Denes Turei
| Snapshot Date: 2025-12-15 13:45 -0500 (Mon, 15 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 27b34f4 |
| git_last_commit_date: 2025-12-10 09:01:42 -0500 (Wed, 10 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-18 12:08 -0500 (Thu, 18 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4882 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4673 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4607 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4671 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.18.3 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.18.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.18.3.tar.gz |
| StartedAt: 2025-12-16 14:27:02 -0000 (Tue, 16 Dec 2025) |
| EndedAt: 2025-12-16 14:54:35 -0000 (Tue, 16 Dec 2025) |
| EllapsedTime: 1652.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.18.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.18.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-12-16 14:28:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-16 14:28:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:28:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-16 14:28:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-15
[2025-12-16 14:28:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-12-15 21:13:47 UTC; unix
[2025-12-16 14:28:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2025-12-16 14:28:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-16 14:28:05] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-12-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-12-16 14:28:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-12-16 14:28:06] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.3(2025-12-15); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-12-16 14:28:06] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-16 14:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-16 14:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-16 14:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-16 14:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-16 14:28:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:06] [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
[2025-12-16 14:28:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-16 14:28:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:28:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-16 14:28:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-15
[2025-12-16 14:28:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-12-15 21:13:47 UTC; unix
[2025-12-16 14:28:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2025-12-16 14:28:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-16 14:28:37] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-12-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-12-16 14:28:37] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-12-16 14:28:37] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.3(2025-12-15); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-12-16 14:28:37] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-16 14:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-16 14:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-16 14:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-16 14:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-16 14:28:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:28:37] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
patch_httr2_keep_handle: no visible binding for global variable
‘handle’
patch_httr2_keep_handle: no visible global function definition for
‘ORIGINAL’
Undefined global functions or variables:
ORIGINAL enzyme_genesymbol handle
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 106.957 0.097 168.455
curated_ligrec_stats 44.084 3.631 201.498
filter_extra_attrs 36.505 6.319 44.576
omnipath-interactions 36.092 2.205 82.385
all_uniprots 32.255 2.374 72.961
uniprot_organisms 26.074 2.466 36.164
extra_attrs_to_cols 21.963 1.490 32.927
nichenet_gr_network_omnipath 20.723 0.960 25.930
extra_attr_values 19.198 1.684 40.780
with_extra_attrs 16.748 2.078 20.990
nichenet_signaling_network_omnipath 14.310 0.689 22.188
go_annot_download 14.003 0.380 33.354
giant_component 13.173 0.521 23.018
omnipath_for_cosmos 11.982 0.620 54.988
extra_attrs 11.022 1.365 18.014
filter_by_resource 11.630 0.677 24.793
translate_ids_multi 10.706 0.809 63.362
has_extra_attrs 10.055 1.398 11.670
pivot_annotations 9.527 0.486 27.173
curated_ligand_receptor_interactions 7.709 0.553 26.896
print_interactions 7.423 0.445 14.370
find_all_paths 7.388 0.157 9.174
filter_intercell 6.584 0.247 16.717
signed_ptms 6.369 0.277 7.692
static_table 6.007 0.181 14.226
pubmed_open 4.941 0.207 5.212
omnipath_query 4.767 0.221 5.034
hpo_download 2.853 0.581 27.392
print_path_vs 2.760 0.202 6.232
enzsub_graph 2.729 0.112 6.425
ensembl_id_mapping_table 2.541 0.197 55.373
annotated_network 1.446 0.285 6.580
biomart_query 1.364 0.044 6.488
metalinksdb_sqlite 1.077 0.251 16.115
translate_ids 1.176 0.056 20.772
uniprot_full_id_mapping_table 1.141 0.063 17.740
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.18.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-12-15 21:14:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-15 21:14:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:07] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-15 21:14:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-15 21:14:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-15 [2025-12-15 21:14:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-12-15 21:13:47 UTC; unix [2025-12-15 21:14:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3 [2025-12-15 21:14:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-12-15 21:14:07] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-12-15; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-12-15 21:14:07] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-12-15 21:14:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.3(2025-12-15); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-12-15 21:14:07] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-12-15 21:14:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-15 21:14:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-15 21:14:07] [TRACE] [OmnipathR] Contains 7 files. [2025-12-15 21:14:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-15 21:14:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-15 21:14:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-15 21:14:07] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-12-15 21:14:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-15 21:14:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-15 21:14:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-15 21:14:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-15 21:14:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:08] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-12-15 21:14:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-15 21:14:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-15 21:14:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-15 21:14:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-15 [2025-12-15 21:14:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-12-15 21:13:47 UTC; unix [2025-12-15 21:14:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3 [2025-12-15 21:14:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-12-15 21:14:11] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-12-15; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-12-15 21:14:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-12-15 21:14:11] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.3(2025-12-15); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-12-15 21:14:11] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-12-15 21:14:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-15 21:14:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-15 21:14:11] [TRACE] [OmnipathR] Contains 1 files. [2025-12-15 21:14:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-15 21:14:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-15 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-15 21:14:11] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-12-15 21:14:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-15 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-15 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-15 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-15 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-15 21:14:11] [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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-12-16 14:52:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-16 14:52:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:52:37] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:52:37] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-16 14:52:37] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-15
[2025-12-16 14:52:37] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-12-15 21:13:47 UTC; unix
[2025-12-16 14:52:37] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.3
[2025-12-16 14:52:37] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-16 14:52:38] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-12-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-12-16 14:52:38] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-12-16 14:52:38] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.3(2025-12-15); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-12-16 14:52:38] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Contains 22 files.
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-16 14:52:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:52:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-16 14:52:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-16 14:52:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-16 14:52:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-16 14:52:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-16 14:52:38] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
58.798 4.611 108.649
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.025 | 0.000 | 0.025 | |
| all_uniprots | 32.255 | 2.374 | 72.961 | |
| ancestors | 0.008 | 0.004 | 0.033 | |
| annotated_network | 1.446 | 0.285 | 6.580 | |
| annotation_categories | 106.957 | 0.097 | 168.455 | |
| annotation_resources | 0.078 | 0.013 | 1.158 | |
| annotations | 0.699 | 0.040 | 2.513 | |
| biomart_query | 1.364 | 0.044 | 6.488 | |
| bioplex1 | 0.008 | 0.004 | 0.012 | |
| bioplex2 | 0.013 | 0.000 | 0.012 | |
| bioplex3 | 0.013 | 0.000 | 0.012 | |
| bioplex_all | 0.012 | 0.000 | 0.012 | |
| bioplex_hct116_1 | 0.008 | 0.004 | 0.012 | |
| bma_motif_es | 0.767 | 0.070 | 3.118 | |
| bma_motif_vs | 0.258 | 0.017 | 1.416 | |
| chalmers_gem | 0.013 | 0.000 | 0.029 | |
| chalmers_gem_id_mapping_table | 0.012 | 0.000 | 0.021 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.009 | |
| chalmers_gem_metabolites | 0.013 | 0.000 | 0.027 | |
| chalmers_gem_network | 0.014 | 0.000 | 0.023 | |
| chalmers_gem_raw | 0.013 | 0.000 | 0.025 | |
| chalmers_gem_reactions | 0.012 | 0.000 | 0.021 | |
| common_name | 0.149 | 0.000 | 0.296 | |
| complex_genes | 0.769 | 0.055 | 3.686 | |
| complex_resources | 0.076 | 0.007 | 1.168 | |
| complexes | 0.221 | 0.030 | 1.495 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.042 | 0.008 | 0.050 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.709 | 0.553 | 26.896 | |
| curated_ligrec_stats | 44.084 | 3.631 | 201.498 | |
| database_summary | 1.929 | 0.119 | 3.570 | |
| descendants | 0.013 | 0.000 | 0.013 | |
| ensembl_dataset | 0.052 | 0.004 | 0.056 | |
| ensembl_id_mapping_table | 2.541 | 0.197 | 55.373 | |
| ensembl_id_type | 0.003 | 0.000 | 0.003 | |
| ensembl_name | 0.351 | 0.021 | 0.373 | |
| ensembl_organisms | 0.166 | 0.008 | 0.174 | |
| ensembl_organisms_raw | 0.141 | 0.029 | 0.176 | |
| ensembl_orthology | 0.001 | 0.000 | 0.000 | |
| enzsub_graph | 2.729 | 0.112 | 6.425 | |
| enzsub_resources | 0.088 | 0.001 | 0.963 | |
| enzyme_substrate | 1.452 | 0.078 | 3.151 | |
| evex_download | 0.014 | 0.000 | 0.014 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 19.198 | 1.684 | 40.780 | |
| extra_attrs | 11.022 | 1.365 | 18.014 | |
| extra_attrs_to_cols | 21.963 | 1.490 | 32.927 | |
| filter_by_resource | 11.630 | 0.677 | 24.793 | |
| filter_extra_attrs | 36.505 | 6.319 | 44.576 | |
| filter_intercell | 6.584 | 0.247 | 16.717 | |
| filter_intercell_network | 0.024 | 0.006 | 0.030 | |
| find_all_paths | 7.388 | 0.157 | 9.174 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.013 | 0.000 | 0.014 | |
| giant_component | 13.173 | 0.521 | 23.018 | |
| go_annot_download | 14.003 | 0.380 | 33.354 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.014 | 0.000 | 0.014 | |
| guide2pharma_download | 0.010 | 0.004 | 0.014 | |
| harmonizome_download | 0.010 | 0.004 | 0.014 | |
| has_extra_attrs | 10.055 | 1.398 | 11.670 | |
| hmdb_id_mapping_table | 0.010 | 0.004 | 0.013 | |
| hmdb_id_type | 0.003 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.013 | 0.000 | 0.013 | |
| homologene_download | 0.009 | 0.004 | 0.013 | |
| homologene_raw | 0.068 | 0.004 | 0.073 | |
| homologene_uniprot_orthology | 0.005 | 0.008 | 0.013 | |
| hpo_download | 2.853 | 0.581 | 27.392 | |
| htridb_download | 0.015 | 0.000 | 0.016 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.063 | 0.012 | 0.079 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.817 | 0.043 | 1.347 | |
| interaction_graph | 0.493 | 0.028 | 1.554 | |
| interaction_resources | 0.078 | 0.017 | 1.074 | |
| interaction_types | 0.087 | 0.012 | 0.100 | |
| intercell | 0.988 | 0.088 | 2.105 | |
| intercell_categories | 0.700 | 0.064 | 1.276 | |
| intercell_consensus_filter | 1.516 | 0.111 | 3.454 | |
| intercell_generic_categories | 0.094 | 0.008 | 0.103 | |
| intercell_network | 0.005 | 0.008 | 0.014 | |
| intercell_resources | 0.064 | 0.021 | 1.111 | |
| intercell_summary | 0.100 | 0.004 | 0.105 | |
| is_ontology_id | 0.001 | 0.000 | 0.000 | |
| is_swissprot | 0.070 | 0.008 | 0.078 | |
| is_trembl | 0.071 | 0.004 | 0.076 | |
| is_uniprot | 0.010 | 0.004 | 0.015 | |
| kegg_api_templates | 0.000 | 0.001 | 0.002 | |
| kegg_conv | 1.506 | 0.102 | 4.740 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.697 | 0.060 | 1.628 | |
| kegg_find | 0.672 | 0.048 | 1.800 | |
| kegg_info | 0.013 | 0.000 | 0.013 | |
| kegg_link | 0.736 | 0.047 | 2.351 | |
| kegg_list | 0.687 | 0.043 | 4.290 | |
| kegg_open | 0.010 | 0.004 | 0.014 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.015 | 0.013 | 0.028 | |
| kegg_organisms | 0.035 | 0.000 | 0.036 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.015 | 0.000 | 0.015 | |
| kegg_pathway_list | 0.010 | 0.004 | 0.014 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 1.007 | 0.026 | 1.727 | |
| kegg_process | 0.025 | 0.000 | 0.025 | |
| kegg_query | 0.010 | 0.000 | 0.011 | |
| kegg_request | 0.081 | 0.000 | 0.083 | |
| kegg_rm_prefix | 0.760 | 0.085 | 2.159 | |
| kinasephos | 1.067 | 0.068 | 4.234 | |
| latin_name | 0.299 | 0.007 | 0.309 | |
| load_db | 0.116 | 0.012 | 0.132 | |
| metalinksdb_sqlite | 1.077 | 0.251 | 16.115 | |
| metalinksdb_table | 0.262 | 0.036 | 0.304 | |
| metalinksdb_tables | 0.025 | 0.000 | 0.026 | |
| ncbi_taxid | 0.294 | 0.011 | 0.307 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.010 | 0.005 | 0.014 | |
| nichenet_gr_network | 0.038 | 0.000 | 0.039 | |
| nichenet_gr_network_evex | 0.012 | 0.000 | 0.013 | |
| nichenet_gr_network_harmonizome | 0.014 | 0.000 | 0.015 | |
| nichenet_gr_network_htridb | 0.013 | 0.000 | 0.014 | |
| nichenet_gr_network_omnipath | 20.723 | 0.960 | 25.930 | |
| nichenet_gr_network_pathwaycommons | 0.013 | 0.000 | 0.014 | |
| nichenet_gr_network_regnetwork | 0.012 | 0.000 | 0.013 | |
| nichenet_gr_network_remap | 0.013 | 0.000 | 0.013 | |
| nichenet_gr_network_trrust | 0.013 | 0.000 | 0.013 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.030 | 0.008 | 0.038 | |
| nichenet_lr_network_guide2pharma | 0.005 | 0.009 | 0.014 | |
| nichenet_lr_network_omnipath | 0.039 | 0.000 | 0.039 | |
| nichenet_lr_network_ramilowski | 0.013 | 0.000 | 0.013 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.061 | 0.003 | 0.066 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.035 | 0.004 | 0.040 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.037 | 0.004 | 0.042 | |
| nichenet_signaling_network_cpdb | 0.014 | 0.000 | 0.013 | |
| nichenet_signaling_network_evex | 0.010 | 0.004 | 0.014 | |
| nichenet_signaling_network_harmonizome | 0.013 | 0.000 | 0.014 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 14.310 | 0.689 | 22.188 | |
| nichenet_signaling_network_pathwaycommons | 0.180 | 0.000 | 0.182 | |
| nichenet_signaling_network_vinayagam | 0.009 | 0.008 | 0.017 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.119 | 0.028 | 1.052 | |
| oma_code | 0.169 | 0.004 | 0.174 | |
| oma_organisms | 0.089 | 0.013 | 0.106 | |
| oma_pairwise | 0.010 | 0.004 | 0.015 | |
| oma_pairwise_genesymbols | 0.013 | 0.000 | 0.014 | |
| oma_pairwise_translated | 0.010 | 0.004 | 0.014 | |
| omnipath-interactions | 36.092 | 2.205 | 82.385 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.012 | 0.004 | 0.017 | |
| omnipath_cache_clean_db | 0.139 | 0.029 | 0.170 | |
| omnipath_cache_download_ready | 0.654 | 0.098 | 0.785 | |
| omnipath_cache_filter_versions | 0.110 | 0.025 | 0.186 | |
| omnipath_cache_get | 0.107 | 0.008 | 0.118 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.081 | 0.000 | 0.084 | |
| omnipath_cache_load | 0.592 | 0.019 | 3.578 | |
| omnipath_cache_move_in | 0.168 | 0.029 | 0.206 | |
| omnipath_cache_remove | 0.106 | 0.028 | 0.141 | |
| omnipath_cache_save | 0.175 | 0.029 | 0.316 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.093 | 0.013 | 0.113 | |
| omnipath_cache_update_status | 0.214 | 0.008 | 0.225 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.002 | |
| omnipath_for_cosmos | 11.982 | 0.620 | 54.988 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.000 | 0.001 | |
| omnipath_msg | 0.007 | 0.000 | 0.007 | |
| omnipath_query | 4.767 | 0.221 | 5.034 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0.001 | 0.000 | 0.000 | |
| omnipath_set_cachedir | 0.032 | 0.009 | 0.041 | |
| omnipath_set_console_loglevel | 0.002 | 0.004 | 0.007 | |
| omnipath_set_logfile_loglevel | 0.007 | 0.000 | 0.006 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_show_db | 0.073 | 0.032 | 0.108 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.000 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0.000 | 0.001 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.208 | 0.008 | 0.217 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 9.527 | 0.486 | 27.173 | |
| preppi_download | 0.001 | 0.000 | 0.000 | |
| preppi_filter | 0.002 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.620 | 0.019 | 1.942 | |
| print_bma_motif_vs | 0.194 | 0.012 | 1.026 | |
| print_interactions | 7.423 | 0.445 | 14.370 | |
| print_path_es | 0.872 | 0.048 | 2.679 | |
| print_path_vs | 2.760 | 0.202 | 6.232 | |
| pubmed_open | 4.941 | 0.207 | 5.212 | |
| query_info | 0.415 | 0.258 | 1.161 | |
| ramilowski_download | 0.000 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| ramp_id_type | 0.003 | 0.000 | 0.003 | |
| ramp_sqlite | 0.000 | 0.000 | 0.001 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0 | 0 | 0 | |
| recon3d | 0.002 | 0.000 | 0.002 | |
| recon3d_raw | 0 | 0 | 0 | |
| recon3d_raw_vmh | 0 | 0 | 0 | |
| regnetwork_directions | 0.000 | 0.001 | 0.001 | |
| regnetwork_download | 0.000 | 0.001 | 0.001 | |
| relations_list_to_table | 0.105 | 0.017 | 1.257 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.078 | 0.020 | 0.348 | |
| remap_dorothea_download | 0.000 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.472 | 0.254 | 1.230 | |
| resources | 0.077 | 0.004 | 1.072 | |
| resources_colname | 1.169 | 0.033 | 3.437 | |
| resources_in | 4.683 | 0.201 | 4.932 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 6.369 | 0.277 | 7.692 | |
| simplify_intercell_network | 0.000 | 0.001 | 0.001 | |
| static_table | 6.007 | 0.181 | 14.226 | |
| static_tables | 0.167 | 0.008 | 0.342 | |
| stitch_actions | 0.000 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.000 | 0.001 | 0.001 | |
| stitch_remove_prefixes | 0.005 | 0.004 | 0.009 | |
| swap_relations | 0.079 | 0.025 | 0.355 | |
| swissprots_only | 0.155 | 0.004 | 0.160 | |
| tfcensus_download | 0.574 | 0.019 | 0.616 | |
| translate_ids | 1.176 | 0.056 | 20.772 | |
| translate_ids_multi | 10.706 | 0.809 | 63.362 | |
| trembls_only | 0.155 | 0.004 | 0.160 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.141 | 0.063 | 17.740 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| uniprot_id_type | 0.003 | 0.000 | 0.003 | |
| uniprot_idmapping_id_types | 0.467 | 0.033 | 1.422 | |
| uniprot_organisms | 26.074 | 2.466 | 36.164 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.002 | |
| vinayagam_download | 0.001 | 0.000 | 0.000 | |
| walk_ontology_tree | 0.002 | 0.000 | 0.001 | |
| with_extra_attrs | 16.748 | 2.078 | 20.990 | |
| with_references | 0.928 | 0.059 | 2.919 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |