Denes Turei
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: 3e11391 |
| git_last_commit_date: 2026-04-29 06:26:56 -0400 (Wed, 29 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:33 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 1505/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 4.1.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
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. |
| Package: OmnipathR |
| Version: 4.1.0 |
| 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_4.1.0.tar.gz |
| StartedAt: 2026-05-06 02:31:30 -0400 (Wed, 06 May 2026) |
| EndedAt: 2026-05-06 03:08:19 -0400 (Wed, 06 May 2026) |
| EllapsedTime: 2208.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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###
### 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_4.1.0.tar.gz
###
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* 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: 2026-05-06 06:31:31 UTC
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘4.1.0’
* 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
[2026-05-06 02:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-06 02:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:00] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:32:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-06 02:32:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-05
[2026-05-06 02:32:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-05 19:08:53 UTC; unix
[2026-05-06 02:32:00] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-06 02:32:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-06 02:32:01] [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=2026-05-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-06 02:32:01] [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]
[2026-05-06 02:32:01] [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 2.3.1(2026-05-04); 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 4.1.0(2026-05-05); 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)
[2026-05-06 02:32:01] [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
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-06 02:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-06 02:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-06 02:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-06 02:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-06 02:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:01] [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
[2026-05-06 02:32:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-06 02:32:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:17] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:32:17] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-06 02:32:17] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-05
[2026-05-06 02:32:17] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-05 19:08:53 UTC; unix
[2026-05-06 02:32:17] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-06 02:32:17] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-06 02:32:18] [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=2026-05-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-06 02:32:18] [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]
[2026-05-06 02:32:18] [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 2.3.1(2026-05-04); 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 4.1.0(2026-05-05); 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)
[2026-05-06 02:32:18] [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
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-06 02:32:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-06 02:32:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-06 02:32:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-06 02:32:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-06 02:32:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:32:18] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 80.800 0.139 82.845
filter_extra_attrs 50.504 6.745 80.772
curated_ligrec_stats 47.201 4.409 131.000
omnipath-interactions 35.116 2.402 64.074
nichenet_gr_network_omnipath 31.180 1.588 50.649
nichenet_signaling_network_omnipath 30.859 1.505 39.614
all_uniprots 25.657 1.753 41.296
giant_component 15.910 0.866 20.293
has_extra_attrs 12.933 1.584 19.558
extra_attrs_to_cols 12.872 1.360 14.121
pivot_annotations 12.930 0.778 21.456
extra_attr_values 12.223 1.272 15.638
omnipath_for_cosmos 12.694 0.430 46.296
go_annot_download 12.116 0.879 12.409
