Denes Turei
| Snapshot Date: 2025-11-20 15:01 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 7ab5630 |
| git_last_commit_date: 2025-11-17 12:48:40 -0500 (Mon, 17 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-24 12:07 -0500 (Mon, 24 Nov 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" | 4873 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4654 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4600 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 3.18.2 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 3.18.2 |
| 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_3.18.2.tar.gz |
| StartedAt: 2025-11-21 13:50:15 -0000 (Fri, 21 Nov 2025) |
| EndedAt: 2025-11-21 14:15:19 -0000 (Fri, 21 Nov 2025) |
| EllapsedTime: 1503.7 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_3.18.2.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 ‘3.18.2’
* 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
[2025-11-21 13:51:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-21 13:51:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:06] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 13:51:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-21 13:51:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-20
[2025-11-21 13:51:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-11-20 21:55:00 UTC; unix
[2025-11-21 13:51:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-21 13:51:06] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-21 13:51:07] [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=2025-11-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-11-21 13:51:07] [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]
[2025-11-21 13:51:07] [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 3.18.2(2025-11-20); 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)
[2025-11-21 13:51:07] [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
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-21 13:51:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-21 13:51:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-21 13:51:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-21 13:51:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-21 13:51:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:07] [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
[2025-11-21 13:51:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-21 13:51:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:35] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 13:51:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-21 13:51:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-20
[2025-11-21 13:51:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-11-20 21:55:00 UTC; unix
[2025-11-21 13:51:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-21 13:51:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-21 13:51:35] [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=2025-11-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-11-21 13:51:36] [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]
[2025-11-21 13:51:36] [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 3.18.2(2025-11-20); 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)
[2025-11-21 13:51:36] [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
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-21 13:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-21 13:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-21 13:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-21 13:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-21 13:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 13:51:36] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
Undefined global functions or variables:
enzyme_genesymbol
* 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 106.889 0.018 120.816
curated_ligrec_stats 44.274 4.914 189.452
filter_extra_attrs 37.624 5.547 52.858
omnipath-interactions 35.814 2.385 78.573
all_uniprots 32.269 2.590 96.522
uniprot_organisms 26.047 2.031 49.460
extra_attrs_to_cols 21.424 1.472 38.324
extra_attr_values 18.803 1.649 45.046
nichenet_gr_network_omnipath 19.312 0.932 25.716
with_extra_attrs 15.849 1.583 19.299
nichenet_signaling_network_omnipath 14.378 0.799 19.121
go_annot_download 13.527 0.511 26.532
