Denes Turei
| Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_23 |
| git_last_commit: a4e9224 |
| git_last_commit_date: 2026-04-29 06:27:44 -0400 (Wed, 29 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-07 11:35 -0400 (Thu, 07 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4990 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4723 |
| 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 1541/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 4.0.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | OK | ERROR | ERROR | |||||||||
| 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: 4.0.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_4.0.0.tar.gz |
| StartedAt: 2026-05-07 03:00:43 -0400 (Thu, 07 May 2026) |
| EndedAt: 2026-05-07 03:40:21 -0400 (Thu, 07 May 2026) |
| EllapsedTime: 2378.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_4.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-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: 2026-05-07 07:00:44 UTC
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘4.0.0’
* 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
[2026-05-07 03:01:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-07 03:01:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:23] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:01:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-07 03:01:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-06
[2026-05-07 03:01:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-06 19:18:35 UTC; unix
[2026-05-07 03:01:23] [INFO] [OmnipathR] Package `OmnipathR` version: 4.0.0
[2026-05-07 03:01:23] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-05-07 03:01:28] [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=2026-05-07; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-05-07 03:01:28] [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-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-07 03:01:28] [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 4.0.0(2026-05-06); 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)
[2026-05-07 03:01:28] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-07 03:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-07 03:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-07 03:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-07 03:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-07 03:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:28] [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
[2026-05-07 03:01:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-07 03:01:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:01:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-07 03:01:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-06
[2026-05-07 03:01:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-06 19:18:35 UTC; unix
[2026-05-07 03:01:53] [INFO] [OmnipathR] Package `OmnipathR` version: 4.0.0
[2026-05-07 03:01:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-05-07 03:01:59] [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=2026-05-07; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-05-07 03:01:59] [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-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-07 03:01:59] [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 4.0.0(2026-05-06); 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)
[2026-05-07 03:01:59] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-07 03:01:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-07 03:01:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-07 03:01:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-07 03:01:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-07 03:01:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:01:59] [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 79.568 0.201 81.191
curated_ligrec_stats 47.550 3.920 123.092
omnipath-interactions 36.503 3.850 65.876
filter_extra_attrs 30.232 6.210 39.474
extra_attrs_to_cols 28.340 3.175 42.870
extra_attr_values 28.138 2.123 42.943
all_uniprots 25.584 2.060 40.198
go_annot_download 24.824 1.467 33.918
nichenet_gr_network_omnipath 21.060 1.506 27.194
has_extra_attrs 18.389 2.130 24.832
nichenet_signaling_network_omnipath 17.335 1.085 20.713
filter_by_resource 15.859 1.057 24.542
giant_component 15.286 1.074 25.921
extra_attrs 13.222 2.028 15.870
filter_intercell 13.978 1.199 25.077
pivot_annotations 10.662 1.103 18.645
with_extra_attrs 10.094 1.660 11.620
omnipath_for_cosmos 9.923 0.915 107.807
find_all_paths 8.946 0.382 9.308
curated_ligand_receptor_interactions 7.666 1.633 18.943
