Denes Turei
| Snapshot Date: 2025-12-03 13:40 -0500 (Wed, 03 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: 0f1c5d0 |
| git_last_commit_date: 2025-11-17 12:47:44 -0500 (Mon, 17 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-04 11:35 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 1490/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.2 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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. |
| Package: OmnipathR |
| Version: 3.19.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.19.2.tar.gz |
| StartedAt: 2025-12-04 02:00:47 -0500 (Thu, 04 Dec 2025) |
| EndedAt: 2025-12-04 02:21:19 -0500 (Thu, 04 Dec 2025) |
| EllapsedTime: 1232.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.19.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.2’
* 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 whether startup messages can be suppressed ... NOTE
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-04 02:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:01:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-04 02:01:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-03
[2025-12-04 02:01:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-03 20:07:13 UTC; unix
[2025-12-04 02:01:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2
[2025-12-04 02:01:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-04 02:01:05] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-04; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-04 02:01:05] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-04 02:01:05] [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 0.6.39(2025-11-19); 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 3.19.2(2025-12-03); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-04 02:01:05] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-04 02:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-04 02:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-04 02:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-04 02:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-04 02:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:05] [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
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-04 02:01:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:17] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:01:17] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-04 02:01:17] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-03
[2025-12-04 02:01:17] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-03 20:07:13 UTC; unix
[2025-12-04 02:01:17] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2
[2025-12-04 02:01:17] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-04 02:01:17] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-04; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-04 02:01:17] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-04 02:01:17] [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 0.6.39(2025-11-19); 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 3.19.2(2025-12-03); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-04 02:01:17] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-04 02:01:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-04 02:01:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-04 02:01:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-04 02:01:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-04 02:01:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:01:17] [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 40.585 0.073 44.509
curated_ligrec_stats 17.166 2.710 150.745
omnipath-interactions 13.663 1.513 85.344
filter_extra_attrs 10.399 4.557 23.553
all_uniprots 8.296 1.137 34.448
uniprot_organisms 6.149 0.964 13.330
go_annot_download 6.515 0.473 8.490
nichenet_gr_network_omnipath 6.217 0.740 21.612
extra_attrs_to_cols 5.567 1.092 9.238
extra_attr_values 5.026 1.182 37.465
pivot_annotations 5.449 0.748 135.227
with_extra_attrs 4.989 1.051 11.860
nichenet_signaling_network_omnipath 5.303 0.629 21.838
giant_component 4.895 0.486 12.067
omnipath_for_cosmos 4.335 0.375 49.012
translate_ids_multi 4.188 0.325 45.455
extra_attrs 3.216 1.109 5.019
filter_by_resource 3.611 0.274 8.199
has_extra_attrs 2.777 0.892 6.310
