-27 02:17:43] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-27 02:17:43] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-27 02:17:44] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-26); 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 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.3(2026-04-20); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-27 02:17:44] [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
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Contains 1 files.
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:17:44] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: all_uniprots
> ### Title: A table with all UniProt records
> ### Aliases: all_uniprots
> 
> ### ** Examples
> 
> human_swissprot_entries <- all_uniprots(fields = 'id')
[2026-04-27 02:18:25] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-04-27 02:18:25] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-04-27 02:18:25] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-04-27 02:18:25] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-04-27 02:18:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:26] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:26] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-04-27 02:18:26] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-27 02:18:26] [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]
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.630583s from rescued.omnipathdb.org (63.2 Kb/s); Redirect: 0s, DNS look up: 0.003408s, Connection: 0.004184s, Pretransfer: 0.348627s, First byte at: 0.491325s
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 27 Apr 2026 06:18:26 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Mon, 27 Apr 2026 07:18:26 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-04-27 02:18:26] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 27 Apr 2026 06:18:26 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Mon, 27 Apr 2026 07:18:26 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-04-27 02:18:27] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:27] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-27 02:18:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:27] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-27 02:18:27] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-27 02:18:27] [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]
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] Downloaded 4 Kb in 0.396007s from omabrowser.org (10.1 Kb/s); Redirect: 0s, DNS look up: 0.002666s, Connection: 0.015451s, Pretransfer: 0.080455s, First byte at: 0.39587s
[2026-04-27 02:18:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 27 Apr 2026 06:18:27 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=MM%2FUTe8kCpzqiq0xdcwB4tzi3k9RjwYGmxHfST%2Fhagjh83JAJqbYoISFNi9sAMIGRbIQCgK72IttW7md%2B%2FNPA%2BwMr1X%2FANuzaQbbVlVzVerBdC%2FHYYzd0Qi31Hvx3pel6g%3D%3D"}]}; cf-ray: 9f2bb5c18a1aec0a-IAD; alt-svc: h3=":443"; ma=86400
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-27 02:18:28] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-27 02:18:28] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:28] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-27 02:18:28] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-27 02:18:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-27 02:18:55] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:55] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:55] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-04-27 02:18:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-04-27 02:18:56] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:56] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-04-27 02:18:56] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-27 02:18:56] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:18:56] [INFO]    [OmnipathR] Cache item `80e22dce504c916061293773267b3f34dea718f3` version 1: status changed from `unknown` to `started`.
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/80e22dce504c916061293773267b3f34dea718f3-1.rds`.
[2026-04-27 02:18:56] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-27 02:18:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-27 02:18:56] [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]
[2026-04-27 02:18:57] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-27 02:18:58] [TRACE]   [OmnipathR] Downloaded 27 bytes in 1.742468s from rest.uniprot.org (15 bytes/s); Redirect: 0s, DNS look up: 0.017419s, Connection: 0.018171s, Pretransfer: 0.572567s, First byte at: 1.742393s
[2026-04-27 02:18:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 27 Apr 2026 06:18:57 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-27 02:20:57] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-27 02:21:02] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-27 02:21:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-27 02:21:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-27 02:21:02] [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]
[2026-04-27 02:21:04] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-27 02:21:04] [TRACE]   [OmnipathR] Downloaded 27 bytes in 2.150213s from rest.uniprot.org (12 bytes/s); Redirect: 0s, DNS look up: 0.001849s, Connection: 0.002835s, Pretransfer: 0.518516s, First byte at: 2.150164s
[2026-04-27 02:21:04] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 27 Apr 2026 06:21:04 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-27 02:22:04] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-27 02:22:09] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-27 02:22:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-27 02:22:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-27 02:22:09] [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]
[2026-04-27 02:22:11] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-27 02:22:11] [TRACE]   [OmnipathR] Downloaded 27 bytes in 1.696052s from rest.uniprot.org (15 bytes/s); Redirect: 0s, DNS look up: 0.001865s, Connection: 0.002806s, Pretransfer: 0.287193s, First byte at: 1.695995s
[2026-04-27 02:22:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 27 Apr 2026 06:22:11 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-27 02:24:44] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-27 02:24:44] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-27 02:24:44] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-26
[2026-04-27 02:24:44] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-26 19:09:52 UTC; unix
[2026-04-27 02:24:44] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-27 02:24:44] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-04-27 02:24:45] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-27 02:24:45] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-27 02:24:45] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-26); 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 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); 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 0.7.3(2026-04-11); vroom 1.7.1(2026-03-31); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-27 02:24:45] [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
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  : 
  Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Calls: all_uniprots ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
* 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-3.24-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.99.0’
** 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
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-26
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-26 19:09:52 UTC; unix
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-26 15:10:07] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-26 15:10:07] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-26); 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 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.3(2026-04-20); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-26 15:10:07] [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
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Contains 20 files.
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:07] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2026-04-26 15:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-26 15:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-26
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-26 19:09:52 UTC; unix
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-26 15:10:10] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-26 15:10:10] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-26); 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 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.3(2026-04-20); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-26 15:10:10] [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
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Contains 1 files.
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-26 15:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-26 15:10:10] [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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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> #!/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)
[2026-04-27 02:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:24:52] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:24:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-27 02:24:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-26
[2026-04-27 02:24:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-26 19:09:52 UTC; unix
[2026-04-27 02:24:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-27 02:24:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-04-27 02:24:53] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-27 02:24:54] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.24-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-27 02:24:54] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); 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 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-26); 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 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-27 02:24:54] [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
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Contains 5 files.
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:24:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-27 02:24:54] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
> 
> proc.time()
   user  system elapsed 
 77.604   7.027 132.013

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.0200.0010.021