giant_component 12.528 0.567 19.754
omnipath_for_cosmos 11.903 0.753 31.667
extra_attrs 11.280 1.299 20.352
filter_by_resource 11.629 0.561 20.284
has_extra_attrs 9.783 1.293 11.096
translate_ids_multi 10.072 0.495 27.138
pivot_annotations 9.674 0.405 29.520
curated_ligand_receptor_interactions 7.787 0.812 26.093
find_all_paths 7.702 0.446 13.753
print_interactions 7.392 0.354 14.478
filter_intercell 6.653 0.198 19.015
signed_ptms 6.376 0.323 7.803
pubmed_open 5.295 0.664 5.975
static_table 5.713 0.225 11.544
resources_in 4.704 0.328 5.047
hpo_download 3.042 0.539 22.638
print_path_vs 2.850 0.191 6.594
enzsub_graph 2.692 0.195 6.664
ensembl_id_mapping_table 2.677 0.143 20.691
database_summary 1.927 0.203 19.765
annotated_network 1.442 0.126 6.495
metalinksdb_sqlite 1.243 0.171 14.395
translate_ids 1.159 0.058 11.625
uniprot_full_id_mapping_table 1.025 0.055 13.510
* 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 ‘3.18.2’ ** 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 [2025-11-20 21:55:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-20 21:55:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:20] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-11-20 21:55:20] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-20 21:55:20] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-20 [2025-11-20 21:55:20] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-11-20 21:55:00 UTC; unix [2025-11-20 21:55:20] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2 [2025-11-20 21:55:20] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-11-20 21:55:20] [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=2025-11-20; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-11-20 21:55:20] [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] [2025-11-20 21:55:21] [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 3.18.2(2025-11-20); 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) [2025-11-20 21:55:21] [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 [2025-11-20 21:55:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-20 21:55:21] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-11-20 21:55:21] [TRACE] [OmnipathR] Contains 7 files. [2025-11-20 21:55:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-20 21:55:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-20 21:55:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-11-20 21:55:21] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-11-20 21:55:21] [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). [2025-11-20 21:55:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:21] [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). [2025-11-20 21:55:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-20 21:55:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:21] [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). [2025-11-20 21:55:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:21] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-11-20 21:55:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-20 21:55:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-11-20 21:55:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-20 21:55:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-20 [2025-11-20 21:55:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-11-20 21:55:00 UTC; unix [2025-11-20 21:55:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2 [2025-11-20 21:55:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-11-20 21:55:24] [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=2025-11-20; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-11-20 21:55:24] [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] [2025-11-20 21:55:24] [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 3.18.2(2025-11-20); 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) [2025-11-20 21:55:24] [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 [2025-11-20 21:55:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-20 21:55:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-11-20 21:55:24] [TRACE] [OmnipathR] Contains 1 files. [2025-11-20 21:55:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-20 21:55:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-20 21:55:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-11-20 21:55:24] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-11-20 21:55:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-20 21:55:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-20 21:55:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-20 21:55:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-20 21:55:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-20 21:55:24] [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)