curated_ligand_receptor_interactions 2.857 0.700 30.352
filter_intercell 3.123 0.218 11.930
print_interactions 2.708 0.253 38.697
ensembl_id_mapping_table 1.365 0.135 30.647
print_path_vs 1.081 0.132 5.871
enzsub_graph 0.924 0.090 5.211
metalinksdb_sqlite 0.582 0.205 29.796
kegg_conv 0.660 0.099 22.902
biomart_query 0.610 0.085 8.196
annotated_network 0.577 0.066 5.653
translate_ids 0.504 0.111 10.508
kinasephos 0.505 0.096 25.934
uniprot_full_id_mapping_table 0.475 0.101 12.591
with_references 0.441 0.058 5.395
kegg_rm_prefix 0.341 0.050 12.895
kegg_link 0.325 0.045 6.126
* 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
‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.2’ ** 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 [2025-12-03 15:07:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-03 15:07:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:18] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-12-03 15:07:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-03 15:07:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-03 [2025-12-03 15:07:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-03 20:07:13 UTC; unix [2025-12-03 15:07:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-03 15:07:18] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-03 15:07:19] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-03; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-12-03 15:07:19] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-12-03 15:07:19] [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 0.6.39(2025-11-19); 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 3.19.2(2025-12-03); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-03 15:07:19] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-12-03 15:07:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-03 15:07:19] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-12-03 15:07:19] [TRACE] [OmnipathR] Contains 1 files. [2025-12-03 15:07:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-03 15:07:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-03 15:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-12-03 15:07:19] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-12-03 15:07:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-03 15:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-03 15:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-03 15:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-03 15:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:19] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-12-03 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-03 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-12-03 15:07:20] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-03 15:07:20] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-03 [2025-12-03 15:07:20] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-03 20:07:13 UTC; unix [2025-12-03 15:07:20] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-03 15:07:20] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-03 15:07:20] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-03; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-12-03 15:07:20] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-12-03 15:07:20] [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 0.6.39(2025-11-19); 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 3.19.2(2025-12-03); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-03 15:07:20] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-12-03 15:07:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-03 15:07:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-12-03 15:07:20] [TRACE] [OmnipathR] Contains 1 files. [2025-12-03 15:07:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-03 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-03 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-12-03 15:07:20] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-12-03 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-03 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-03 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-03 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-03 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-03 15:07:20] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin20