translate_ids_multi 6.547 0.649 7.161
print_interactions 6.346 0.490 10.632
static_table 5.986 0.397 7.119
kegg_conv 4.739 0.376 16.848
signed_ptms 4.493 0.225 5.318
ensembl_id_mapping_table 2.718 0.281 27.347
kegg_picture 2.474 0.122 6.246
metalinksdb_sqlite 1.966 0.519 11.631
kegg_find 1.805 0.230 6.671
kegg_ddi 1.702 0.152 5.012
translate_ids 1.437 0.369 11.512
kegg_rm_prefix 1.538 0.210 6.567
kinasephos 1.459 0.249 17.637
kegg_link 1.429 0.226 7.860
uniprot_full_id_mapping_table 1.355 0.171 13.878
biomart_query 1.231 0.174 12.260
* 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-3.23-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘4.0.0’ ** 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 [2026-05-06 15:18:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-06 15:18:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:50] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-06 15:18:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-06 15:18:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-06 [2026-05-06 15:18:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-06 19:18:35 UTC; unix [2026-05-06 15:18:50] [INFO] [OmnipathR] Package `OmnipathR` version: 4.0.0 [2026-05-06 15:18:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-05-06 15:18:51] [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=1.8.25 @ /usr/local/bin/quarto] [2026-05-06 15:18:51] [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-3.23-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 15:18:51] [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 4.0.0(2026-05-06); 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 15:18:51] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-06 15:18:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-06 15:18:51] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-06 15:18:51] [TRACE] [OmnipathR] Contains 20 files. [2026-05-06 15:18:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-06 15:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-06 15:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-06 15:18:51] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-05-06 15:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-06 15:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-06 15:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-06 15:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-06 15:18:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:51] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-05-06 15:18:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-06 15:18:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-06 15:18:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-06 15:18:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-06 [2026-05-06 15:18:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-06 19:18:35 UTC; unix [2026-05-06 15:18:53] [INFO] [OmnipathR] Package `OmnipathR` version: 4.0.0 [2026-05-06 15:18:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-05-06 15:18:54] [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=1.8.25 @ /usr/local/bin/quarto] [2026-05-06 15:18:54] [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-3.23-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 15:18:54] [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); 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 4.0.0(2026-05-06); 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 15:18:54] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-06 15:18:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-06 15:18:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-06 15:18:54] [TRACE] [OmnipathR] Contains 1 files. [2026-05-06 15:18:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-06 15:18:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-06 15:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-06 15:18:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-05-06 15:18:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-06 15:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-06 15:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-06 15:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-06 15:18:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-06 15:18:54] [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)
[2026-05-07 03:20:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-07 03:20:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:20:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:20:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-07 03:20:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-06