[2025-11-21 14:13:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-21 14:13:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 14:13:21] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 14:13:21] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-21 14:13:21] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-20
[2025-11-21 14:13:21] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-11-20 21:55:00 UTC; unix
[2025-11-21 14:13:21] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-21 14:13:21] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-21 14:13:22] [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=2025-11-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-11-21 14:13:22] [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]
[2025-11-21 14:13:22] [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 3.18.2(2025-11-20); 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)
[2025-11-21 14:13:22] [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
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Contains 22 files.
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-21 14:13:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 14:13:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-11-21 14:13:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-21 14:13:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 14:13:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-21 14:13:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 14:13:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-21 14:13:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 14:13:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-21 14:13:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-21 14:13:23] [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
58.043 4.468 108.217
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.025 | 0.001 | 0.026 | |
| all_uniprots | 32.269 | 2.590 | 96.522 | |
| ancestors | 0.014 | 0.000 | 0.014 | |
| annotated_network | 1.442 | 0.126 | 6.495 | |
| annotation_categories | 106.889 | 0.018 | 120.816 | |
| annotation_resources | 0.073 | 0.016 | 1.191 | |
| annotations | 0.662 | 0.062 | 3.031 | |
| biomart_query | 1.344 | 0.064 | 3.668 | |
| bioplex1 | 0.015 | 0.000 | 0.014 | |
| bioplex2 | 0.013 | 0.000 | 0.013 | |
| bioplex3 | 0.013 | 0.000 | 0.013 | |
| bioplex_all | 0.013 | 0.000 | 0.013 | |
| bioplex_hct116_1 | 0.010 | 0.004 | 0.013 | |
| bma_motif_es | 0.763 | 0.022 | 2.851 | |
| bma_motif_vs | 0.246 | 0.024 | 1.417 | |
| chalmers_gem | 0.013 | 0.000 | 0.014 | |
| chalmers_gem_id_mapping_table | 0.013 | 0.000 | 0.014 | |
| chalmers_gem_id_type | 0.003 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.013 | 0.000 | 0.013 | |
| chalmers_gem_network | 0.012 | 0.000 | 0.012 | |
| chalmers_gem_raw | 0.008 | 0.004 | 0.012 | |
| chalmers_gem_reactions | 0.043 | 0.000 | 0.051 | |
| common_name | 0.138 | 0.008 | 0.217 | |
| complex_genes | 0.733 | 0.085 | 3.170 | |
| complex_resources | 0.082 | 0.004 | 1.140 | |
| complexes | 0.200 | 0.029 | 1.330 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.045 | 0.000 | 0.084 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.787 | 0.812 | 26.093 | |
| curated_ligrec_stats | 44.274 | 4.914 | 189.452 | |
| database_summary | 1.927 | 0.203 | 19.765 | |
| descendants | 0.012 | 0.000 | 0.012 | |
| ensembl_dataset | 0.059 | 0.000 | 0.059 | |
| ensembl_id_mapping_table | 2.677 | 0.143 | 20.691 | |
| ensembl_id_type | 0.002 | 0.000 | 0.003 | |
| ensembl_name | 0.368 | 0.000 | 0.369 | |
| ensembl_organisms | 0.150 | 0.016 | 0.166 | |
| ensembl_organisms_raw | 0.140 | 0.020 | 0.162 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.692 | 0.195 | 6.664 | |
| enzsub_resources | 0.086 | 0.005 | 1.128 | |
| enzyme_substrate | 1.435 | 0.043 | 2.871 | |
| evex_download | 0.014 | 0.000 | 0.025 | |
| evidences | 0.001 | 0.000 | 0.000 | |
| extra_attr_values | 18.803 | 1.649 | 45.046 | |
| extra_attrs | 11.280 | 1.299 | 20.352 | |
| extra_attrs_to_cols | 21.424 | 1.472 | 38.324 | |
| filter_by_resource | 11.629 | 0.561 | 20.284 | |
| filter_extra_attrs | 37.624 | 5.547 | 52.858 | |
| filter_intercell | 6.653 | 0.198 | 19.015 | |
| filter_intercell_network | 0.027 | 0.000 | 0.027 | |
| find_all_paths | 7.702 | 0.446 | 13.753 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.011 | 0.003 | 0.014 | |
| giant_component | 12.528 | 0.567 | 19.754 | |
| go_annot_download | 13.527 | 0.511 | 26.532 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.013 | 0.000 | 0.014 | |
| guide2pharma_download | 0.014 | 0.000 | 0.016 | |
| harmonizome_download | 0.014 | 0.000 | 0.018 | |
| has_extra_attrs | 9.783 | 1.293 | 11.096 | |
| hmdb_id_mapping_table | 0.013 | 0.000 | 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 | 0.011 | 0.004 | 0.015 | |
| homologene_raw | 0.073 | 0.000 | 0.072 | |
| homologene_uniprot_orthology | 0.014 | 0.000 | 0.014 | |
| hpo_download | 3.042 | 0.539 | 22.638 | |
| htridb_download | 0.009 | 0.004 | 0.013 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.054 | 0.009 | 0.063 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.770 | 0.035 | 1.341 | |
| interaction_graph | 0.499 | 0.016 | 1.599 | |
| interaction_resources | 0.086 | 0.004 | 1.163 | |
| interaction_types | 0.092 | 0.004 | 0.095 | |
| intercell | 0.923 | 0.087 | 2.116 | |
| intercell_categories | 0.772 | 0.036 | 1.340 | |
| intercell_consensus_filter | 1.528 | 0.078 | 3.600 | |
| intercell_generic_categories | 0.087 | 0.008 | 0.096 | |
| intercell_network | 0.012 | 0.000 | 0.013 | |
| intercell_resources | 0.072 | 0.009 | 0.957 | |
| intercell_summary | 0.103 | 0.000 | 0.104 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.071 | 0.003 | 0.076 | |
| is_trembl | 0.070 | 0.004 | 0.074 | |
| is_uniprot | 0.010 | 0.003 | 0.014 | |
| kegg_api_templates | 0.002 | 0.000 | 0.003 | |
| kegg_conv | 1.509 | 0.104 | 4.367 | |
| kegg_databases | 0.000 | 0.000 | 0.001 | |
| kegg_ddi | 0.635 | 0.057 | 1.987 | |
| kegg_find | 0.660 | 0.094 | 2.297 | |
| kegg_info | 0.012 | 0.000 | 0.013 | |
| kegg_link | 0.779 | 0.047 | 2.467 | |
| kegg_list | 0.666 | 0.114 | 1.221 | |
| kegg_open | 0.009 | 0.004 | 0.013 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.014 | 0.013 | 0.025 | |
| kegg_organisms | 0.029 | 0.004 | 0.033 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.013 | 0.000 | 0.013 | |
| kegg_pathway_list | 0.015 | 0.000 | 0.015 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.017 | 0.030 | 1.826 | |
| kegg_process | 0.019 | 0.008 | 0.028 | |
| kegg_query | 0.013 | 0.000 | 0.013 | |
| kegg_request | 0.089 | 0.000 | 0.089 | |
| kegg_rm_prefix | 0.808 | 0.096 | 2.316 | |
| kinasephos | 1.038 | 0.063 | 3.511 | |
| latin_name | 0.288 | 0.012 | 0.302 | |
| load_db | 0.114 | 0.000 | 0.115 | |
| metalinksdb_sqlite | 1.243 | 0.171 | 14.395 | |
| metalinksdb_table | 0.247 | 0.041 | 0.289 | |
| metalinksdb_tables | 0.023 | 0.004 | 0.026 | |
| ncbi_taxid | 0.299 | 0.007 | 0.307 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.011 | 0.005 | 0.014 | |
| nichenet_gr_network | 0.034 | 0.004 | 0.038 | |
| nichenet_gr_network_evex | 0.013 | 0.000 | 0.013 | |
| nichenet_gr_network_harmonizome | 0.009 | 0.004 | 0.013 | |
| nichenet_gr_network_htridb | 0.012 | 0.000 | 0.012 | |
| nichenet_gr_network_omnipath | 19.312 | 0.932 | 25.716 | |
| nichenet_gr_network_pathwaycommons | 0.014 | 0.000 | 0.014 | |
| nichenet_gr_network_regnetwork | 0.011 | 0.000 | 0.012 | |
| nichenet_gr_network_remap | 0.012 | 0.000 | 0.012 | |
| nichenet_gr_network_trrust | 0.012 | 0.000 | 0.012 | |
| nichenet_ligand_activities | 0.001 | 0.000 | 0.000 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.036 | 0.000 | 0.036 | |
| nichenet_lr_network_guide2pharma | 0.012 | 0.000 | 0.012 | |
| nichenet_lr_network_omnipath | 0.031 | 0.004 | 0.035 | |
| nichenet_lr_network_ramilowski | 0.011 | 0.000 | 0.011 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.054 | 0.004 | 0.058 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.035 | 0.000 | 0.035 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.036 | 0.000 | 0.036 | |
| nichenet_signaling_network_cpdb | 0.011 | 0.000 | 0.011 | |
| nichenet_signaling_network_evex | 0.012 | 0.000 | 0.012 | |
| nichenet_signaling_network_harmonizome | 0.012 | 0.000 | 0.012 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 14.378 | 0.799 | 19.121 | |
| nichenet_signaling_network_pathwaycommons | 0.010 | 0.005 | 0.014 | |
| nichenet_signaling_network_vinayagam | 0.014 | 0.000 | 0.014 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.115 | 0.008 | 1.211 | |
| oma_code | 0.159 | 0.000 | 0.162 | |
| oma_organisms | 0.081 | 0.007 | 0.090 | |
| oma_pairwise | 0.013 | 0.001 | 0.013 | |
| oma_pairwise_genesymbols | 0.013 | 0.000 | 0.013 | |
| oma_pairwise_translated | 0.013 | 0.000 | 0.013 | |
| omnipath-interactions | 35.814 | 2.385 | 78.573 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.010 | 0.004 | 0.013 | |
| omnipath_cache_clean_db | 0.142 | 0.012 | 0.153 | |
| omnipath_cache_download_ready | 0.642 | 0.061 | 0.720 | |
| omnipath_cache_filter_versions | 0.122 | 0.003 | 0.148 | |
| omnipath_cache_get | 0.104 | 0.012 | 0.118 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.002 | |
| omnipath_cache_latest_or_new | 0.078 | 0.004 | 0.084 | |
| omnipath_cache_load | 0.517 | 0.041 | 3.295 | |
| omnipath_cache_move_in | 0.283 | 0.014 | 0.307 | |
| omnipath_cache_remove | 0.107 | 0.020 | 0.134 | |
| omnipath_cache_save | 0.183 | 0.020 | 0.315 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.081 | 0.020 | 0.108 | |
| omnipath_cache_update_status | 0.096 | 0.021 | 0.117 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 11.903 | 0.753 | 31.667 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.002 | 0.000 | 0.002 | |
| omnipath_msg | 0.006 | 0.000 | 0.007 | |
| omnipath_query | 4.718 | 0.145 | 4.867 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.031 | 0.004 | 0.035 | |
| omnipath_set_console_loglevel | 0.005 | 0.000 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.004 | 0.000 | 0.005 | |
| omnipath_set_loglevel | 0.002 | 0.000 | 0.003 | |
| omnipath_show_db | 0.079 | 0.008 | 0.088 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.191 | 0.008 | 0.199 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 9.674 | 0.405 | 29.520 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.548 | 0.052 | 2.203 | |
| print_bma_motif_vs | 0.176 | 0.016 | 1.269 | |
| print_interactions | 7.392 | 0.354 | 14.478 | |
| print_path_es | 0.836 | 0.066 | 3.038 | |
| print_path_vs | 2.850 | 0.191 | 6.594 | |
| pubmed_open | 5.295 | 0.664 | 5.975 | |
| query_info | 0.407 | 0.053 | 0.989 | |
| ramilowski_download | 0.001 | 0.000 | 0.000 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| ramp_id_type | 0.003 | 0.000 | 0.002 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| recon3d | 0.003 | 0.000 | 0.002 | |
| recon3d_raw | 0.001 | 0.000 | 0.000 | |
| recon3d_raw_vmh | 0.001 | 0.000 | 0.000 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.097 | 0.020 | 1.429 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.099 | 0.027 | 0.379 | |
| remap_dorothea_download | 0.000 | 0.001 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.462 | 0.073 | 1.071 | |
| resources | 0.070 | 0.004 | 1.336 | |
| resources_colname | 1.115 | 0.108 | 3.452 | |
| resources_in | 4.704 | 0.328 | 5.047 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 6.376 | 0.323 | 7.803 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 5.713 | 0.225 | 11.544 | |
| static_tables | 0.145 | 0.008 | 0.331 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.010 | 0.000 | 0.009 | |
| swap_relations | 0.085 | 0.016 | 0.338 | |
| swissprots_only | 0.155 | 0.004 | 0.159 | |
| tfcensus_download | 0.506 | 0.053 | 0.722 | |
| translate_ids | 1.159 | 0.058 | 11.625 | |
| translate_ids_multi | 10.072 | 0.495 | 27.138 | |
| trembls_only | 0.215 | 0.008 | 0.223 | |
| trrust_download | 0.001 | 0.000 | 0.000 | |
| uniprot_full_id_mapping_table | 1.025 | 0.055 | 13.510 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.000 | 0.000 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.002 | 0.000 | 0.003 | |
| uniprot_idmapping_id_types | 0.488 | 0.015 | 1.603 | |
| uniprot_organisms | 26.047 | 2.031 | 49.460 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
| vinayagam_download | 0.000 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.002 | 0.000 | 0.001 | |
| with_extra_attrs | 15.849 | 1.583 | 19.299 | |
| with_references | 0.962 | 0.044 | 3.122 | |
| zenodo_download | 0.001 | 0.000 | 0.002 | |