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> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-12-04 02:19:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-04 02:19:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:19:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:19:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-04 02:19:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-03
[2025-12-04 02:19:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-03 20:07:13 UTC; unix
[2025-12-04 02:19:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2
[2025-12-04 02:19:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-04 02:19:50] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-04; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-04 02:19:50] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-04 02:19:51] [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); 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 0.6.39(2025-11-19); 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 3.19.2(2025-12-03); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.1(2025-11-25); 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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-04 02:19:51] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Contains 22 files.
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-04 02:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:19:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-04 02:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-04 02:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-04 02:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:19:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-04 02:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-04 02:19:51] [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
16.971 2.384 81.624
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.006 | 0.002 | 0.016 | |
| all_uniprots | 8.296 | 1.137 | 34.448 | |
| ancestors | 0.003 | 0.001 | 0.012 | |
| annotated_network | 0.577 | 0.066 | 5.653 | |
| annotation_categories | 40.585 | 0.073 | 44.509 | |
| annotation_resources | 0.036 | 0.009 | 1.043 | |
| annotations | 0.334 | 0.036 | 2.267 | |
| biomart_query | 0.610 | 0.085 | 8.196 | |
| bioplex1 | 0.003 | 0.000 | 0.003 | |
| bioplex2 | 0.003 | 0.001 | 0.012 | |
| bioplex3 | 0.003 | 0.001 | 0.004 | |
| bioplex_all | 0.004 | 0.001 | 0.018 | |
| bioplex_hct116_1 | 0.003 | 0.001 | 0.033 | |
| bma_motif_es | 0.353 | 0.051 | 2.720 | |
| bma_motif_vs | 0.128 | 0.017 | 1.080 | |
| chalmers_gem | 0.006 | 0.001 | 0.007 | |
| chalmers_gem_id_mapping_table | 0.006 | 0.001 | 0.007 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.001 | 0.007 | |
| chalmers_gem_network | 0.007 | 0.001 | 0.007 | |
| chalmers_gem_raw | 0.006 | 0.001 | 0.007 | |
| chalmers_gem_reactions | 0.006 | 0.001 | 0.008 | |
| common_name | 0.052 | 0.004 | 0.088 | |
| complex_genes | 0.310 | 0.038 | 3.110 | |
| complex_resources | 0.022 | 0.005 | 1.125 | |
| complexes | 0.069 | 0.012 | 0.993 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.004 | 0.001 | 0.030 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 2.857 | 0.700 | 30.352 | |
| curated_ligrec_stats | 17.166 | 2.710 | 150.745 | |
| database_summary | 0.638 | 0.079 | 3.676 | |
| descendants | 0.003 | 0.001 | 0.011 | |
| ensembl_dataset | 0.021 | 0.001 | 0.042 | |
| ensembl_id_mapping_table | 1.365 | 0.135 | 30.647 | |
| ensembl_id_type | 0.001 | 0.000 | 0.001 | |
| ensembl_name | 0.244 | 0.009 | 0.306 | |
| ensembl_organisms | 0.038 | 0.008 | 0.140 | |
| ensembl_organisms_raw | 0.042 | 0.014 | 0.130 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 0.924 | 0.090 | 5.211 | |
| enzsub_resources | 0.023 | 0.006 | 1.044 | |
| enzyme_substrate | 0.704 | 0.065 | 4.084 | |
| evex_download | 0.009 | 0.001 | 0.031 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 5.026 | 1.182 | 37.465 | |
| extra_attrs | 3.216 | 1.109 | 5.019 | |
| extra_attrs_to_cols | 5.567 | 1.092 | 9.238 | |
| filter_by_resource | 3.611 | 0.274 | 8.199 | |
| filter_extra_attrs | 10.399 | 4.557 | 23.553 | |
| filter_intercell | 3.123 | 0.218 | 11.930 | |
| filter_intercell_network | 0.006 | 0.000 | 0.006 | |
| find_all_paths | 2.682 | 0.184 | 3.007 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_ontology_db | 0.002 | 0.001 | 0.003 | |
| giant_component | 4.895 | 0.486 | 12.067 | |
| go_annot_download | 6.515 | 0.473 | 8.490 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.002 | 0.000 | 0.004 | |
| guide2pharma_download | 0.002 | 0.000 | 0.003 | |
| harmonizome_download | 0.003 | 0.001 | 0.022 | |
| has_extra_attrs | 2.777 | 0.892 | 6.310 | |
| hmdb_id_mapping_table | 0.002 | 0.001 | 0.003 | |
| hmdb_id_type | 0.001 | 0.000 | 0.001 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.003 | 0.001 | 0.003 | |
| homologene_download | 0.002 | 0.001 | 0.004 | |
| homologene_raw | 0.025 | 0.002 | 0.033 | |
| homologene_uniprot_orthology | 0.003 | 0.001 | 0.005 | |
| hpo_download | 1.265 | 0.122 | 1.947 | |
| htridb_download | 0.003 | 0.001 | 0.003 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.014 | 0.003 | 0.031 | |
| inbiomap_download | 0.000 | 0.001 | 0.000 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.314 | 0.034 | 2.965 | |
| interaction_graph | 0.167 | 0.016 | 1.358 | |
| interaction_resources | 0.022 | 0.008 | 1.116 | |
| interaction_types | 0.028 | 0.003 | 0.060 | |
| intercell | 0.380 | 0.046 | 3.288 | |
| intercell_categories | 0.290 | 0.033 | 0.819 | |
| intercell_consensus_filter | 0.667 | 0.074 | 3.682 | |
| intercell_generic_categories | 0.034 | 0.004 | 0.116 | |
| intercell_network | 0.002 | 0.001 | 0.003 | |
| intercell_resources | 0.023 | 0.004 | 0.811 | |
| intercell_summary | 0.030 | 0.009 | 0.071 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.022 | 0.003 | 0.035 | |
| is_trembl | 0.025 | 0.003 | 0.039 | |
| is_uniprot | 0.004 | 0.001 | 0.005 | |
| kegg_api_templates | 0.000 | 0.002 | 0.003 | |
| kegg_conv | 0.660 | 0.099 | 22.902 | |
| kegg_databases | 0.000 | 0.001 | 0.000 | |
| kegg_ddi | 0.289 | 0.036 | 1.798 | |
| kegg_find | 0.279 | 0.037 | 1.999 | |
| kegg_info | 0.002 | 0.001 | 0.003 | |
| kegg_link | 0.325 | 0.045 | 6.126 | |
| kegg_list | 0.285 | 0.035 | 1.397 | |
| kegg_open | 0.004 | 0.000 | 0.019 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.008 | 0.035 | 0.057 | |
| kegg_organisms | 0.009 | 0.004 | 0.029 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.004 | 0.001 | 0.007 | |
| kegg_pathway_list | 0.002 | 0.000 | 0.003 | |
| kegg_pathways_download | 0.001 | 0.001 | 0.000 | |
| kegg_picture | 0.574 | 0.024 | 4.484 | |
| kegg_process | 0.006 | 0.001 | 0.007 | |
| kegg_query | 0.003 | 0.000 | 0.003 | |
| kegg_request | 0.025 | 0.004 | 0.046 | |
| kegg_rm_prefix | 0.341 | 0.050 | 12.895 | |
| kinasephos | 0.505 | 0.096 | 25.934 | |
| latin_name | 0.115 | 0.007 | 0.150 | |
| load_db | 0.028 | 0.007 | 0.117 | |
| metalinksdb_sqlite | 0.582 | 0.205 | 29.796 | |
| metalinksdb_table | 0.095 | 0.022 | 0.135 | |
| metalinksdb_tables | 0.007 | 0.001 | 0.008 | |
| ncbi_taxid | 0.099 | 0.005 | 0.105 | |
| nichenet_build_model | 0.000 | 0.001 | 0.000 | |
| nichenet_expression_data | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network | 0.010 | 0.003 | 0.013 | |
| nichenet_gr_network_evex | 0.003 | 0.000 | 0.004 | |
| nichenet_gr_network_harmonizome | 0.004 | 0.001 | 0.005 | |
| nichenet_gr_network_htridb | 0.003 | 0.001 | 0.003 | |
| nichenet_gr_network_omnipath | 6.217 | 0.740 | 21.612 | |
| nichenet_gr_network_pathwaycommons | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network_regnetwork | 0.003 | 0.001 | 0.006 | |
| nichenet_gr_network_remap | 0.003 | 0.001 | 0.003 | |
| nichenet_gr_network_trrust | 0.002 | 0.001 | 0.004 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.000 | |
| nichenet_lr_network | 0.010 | 0.002 | 0.024 | |
| nichenet_lr_network_guide2pharma | 0.003 | 0.001 | 0.004 | |
| nichenet_lr_network_omnipath | 0.033 | 0.003 | 0.042 | |
| nichenet_lr_network_ramilowski | 0.003 | 0.000 | 0.004 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.013 | 0.003 | 0.017 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.008 | 0.002 | 0.010 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network | 0.009 | 0.002 | 0.013 | |
| nichenet_signaling_network_cpdb | 0.002 | 0.000 | 0.003 | |
| nichenet_signaling_network_evex | 0.002 | 0.000 | 0.003 | |
| nichenet_signaling_network_harmonizome | 0.002 | 0.001 | 0.007 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.001 | 0.000 | |
| nichenet_signaling_network_omnipath | 5.303 | 0.629 | 21.838 | |
| nichenet_signaling_network_pathwaycommons | 0.003 | 0.001 | 0.004 | |
| nichenet_signaling_network_vinayagam | 0.003 | 0.001 | 0.004 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.045 | 0.013 | 0.626 | |
| oma_code | 0.052 | 0.003 | 0.063 | |
| oma_organisms | 0.030 | 0.008 | 0.043 | |
| oma_pairwise | 0.004 | 0.000 | 0.004 | |
| oma_pairwise_genesymbols | 0.004 | 0.000 | 0.004 | |
| oma_pairwise_translated | 0.002 | 0.001 | 0.003 | |
| omnipath-interactions | 13.663 | 1.513 | 85.344 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_clean | 0.004 | 0.002 | 0.006 | |
| omnipath_cache_clean_db | 0.062 | 0.013 | 0.082 | |
| omnipath_cache_download_ready | 0.333 | 0.083 | 1.527 | |
| omnipath_cache_filter_versions | 0.060 | 0.018 | 0.103 | |
| omnipath_cache_get | 0.051 | 0.013 | 0.066 | |
| omnipath_cache_key | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.035 | 0.010 | 0.051 | |
| omnipath_cache_load | 0.325 | 0.044 | 4.789 | |
| omnipath_cache_move_in | 0.122 | 0.028 | 0.173 | |
| omnipath_cache_remove | 0.057 | 0.019 | 0.099 | |
| omnipath_cache_save | 0.090 | 0.025 | 1.256 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_set_ext | 0.033 | 0.013 | 0.539 | |
| omnipath_cache_update_status | 0.052 | 0.011 | 0.067 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 4.335 | 0.375 | 49.012 | |
| omnipath_load_config | 0.000 | 0.001 | 0.000 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.001 | 0.001 | |
| omnipath_msg | 0.004 | 0.001 | 0.005 | |
| omnipath_query | 2.119 | 0.126 | 2.380 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.058 | 0.004 | 0.063 | |
| omnipath_set_console_loglevel | 0.003 | 0.000 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.001 | 0.001 | 0.002 | |
| omnipath_show_db | 0.05 | 0.01 | 0.06 | |
| omnipath_unlock_cache_db | 0.000 | 0.001 | 0.000 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.000 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.100 | 0.007 | 0.109 | |
| pathwaycommons_download | 0.000 | 0.000 | 0.001 | |
| pivot_annotations | 5.449 | 0.748 | 135.227 | |
| preppi_download | 0.000 | 0.001 | 0.001 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.297 | 0.042 | 1.807 | |
| print_bma_motif_vs | 0.056 | 0.012 | 1.967 | |
| print_interactions | 2.708 | 0.253 | 38.697 | |
| print_path_es | 0.397 | 0.047 | 3.037 | |
| print_path_vs | 1.081 | 0.132 | 5.871 | |
| pubmed_open | 1.752 | 0.095 | 2.010 | |
| query_info | 0.241 | 0.023 | 0.634 | |
| ramilowski_download | 0.001 | 0.000 | 0.000 | |
| ramp_id_mapping_table | 0.000 | 0.001 | 0.001 | |
| ramp_id_type | 0.001 | 0.000 | 0.001 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |
| recon3d | 0.001 | 0.000 | 0.001 | |
| recon3d_raw | 0 | 0 | 0 | |
| recon3d_raw_vmh | 0 | 0 | 0 | |
| regnetwork_directions | 0.000 | 0.001 | 0.000 | |
| regnetwork_download | 0.000 | 0.000 | 0.001 | |
| relations_list_to_table | 0.031 | 0.015 | 1.623 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.022 | 0.011 | 0.183 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.000 | 0.000 | 0.001 | |
| resource_info | 0.236 | 0.036 | 1.652 | |
| resources | 0.017 | 0.008 | 1.025 | |
| resources_colname | 0.613 | 0.036 | 4.378 | |
| resources_in | 1.510 | 0.086 | 1.703 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 2.241 | 0.118 | 3.448 | |
| simplify_intercell_network | 0.000 | 0.000 | 0.001 | |
| static_table | 2.971 | 0.174 | 4.409 | |
| static_tables | 0.017 | 0.004 | 0.027 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0.001 | 0.000 | 0.000 | |
| stitch_remove_prefixes | 0.005 | 0.001 | 0.005 | |
| swap_relations | 0.033 | 0.017 | 0.430 | |
| swissprots_only | 0.061 | 0.005 | 0.068 | |
| tfcensus_download | 0.282 | 0.036 | 1.522 | |
| translate_ids | 0.504 | 0.111 | 10.508 | |
| translate_ids_multi | 4.188 | 0.325 | 45.455 | |
| trembls_only | 0.049 | 0.003 | 0.059 | |
| trrust_download | 0.000 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 0.475 | 0.101 | 12.591 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0 | 0 | 0 | |
| uniprot_id_type | 0.000 | 0.000 | 0.001 | |
| uniprot_idmapping_id_types | 0.253 | 0.022 | 1.222 | |
| uniprot_organisms | 6.149 | 0.964 | 13.330 | |
| unique_intercell_network | 0 | 0 | 0 | |
| unnest_evidences | 0.000 | 0.000 | 0.001 | |
| uploadlists_id_type | 0.000 | 0.000 | 0.001 | |
| vinayagam_download | 0.001 | 0.000 | 0.001 | |
| walk_ontology_tree | 0 | 0 | 0 | |
| with_extra_attrs | 4.989 | 1.051 | 11.860 | |
| with_references | 0.441 | 0.058 | 5.395 | |
| zenodo_download | 0.000 | 0.000 | 0.001 | |