with_extra_attrs 10.691 1.395 11.973
find_all_paths 11.444 0.404 15.659
print_interactions 10.202 0.598 15.857
filter_intercell 9.622 0.837 15.333
translate_ids_multi 8.408 0.598 31.938
extra_attrs 7.478 0.834 8.338
curated_ligand_receptor_interactions 7.467 0.773 18.605
filter_by_resource 7.688 0.349 10.006
pubmed_open 7.158 0.179 7.514
static_table 6.056 0.284 7.091
omnipath_query 5.091 0.113 5.161
signed_ptms 4.419 0.129 5.289
kegg_conv 3.646 0.560 17.709
print_path_vs 3.091 0.129 5.146
kegg_link 2.274 0.161 8.461
metalinksdb_sqlite 1.853 0.261 12.464
annotated_network 1.898 0.134 5.217
kinasephos 1.753 0.224 27.961
kegg_rm_prefix 1.789 0.184 6.926
kegg_picture 1.653 0.032 5.886
translate_ids 1.356 0.094 10.509
uniprot_full_id_mapping_table 1.239 0.210 12.080
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.24-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
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 ‘4.1.0’ ** 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 [2026-05-05 15:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-05 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-05 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-05 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-05 [2026-05-05 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-05 19:08:53 UTC; unix [2026-05-05 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-05 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-05 15:09:08] [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=2026-05-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-05-05 15:09:08] [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] [2026-05-05 15:09:08] [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 2.3.1(2026-05-04); 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 4.1.0(2026-05-05); 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) [2026-05-05 15:09:08] [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 [2026-05-05 15:09:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-05 15:09:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-05 15:09:08] [TRACE] [OmnipathR] Contains 8 files. [2026-05-05 15:09:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-05 15:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-05 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-05 15:09:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-05-05 15:09:08] [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). [2026-05-05 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:08] [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). [2026-05-05 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-05 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:08] [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). [2026-05-05 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:08] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-05-05 15:09:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-05 15:09:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-05 15:09:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-05 15:09:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-05 [2026-05-05 15:09:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-05 19:08:53 UTC; unix [2026-05-05 15:09:10] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-05 15:09:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-05 15:09:11] [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=2026-05-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-05-05 15:09:11] [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] [2026-05-05 15:09:11] [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 2.3.1(2026-05-04); 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 4.1.0(2026-05-05); 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) [2026-05-05 15:09:11] [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 [2026-05-05 15:09:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-05 15:09:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-05 15:09:11] [TRACE] [OmnipathR] Contains 1 files. [2026-05-05 15:09:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-05 15:09:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-05 15:09:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-05 15:09:11] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-05-05 15:09:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-05 15:09:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-05 15:09:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-05 15:09:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-05 15:09:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-05 15:09:11] [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 4.6.0 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