[2026-05-07 03:20:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-06 19:18:35 UTC; unix
[2026-05-07 03:20:36] [INFO] [OmnipathR] Package `OmnipathR` version: 4.0.0
[2026-05-07 03:20:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-05-07 03:20:37] [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=2026-05-07; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-05-07 03:20:37] [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-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-07 03:20:37] [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 4.0.0(2026-05-06); 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)
[2026-05-07 03:20:37] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-07 03:20:37] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-07 03:20:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:20:37] [TRACE] [OmnipathR] Contains 95 files.
[2026-05-07 03:20:37] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-07 03:20:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-07 03:20:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:20:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-07 03:20:38] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-05-07 03:20:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-07 03:20:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:20:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-07 03:20:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:20:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-07 03:20:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:20:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-07 03:20:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-07 03:20:38] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
49.556 4.150 83.040
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.016 | 0.003 | 0.019 | |
| all_uniprots | 25.584 | 2.060 | 40.198 | |
| ancestors | 0.009 | 0.002 | 0.010 | |
| annotated_network | 1.750 | 0.285 | 4.835 | |
| annotation_categories | 79.568 | 0.201 | 81.191 | |
| annotation_resources | 0.158 | 0.018 | 0.896 | |
| annotations | 0.769 | 0.201 | 1.815 | |
| biomart_query | 1.231 | 0.174 | 12.260 | |
| bioplex1 | 0.010 | 0.002 | 0.011 | |
| bioplex2 | 0.008 | 0.003 | 0.010 | |
| bioplex3 | 0.008 | 0.002 | 0.010 | |
| bioplex_all | 0.009 | 0.001 | 0.010 | |
| bioplex_hct116_1 | 0.008 | 0.002 | 0.010 | |
| bma_motif_es | 0.783 | 0.199 | 1.992 | |
| bma_motif_vs | 0.357 | 0.026 | 1.087 | |
| chalmers_gem | 0.010 | 0.001 | 0.011 | |
| chalmers_gem_id_mapping_table | 0.026 | 0.004 | 0.030 | |
| chalmers_gem_id_type | 0.000 | 0.000 | 0.001 | |
| chalmers_gem_metabolites | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_network | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_raw | 0.008 | 0.000 | 0.009 | |
| chalmers_gem_reactions | 0.009 | 0.000 | 0.009 | |
| common_name | 0.123 | 0.004 | 0.127 | |
| complex_genes | 0.866 | 0.106 | 2.619 | |
| complex_resources | 0.159 | 0.020 | 1.023 | |
| complexes | 0.369 | 0.031 | 1.044 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.008 | 0.001 | 0.009 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 7.666 | 1.633 | 18.943 | |
| curated_ligrec_stats | 47.550 | 3.920 | 123.092 | |
| database_summary | 1.806 | 0.123 | 3.134 | |
| descendants | 0.009 | 0.002 | 0.011 | |
| ensembl_dataset | 0.053 | 0.001 | 0.053 | |
| ensembl_id_mapping_table | 2.718 | 0.281 | 27.347 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.587 | 0.006 | 0.593 | |
| ensembl_organisms | 0.137 | 0.011 | 0.146 | |
| ensembl_organisms_raw | 0.124 | 0.013 | 0.136 | |
| ensembl_orthology | 0.001 | 0.000 | 0.001 | |
| enzsub_graph | 2.061 | 0.114 | 4.029 | |
| enzsub_resources | 0.210 | 0.008 | 0.858 | |
| enzyme_substrate | 0.954 | 0.046 | 1.681 | |
| evex_download | 0.008 | 0.001 | 0.010 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 28.138 | 2.123 | 42.943 | |
| extra_attrs | 13.222 | 2.028 | 15.870 | |
| extra_attrs_to_cols | 28.340 | 3.175 | 42.870 | |
| filter_by_resource | 15.859 | 1.057 | 24.542 | |
| filter_extra_attrs | 30.232 | 6.210 | 39.474 | |
| filter_intercell | 13.978 | 1.199 | 25.077 | |
| filter_intercell_network | 0.051 | 0.006 | 0.058 | |
| find_all_paths | 8.946 | 0.382 | 9.308 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0.000 | 0.001 | 0.000 | |
| get_ontology_db | 0.006 | 0.003 | 0.009 | |
| giant_component | 15.286 | 1.074 | 25.921 | |
| go_annot_download | 24.824 | 1.467 | 33.918 | |
| go_annot_slim | 0.001 | 0.000 | 0.001 | |
| go_ontology_download | 0.025 | 0.002 | 0.053 | |
| guide2pharma_download | 0.022 | 0.002 | 0.050 | |
| harmonizome_download | 0.019 | 0.001 | 0.023 | |
| has_extra_attrs | 18.389 | 2.130 | 24.832 | |
| hmdb_id_mapping_table | 0.023 | 0.001 | 0.025 | |
| hmdb_id_type | 0.000 | 0.002 | 0.002 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0.001 | 0.001 | 0.003 | |
| hmdb_table | 0.026 | 0.000 | 0.026 | |
| homologene_download | 0.021 | 0.001 | 0.022 | |
| homologene_raw | 0.119 | 0.004 | 0.125 | |
| homologene_uniprot_orthology | 0.020 | 0.004 | 0.024 | |
| hpo_download | 0.017 | 0.002 | 0.019 | |
| htridb_download | 0.018 | 0.000 | 0.018 | |
| id_translation_resources | 0.000 | 0.001 | 0.000 | |
| id_types | 0.113 | 0.004 | 0.117 | |
| inbiomap_download | 0.000 | 0.001 | 0.000 | |
| inbiomap_raw | 0.001 | 0.000 | 0.001 | |
| interaction_datasets | 0.958 | 0.035 | 1.301 | |
| interaction_graph | 0.441 | 0.022 | 1.221 | |
| interaction_resources | 0.169 | 0.010 | 0.896 | |
| interaction_types | 0.138 | 0.007 | 0.145 | |
| intercell | 1.626 | 0.555 | 2.906 | |
| intercell_categories | 1.311 | 0.169 | 1.663 | |
| intercell_consensus_filter | 2.546 | 0.248 | 4.144 | |
| intercell_generic_categories | 0.213 | 0.007 | 0.359 | |
| intercell_network | 0.023 | 0.001 | 0.033 | |
| intercell_resources | 0.182 | 0.006 | 1.072 | |
| intercell_summary | 0.142 | 0.032 | 0.241 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.542 | 0.110 | 0.844 | |
| is_trembl | 0.528 | 0.070 | 0.943 | |
| is_uniprot | 0.015 | 0.003 | 0.018 | |
| kegg_api_templates | 0.001 | 0.006 | 0.007 | |
| kegg_conv | 4.739 | 0.376 | 16.848 | |
| kegg_databases | 0.003 | 0.000 | 0.007 | |
| kegg_ddi | 1.702 | 0.152 | 5.012 | |
| kegg_find | 1.805 | 0.230 | 6.671 | |
| kegg_info | 0.027 | 0.004 | 0.062 | |
| kegg_link | 1.429 | 0.226 | 7.860 | |
| kegg_list | 0.757 | 0.136 | 1.784 | |
| kegg_open | 0.006 | 0.003 | 0.009 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.013 | 0.084 | 0.097 | |
| kegg_organisms | 0.017 | 0.004 | 0.021 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.008 | 0.002 | 0.010 | |
| kegg_pathway_list | 0.009 | 0.000 | 0.008 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 2.474 | 0.122 | 6.246 | |
| kegg_process | 0.013 | 0.006 | 0.019 | |
| kegg_query | 0.007 | 0.001 | 0.009 | |
| kegg_request | 0.061 | 0.007 | 0.068 | |
| kegg_rm_prefix | 1.538 | 0.210 | 6.567 | |
| kinasephos | 1.459 | 0.249 | 17.637 | |
| latin_name | 0.276 | 0.036 | 0.310 | |
| load_db | 0.529 | 0.118 | 0.657 | |
| macdb_metabolite_cancer_associations | 0.008 | 0.001 | 0.009 | |
| metabolic_atlas_list_gems | 0 | 0 | 0 | |
| metabolic_atlas_list_models | 0.000 | 0.001 | 0.000 | |
| metabolic_atlas_models | 0 | 0 | 0 | |
| metalinksdb_sqlite | 1.966 | 0.519 | 11.631 | |
| metalinksdb_table | 0.242 | 0.035 | 0.272 | |
| metalinksdb_tables | 0.019 | 0.004 | 0.023 | |
| metatlas_gem_genes | 0.010 | 0.002 | 0.012 | |
| metatlas_gem_metabolites | 0.011 | 0.000 | 0.011 | |
| metatlas_gem_reactions | 0.008 | 0.002 | 0.010 | |
| metatlas_gem_sbml | 0.007 | 0.003 | 0.011 | |
| metatlas_gem_tsv | 0.016 | 0.005 | 0.020 | |
| ncbi_taxid | 0.260 | 0.018 | 0.276 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.011 | 0.000 | 0.011 | |
| nichenet_gr_network | 0.025 | 0.001 | 0.027 | |
| nichenet_gr_network_evex | 0.007 | 0.002 | 0.009 | |
| nichenet_gr_network_harmonizome | 0.008 | 0.001 | 0.009 | |
| nichenet_gr_network_htridb | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_omnipath | 21.060 | 1.506 | 27.194 | |
| nichenet_gr_network_pathwaycommons | 0.009 | 0.000 | 0.010 | |
| nichenet_gr_network_regnetwork | 0.049 | 0.001 | 0.049 | |
| nichenet_gr_network_remap | 0.008 | 0.001 | 0.008 | |
| nichenet_gr_network_trrust | 0.007 | 0.002 | 0.008 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.024 | 0.001 | 0.023 | |
| nichenet_lr_network_guide2pharma | 0.007 | 0.002 | 0.008 | |
| nichenet_lr_network_omnipath | 0.021 | 0.003 | 0.024 | |
| nichenet_lr_network_ramilowski | 0.008 | 0.000 | 0.009 | |
| nichenet_main | 0.000 | 0.001 | 0.001 | |
| nichenet_networks | 0.040 | 0.001 | 0.041 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.020 | 0.004 | 0.024 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network | 0.021 | 0.004 | 0.025 | |
| nichenet_signaling_network_cpdb | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_evex | 0.008 | 0.000 | 0.009 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.001 | 0.008 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 17.335 | 1.085 | 20.713 | |
| nichenet_signaling_network_pathwaycommons | 0.009 | 0.001 | 0.010 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.001 | 0.009 | |
| nichenet_test | 0.001 | 0.000 | 0.001 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.165 | 0.031 | 0.387 | |
| oma_code | 0.219 | 0.006 | 0.225 | |
| oma_organisms | 0.063 | 0.003 | 0.066 | |
| oma_pairwise | 0.010 | 0.000 | 0.011 | |
| oma_pairwise_genesymbols | 0.007 | 0.002 | 0.009 | |
| oma_pairwise_translated | 0.01 | 0.00 | 0.01 | |
| omnipath-interactions | 36.503 | 3.850 | 65.876 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.009 | 0.002 | 0.011 | |
| omnipath_cache_clean_db | 0.106 | 0.032 | 0.137 | |
| omnipath_cache_download_ready | 0.848 | 0.203 | 1.076 | |
| omnipath_cache_filter_versions | 0.698 | 0.193 | 0.901 | |
| omnipath_cache_get | 0.891 | 0.220 | 1.268 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.525 | 0.101 | 0.628 | |
| omnipath_cache_load | 1.977 | 0.299 | 4.614 | |
| omnipath_cache_move_in | 2.129 | 0.510 | 4.054 | |
| omnipath_cache_remove | 1.448 | 0.284 | 1.748 | |
| omnipath_cache_save | 1.026 | 0.228 | 1.369 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.759 | 0.126 | 0.892 | |
| omnipath_cache_update_status | 0.794 | 0.201 | 0.998 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 9.923 | 0.915 | 107.807 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.002 | 0.000 | 0.002 | |
| omnipath_msg | 0.004 | 0.002 | 0.005 | |
| omnipath_query | 3.192 | 0.178 | 3.345 | |
| omnipath_reset_config | 0.001 | 0.000 | 0.000 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.061 | 0.011 | 0.070 | |
| omnipath_set_console_loglevel | 0.003 | 0.000 | 0.004 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.000 | 0.004 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.002 | |
| omnipath_show_db | 0.052 | 0.010 | 0.060 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0.000 | 0.001 | 0.000 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.168 | 0.007 | 0.175 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 10.662 | 1.103 | 18.645 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.300 | 0.010 | 0.954 | |
| print_bma_motif_vs | 0.296 | 0.037 | 1.124 | |
| print_interactions | 6.346 | 0.490 | 10.632 | |
| print_path_es | 0.443 | 0.047 | 1.244 | |
| print_path_vs | 1.781 | 0.234 | 3.298 | |
| pubmed_open | 3.501 | 0.255 | 3.719 | |
| query_info | 0.061 | 0.000 | 0.061 | |
| ramilowski_download | 0.000 | 0.001 | 0.001 | |
| ramp_id_mapping_table | 0.000 | 0.001 | 0.001 | |
| ramp_id_type | 0.000 | 0.000 | 0.001 | |
| ramp_sqlite | 0.000 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |
| reactome_chebi | 0.000 | 0.000 | 0.001 | |
| reactome_chebi_pathways | 0.001 | 0.000 | 0.000 | |
| reactome_pathway_relations | 0.000 | 0.001 | 0.000 | |
| reactome_pathways | 0 | 0 | 0 | |
| recon3d | 0.001 | 0.001 | 0.002 | |
| recon3d_raw | 0.000 | 0.000 | 0.001 | |
| recon3d_raw_vmh | 0.000 | 0.000 | 0.001 | |
| regnetwork_directions | 0.000 | 0.001 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.153 | 0.080 | 0.346 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.078 | 0.031 | 0.153 | |
| remap_dorothea_download | 0.000 | 0.001 | 0.001 | |
| remap_filtered | 0.000 | 0.001 | 0.000 | |
| remap_tf_target_download | 0.000 | 0.001 | 0.000 | |
| resource_info | 0.938 | 0.227 | 1.354 | |
| resources | 0.142 | 0.037 | 0.928 | |
| resources_colname | 1.488 | 0.277 | 3.522 | |
| resources_in | 3.243 | 0.348 | 3.595 | |
| show_network | 0.000 | 0.001 | 0.000 | |
| signed_ptms | 4.493 | 0.225 | 5.318 | |
| simplify_intercell_network | 0.001 | 0.001 | 0.001 | |
| static_table | 5.986 | 0.397 | 7.119 | |
| static_tables | 0.051 | 0.006 | 0.062 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.000 | 0.001 | 0.001 | |
| stitch_remove_prefixes | 0.005 | 0.001 | 0.006 | |
| swap_relations | 0.075 | 0.018 | 0.135 | |
| swissprots_only | 0.129 | 0.000 | 0.130 | |
| tfcensus_download | 0.799 | 0.125 | 1.052 | |
| translate_ids | 1.437 | 0.369 | 11.512 | |
| translate_ids_multi | 6.547 | 0.649 | 7.161 | |
| trembls_only | 0.130 | 0.001 | 0.130 | |
| trrust_download | 0.000 | 0.001 | 0.001 | |
| uniprot_full_id_mapping_table | 1.355 | 0.171 | 13.878 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.000 | 0.000 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.001 | 0.000 | 0.001 | |
| uniprot_idmapping_id_types | 0.830 | 0.122 | 1.373 | |
| uniprot_organisms | 0.102 | 0.010 | 0.113 | |
| unique_intercell_network | 0.000 | 0.001 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.001 | 0.000 | 0.000 | |
| vinayagam_download | 0.000 | 0.001 | 0.001 | |
| walk_ontology_tree | 0.000 | 0.001 | 0.002 | |
| wikipathways_metabolites | 0 | 0 | 0 | |
| wikipathways_metabolites_sparql | 0.001 | 0.000 | 0.000 | |
| wikipathways_pathways | 0 | 0 | 0 | |
| with_extra_attrs | 10.094 | 1.660 | 11.620 | |
| with_references | 0.398 | 0.026 | 1.174 | |
| zenodo_download | 0.000 | 0.001 | 0.001 | |