'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)
[2026-05-06 02:49:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-06 02:49:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:49:44] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:49:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-06 02:49:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-05
[2026-05-06 02:49:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-05 19:08:53 UTC; unix
[2026-05-06 02:49:44] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-06 02:49:44] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-06 02:49:44] [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=2026-05-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-06 02:49:44] [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]
[2026-05-06 02:49:45] [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); 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 2.3.1(2026-05-04); 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 4.1.0(2026-05-05); 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)
[2026-05-06 02:49:45] [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
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Contains 95 files.
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-06 02:49:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:49:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-06 02:49:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-06 02:49:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-06 02:49:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.24-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-06 02:49:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-06 02:49:45] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
49.024 3.639 86.405
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.014 | 0.004 | 0.018 | |
| all_uniprots | 25.657 | 1.753 | 41.296 | |
| ancestors | 0.008 | 0.001 | 0.010 | |
| annotated_network | 1.898 | 0.134 | 5.217 | |
| annotation_categories | 80.800 | 0.139 | 82.845 | |
| annotation_resources | 0.196 | 0.048 | 1.041 | |
| annotations | 0.829 | 0.134 | 1.970 | |
| biomart_query | 1.198 | 0.069 | 4.519 | |
| bioplex1 | 0.009 | 0.000 | 0.009 | |
| bioplex2 | 0.008 | 0.001 | 0.008 | |
| bioplex3 | 0.008 | 0.000 | 0.008 | |
| bioplex_all | 0.008 | 0.000 | 0.009 | |
| bioplex_hct116_1 | 0.007 | 0.001 | 0.008 | |
| bma_motif_es | 0.828 | 0.078 | 1.976 | |
| bma_motif_vs | 0.250 | 0.012 | 1.080 | |
| chalmers_gem | 0.009 | 0.001 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.027 | 0.001 | 0.027 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.000 | |
| chalmers_gem_metabolites | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_network | 0.006 | 0.002 | 0.008 | |
| chalmers_gem_raw | 0.007 | 0.000 | 0.008 | |
| chalmers_gem_reactions | 0.006 | 0.001 | 0.008 | |
| common_name | 0.120 | 0.001 | 0.122 | |
| complex_genes | 0.942 | 0.042 | 2.669 | |
| complex_resources | 0.191 | 0.023 | 1.085 | |
| complexes | 0.303 | 0.021 | 1.096 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.009 | 0.000 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.467 | 0.773 | 18.605 | |
| curated_ligrec_stats | 47.201 | 4.409 | 131.000 | |
| database_summary | 1.853 | 0.115 | 3.099 | |
| descendants | 0.009 | 0.000 | 0.010 | |
| ensembl_dataset | 0.047 | 0.000 | 0.048 | |
| ensembl_id_mapping_table | 1.126 | 0.120 | 1.406 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.268 | 0.000 | 0.267 | |
| ensembl_organisms | 0.105 | 0.008 | 0.111 | |
| ensembl_organisms_raw | 0.335 | 0.007 | 0.341 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.083 | 0.137 | 4.088 | |
| enzsub_resources | 0.200 | 0.025 | 1.047 | |
| enzyme_substrate | 0.972 | 0.048 | 1.798 | |
| evex_download | 0.008 | 0.002 | 0.010 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 12.223 | 1.272 | 15.638 | |
| extra_attrs | 7.478 | 0.834 | 8.338 | |
| extra_attrs_to_cols | 12.872 | 1.360 | 14.121 | |
| filter_by_resource | 7.688 | 0.349 | 10.006 | |
| filter_extra_attrs | 50.504 | 6.745 | 80.772 | |
| filter_intercell | 9.622 | 0.837 | 15.333 | |
| filter_intercell_network | 0.057 | 0.004 | 0.103 | |
| find_all_paths | 11.444 | 0.404 | 15.659 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.025 | 0.001 | 0.026 | |
| giant_component | 15.910 | 0.866 | 20.293 | |
| go_annot_download | 12.116 | 0.879 | 12.409 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.008 | 0.002 | 0.009 | |
| guide2pharma_download | 0.008 | 0.000 | 0.008 | |
| harmonizome_download | 0.007 | 0.002 | 0.008 | |
| has_extra_attrs | 12.933 | 1.584 | 19.558 | |
| hmdb_id_mapping_table | 0.029 | 0.000 | 0.061 | |
| hmdb_id_type | 0.002 | 0.000 | 0.006 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.170 | 0.002 | 0.276 | |
| homologene_download | 0.028 | 0.001 | 0.055 | |
| homologene_raw | 0.131 | 0.005 | 0.272 | |
| homologene_uniprot_orthology | 0.025 | 0.001 | 0.054 | |
| hpo_download | 0.023 | 0.003 | 0.044 | |
| htridb_download | 0.019 | 0.001 | 0.020 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.095 | 0.033 | 0.190 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 2.527 | 0.181 | 4.661 | |
| interaction_graph | 1.098 | 0.028 | 2.793 | |
| interaction_resources | 0.247 | 0.007 | 1.236 | |
| interaction_types | 0.210 | 0.003 | 0.306 | |
| intercell | 2.372 | 0.194 | 3.806 | |
| intercell_categories | 1.137 | 0.064 | 1.410 | |
| intercell_consensus_filter | 1.538 | 0.134 | 2.849 | |
| intercell_generic_categories | 0.100 | 0.002 | 0.101 | |
| intercell_network | 0.012 | 0.002 | 0.013 | |
| intercell_resources | 0.149 | 0.012 | 1.091 | |
| intercell_summary | 0.114 | 0.004 | 0.187 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.338 | 0.043 | 0.380 | |
| is_trembl | 0.334 | 0.043 | 0.378 | |
| is_uniprot | 0.014 | 0.001 | 0.015 | |
| kegg_api_templates | 0.001 | 0.000 | 0.001 | |
| kegg_conv | 3.646 | 0.560 | 17.709 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 1.787 | 0.140 | 4.215 | |
| kegg_find | 1.872 | 0.227 | 4.284 | |
| kegg_info | 0.026 | 0.000 | 0.027 | |
| kegg_link | 2.274 | 0.161 | 8.461 | |
| kegg_list | 2.938 | 0.325 | 4.322 | |
| kegg_open | 0.028 | 0.002 | 0.028 | |
| kegg_operations | 0.001 | 0.000 | 0.000 | |
| kegg_organism_codes | 0.027 | 0.012 | 0.039 | |
| kegg_organisms | 0.067 | 0.002 | 0.069 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.027 | 0.002 | 0.029 | |
| kegg_pathway_list | 0.021 | 0.000 | 0.021 | |
| kegg_pathways_download | 0.001 | 0.000 | 0.000 | |
| kegg_picture | 1.653 | 0.032 | 5.886 | |
| kegg_process | 0.028 | 0.003 | 0.030 | |
| kegg_query | 0.013 | 0.000 | 0.013 | |
| kegg_request | 0.109 | 0.005 | 0.114 | |
| kegg_rm_prefix | 1.789 | 0.184 | 6.926 | |
| kinasephos | 1.753 | 0.224 | 27.961 | |
| latin_name | 0.376 | 0.011 | 0.387 | |
| load_db | 0.466 | 0.076 | 0.536 | |
| macdb_metabolite_cancer_associations | 0.010 | 0.000 | 0.011 | |
| metabolic_atlas_list_gems | 0 | 0 | 0 | |
| metabolic_atlas_list_models | 0 | 0 | 0 | |
| metabolic_atlas_models | 0 | 0 | 0 | |
| metalinksdb_sqlite | 1.853 | 0.261 | 12.464 | |
| metalinksdb_table | 0.467 | 0.071 | 1.070 | |
| metalinksdb_tables | 0.032 | 0.014 | 0.091 | |
| metatlas_gem_genes | 0.022 | 0.001 | 0.046 | |
| metatlas_gem_metabolites | 0.020 | 0.002 | 0.043 | |
| metatlas_gem_reactions | 0.019 | 0.003 | 0.043 | |
| metatlas_gem_sbml | 0.019 | 0.003 | 0.042 | |
| metatlas_gem_tsv | 0.038 | 0.003 | 0.087 | |
| ncbi_taxid | 0.430 | 0.016 | 0.738 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.022 | 0.001 | 0.046 | |
| nichenet_gr_network | 0.057 | 0.005 | 0.122 | |
| nichenet_gr_network_evex | 0.022 | 0.001 | 0.044 | |
| nichenet_gr_network_harmonizome | 0.023 | 0.002 | 0.055 | |
| nichenet_gr_network_htridb | 0.022 | 0.001 | 0.047 | |
| nichenet_gr_network_omnipath | 31.180 | 1.588 | 50.649 | |
| nichenet_gr_network_pathwaycommons | 0.009 | 0.004 | 0.013 | |
| nichenet_gr_network_regnetwork | 0.011 | 0.001 | 0.011 | |
| nichenet_gr_network_remap | 0.011 | 0.000 | 0.010 | |
| nichenet_gr_network_trrust | 0.010 | 0.001 | 0.010 | |
| nichenet_ligand_activities | 0.001 | 0.000 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.040 | 0.001 | 0.040 | |
| nichenet_lr_network_guide2pharma | 0.017 | 0.001 | 0.017 | |
| nichenet_lr_network_omnipath | 0.041 | 0.008 | 0.048 | |
| nichenet_lr_network_ramilowski | 0.017 | 0.000 | 0.017 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.088 | 0.008 | 0.095 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.047 | 0.005 | 0.051 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.052 | 0.001 | 0.052 | |
| nichenet_signaling_network_cpdb | 0.015 | 0.002 | 0.016 | |
| nichenet_signaling_network_evex | 0.016 | 0.001 | 0.017 | |
| nichenet_signaling_network_harmonizome | 0.018 | 0.001 | 0.019 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 30.859 | 1.505 | 39.614 | |
| nichenet_signaling_network_pathwaycommons | 0.021 | 0.002 | 0.022 | |
| nichenet_signaling_network_vinayagam | 0.019 | 0.000 | 0.019 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.425 | 0.036 | 0.836 | |
| oma_code | 0.245 | 0.010 | 0.255 | |
| oma_organisms | 0.118 | 0.017 | 0.158 | |
| oma_pairwise | 0.018 | 0.001 | 0.019 | |
| oma_pairwise_genesymbols | 0.017 | 0.001 | 0.018 | |
| oma_pairwise_translated | 0.015 | 0.002 | 0.017 | |
| omnipath-interactions | 35.116 | 2.402 | 64.074 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.007 | 0.000 | 0.008 | |
| omnipath_cache_clean_db | 0.121 | 0.017 | 0.137 | |
| omnipath_cache_download_ready | 0.803 | 0.124 | 0.957 | |
| omnipath_cache_filter_versions | 0.752 | 0.119 | 0.879 | |
| omnipath_cache_get | 0.707 | 0.156 | 0.865 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_latest_or_new | 0.525 | 0.090 | 0.616 | |
| omnipath_cache_load | 1.295 | 0.152 | 3.891 | |
| omnipath_cache_move_in | 1.081 | 0.159 | 1.247 | |
| omnipath_cache_remove | 0.783 | 0.111 | 0.900 | |
| omnipath_cache_save | 0.865 | 0.122 | 1.104 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.002 | |
| omnipath_cache_set_ext | 0.595 | 0.117 | 0.710 | |
| omnipath_cache_update_status | 0.788 | 0.127 | 0.908 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 12.694 | 0.430 | 46.296 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.002 | 0.001 | 0.002 | |
| omnipath_msg | 0.009 | 0.001 | 0.010 | |
| omnipath_query | 5.091 | 0.113 | 5.161 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.136 | 0.020 | 0.154 | |
| omnipath_set_console_loglevel | 0.008 | 0.001 | 0.008 | |
| omnipath_set_logfile_loglevel | 0.007 | 0.000 | 0.006 | |
| omnipath_set_loglevel | 0.002 | 0.001 | 0.004 | |
| omnipath_show_db | 0.182 | 0.013 | 0.192 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.000 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_name | 0.002 | 0.000 | 0.001 | |
| ontology_name_id | 0.002 | 0.001 | 0.003 | |
| organism_for | 0.327 | 0.005 | 0.330 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 12.930 | 0.778 | 21.456 | |
| preppi_download | 0.001 | 0.000 | 0.000 | |
| preppi_filter | 0.000 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.327 | 0.023 | 1.183 | |
| print_bma_motif_vs | 0.508 | 0.047 | 1.434 | |
| print_interactions | 10.202 | 0.598 | 15.857 | |
| print_path_es | 0.624 | 0.023 | 1.443 | |
| print_path_vs | 3.091 | 0.129 | 5.146 | |
| pubmed_open | 7.158 | 0.179 | 7.514 | |
| query_info | 0.093 | 0.002 | 0.100 | |
| ramilowski_download | 0.000 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| ramp_id_type | 0.002 | 0.000 | 0.001 | |
| ramp_sqlite | 0.001 | 0.000 | 0.000 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| reactome_chebi | 0 | 0 | 0 | |
| reactome_chebi_pathways | 0 | 0 | 0 | |
| reactome_pathway_relations | 0 | 0 | 0 | |
| reactome_pathways | 0 | 0 | 0 | |
| recon3d | 0.001 | 0.001 | 0.003 | |
| recon3d_raw | 0.001 | 0.000 | 0.001 | |
| recon3d_raw_vmh | 0.001 | 0.000 | 0.000 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.232 | 0.012 | 0.392 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.098 | 0.006 | 0.147 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 1.108 | 0.083 | 1.424 | |
| resources | 0.148 | 0.006 | 0.948 | |
| resources_colname | 1.350 | 0.105 | 3.307 | |
| resources_in | 3.357 | 0.044 | 3.416 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 4.419 | 0.129 | 5.289 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 6.056 | 0.284 | 7.091 | |
| static_tables | 0.047 | 0.003 | 0.059 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.007 | 0.000 | 0.006 | |
| swap_relations | 0.070 | 0.007 | 0.118 | |
| swissprots_only | 0.129 | 0.001 | 0.130 | |
| tfcensus_download | 0.815 | 0.076 | 1.133 | |
| translate_ids | 1.356 | 0.094 | 10.509 | |
| translate_ids_multi | 8.408 | 0.598 | 31.938 | |
| trembls_only | 0.126 | 0.000 | 0.127 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.239 | 0.210 | 12.080 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.000 | 0.000 | |
| uniprot_id_mapping_table | 0 | 0 | 0 | |
| uniprot_id_type | 0 | 0 | 0 | |
| uniprot_idmapping_id_types | 0.938 | 0.112 | 1.604 | |
| uniprot_organisms | 0.121 | 0.003 | 0.124 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.001 | 0.000 | 0.001 | |
| vinayagam_download | 0.001 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.001 | |
| wikipathways_metabolites | 0 | 0 | 0 | |
| wikipathways_metabolites_sparql | 0 | 0 | 0 | |
| wikipathways_pathways | 0.001 | 0.000 | 0.001 | |
| with_extra_attrs | 10.691 | 1.395 | 11.973 | |
| with_references | 0.436 | 0.029 | 1.317 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |