Denes Turei
| Snapshot Date: 2026-04-24 13:40 -0400 (Fri, 24 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: 886a999 |
| git_last_commit_date: 2026-04-20 21:32:47 -0400 (Mon, 20 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-25 11:36 -0400 (Sat, 25 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4978 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4722 |
| 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 1539/2415 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.99.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.99.0 |
| 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_3.99.0.tar.gz |
| StartedAt: 2026-04-24 21:17:19 -0400 (Fri, 24 Apr 2026) |
| EndedAt: 2026-04-24 21:33:09 -0400 (Fri, 24 Apr 2026) |
| EllapsedTime: 949.5 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_3.99.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-25 01:17:19 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-04-24 21:17:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-24 21:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:34] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:17:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-24 21:17:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-24
[2026-04-24 21:17:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-24 19:05:54 UTC; unix
[2026-04-24 21:17:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-24 21:17:34] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-24 21:17:35] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-08 r89818); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-24; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-24 21:17:35] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; 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=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-04-24 21:17:35] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-24); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-24 21:17:35] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-24 21:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-24 21:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-24 21:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-24 21:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-24 21:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:35] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-04-24 21:17:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-24 21:17:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:17:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-24 21:17:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-24
[2026-04-24 21:17:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-24 19:05:54 UTC; unix
[2026-04-24 21:17:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-24 21:17:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-24 21:17:43] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-08 r89818); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-24; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-24 21:17:43] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; 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=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-04-24 21:17:44] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-24); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-24 21:17:44] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-24 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-24 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-24 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-24 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-24 21:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:17:44] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 37.336 0.130 38.921
curated_ligrec_stats 15.014 4.554 90.805
filter_extra_attrs 12.531 5.777 25.409
omnipath-interactions 13.305 4.132 42.491
all_uniprots 7.868 1.046 23.140
nichenet_signaling_network_omnipath 7.129 0.744 11.300
nichenet_gr_network_omnipath 6.971 0.742 10.042
extra_attrs_to_cols 5.107 1.125 6.302
extra_attr_values 4.730 1.500 8.459
pivot_annotations 5.160 0.936 15.721
with_extra_attrs 4.694 1.289 6.284
go_annot_download 4.970 0.467 5.473
omnipath_for_cosmos 3.967 1.061 25.522
filter_by_resource 4.017 0.524 9.304
giant_component 3.970 0.478 7.213
print_interactions 3.279 0.975 8.796
static_table 3.306 0.537 10.800
curated_ligand_receptor_interactions 2.773 0.816 13.454
filter_intercell 2.764 0.278 7.121
kegg_conv 0.840 0.472 12.204
kinasephos 0.670 0.626 198.889
metalinksdb_sqlite 0.565 0.479 10.309
translate_ids 0.667 0.361 141.103
uniprot_full_id_mapping_table 0.594 0.272 12.712
kegg_rm_prefix 0.404 0.192 5.004
kegg_link 0.350 0.187 6.359
* 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/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.99.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-04-24 15:06:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-24 15:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:00] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-04-24 15:06:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-24 15:06:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-24 [2026-04-24 15:06:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-24 19:05:54 UTC; unix [2026-04-24 15:06:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.99.0 [2026-04-24 15:06:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-24 15:06:00] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-08 r89818); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-24; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-04-24 15:06:00] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; 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=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-04-24 15:06:00] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-24); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-24 15:06:00] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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 [2026-04-24 15:06:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-24 15:06:00] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-04-24 15:06:00] [TRACE] [OmnipathR] Contains 1 files. [2026-04-24 15:06:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-24 15:06:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-24 15:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-04-24 15:06:00] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-04-24 15:06:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-24 15:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-24 15:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-24 15:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-24 15:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:00] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-04-24 15:06:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-24 15:06:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:01] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-04-24 15:06:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-24 15:06:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-24 [2026-04-24 15:06:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-24 19:05:54 UTC; unix [2026-04-24 15:06:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.99.0 [2026-04-24 15:06:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-24 15:06:01] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-08 r89818); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-24; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-04-24 15:06:02] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; 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=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-04-24 15:06:02] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-24); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-04-24 15:06:02] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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 [2026-04-24 15:06:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-24 15:06:02] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-04-24 15:06:02] [TRACE] [OmnipathR] Contains 1 files. [2026-04-24 15:06:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-24 15:06:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-24 15:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-04-24 15:06:02] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-04-24 15:06:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-24 15:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-24 15:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-24 15:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-24 15:06:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-24 15:06:02] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2026-04-24 21:32:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-24 21:32:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:32:09] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:32:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-24 21:32:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-24
[2026-04-24 21:32:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-24 19:05:54 UTC; unix
[2026-04-24 21:32:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.99.0
[2026-04-24 21:32:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-24 21:32:10] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-08 r89818); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-24; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-04-24 21:32:10] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; 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=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-04-24 21:32:10] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.99.0(2026-04-24); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-24 21:32:10] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Contains 93 files.
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-24 21:32:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:32:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-24 21:32:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-24 21:32:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-24 21:32:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-24 21:32:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-24 21:32:10] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
17.627 2.951 52.750
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.007 | 0.002 | 0.009 | |
| all_uniprots | 7.868 | 1.046 | 23.140 | |
| ancestors | 0.003 | 0.001 | 0.004 | |
| annotated_network | 0.541 | 0.110 | 3.648 | |
| annotation_categories | 37.336 | 0.130 | 38.921 | |
| annotation_resources | 0.030 | 0.008 | 0.705 | |
| annotations | 0.292 | 0.068 | 1.441 | |
| biomart_query | 0.328 | 0.131 | 0.730 | |
| bioplex1 | 0.003 | 0.001 | 0.005 | |
| bioplex2 | 0.003 | 0.001 | 0.004 | |
| bioplex3 | 0.003 | 0.001 | 0.005 | |
| bioplex_all | 0.003 | 0.002 | 0.004 | |
| bioplex_hct116_1 | 0.003 | 0.001 | 0.004 | |
| bma_motif_es | 0.272 | 0.067 | 1.331 | |
| bma_motif_vs | 0.075 | 0.014 | 0.807 | |
| chalmers_gem | 0.003 | 0.001 | 0.005 | |
| chalmers_gem_id_mapping_table | 0.002 | 0.001 | 0.004 | |
| chalmers_gem_id_type | 0 | 0 | 0 | |
| chalmers_gem_metabolites | 0.003 | 0.001 | 0.003 | |
| chalmers_gem_network | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_raw | 0.002 | 0.001 | 0.003 | |
| chalmers_gem_reactions | 0.002 | 0.001 | 0.004 | |
| common_name | 0.059 | 0.004 | 0.066 | |
| complex_genes | 0.337 | 0.074 | 2.466 | |
| complex_resources | 0.029 | 0.006 | 0.663 | |
| complexes | 0.107 | 0.019 | 0.796 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.003 | 0.001 | 0.006 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 2.773 | 0.816 | 13.454 | |
| curated_ligrec_stats | 15.014 | 4.554 | 90.805 | |
| database_summary | 0.666 | 0.195 | 2.371 | |
| descendants | 0.004 | 0.001 | 0.005 | |
| ensembl_dataset | 0.020 | 0.001 | 0.020 | |
| ensembl_id_mapping_table | 0.487 | 0.263 | 0.928 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.082 | 0.005 | 0.086 | |
| ensembl_organisms | 0.044 | 0.014 | 0.057 | |
| ensembl_organisms_raw | 0.040 | 0.014 | 0.054 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 0.780 | 0.164 | 2.780 | |
| enzsub_resources | 0.022 | 0.004 | 0.651 | |
| enzyme_substrate | 0.322 | 0.025 | 0.973 | |
| evex_download | 0.003 | 0.001 | 0.005 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 4.730 | 1.500 | 8.459 | |
| extra_attrs | 2.744 | 1.411 | 4.150 | |
| extra_attrs_to_cols | 5.107 | 1.125 | 6.302 | |
| filter_by_resource | 4.017 | 0.524 | 9.304 | |
| filter_extra_attrs | 12.531 | 5.777 | 25.409 | |
| filter_intercell | 2.764 | 0.278 | 7.121 | |
| filter_intercell_network | 0.007 | 0.002 | 0.010 | |
| find_all_paths | 2.229 | 0.160 | 2.402 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.003 | 0.001 | 0.004 | |
| giant_component | 3.970 | 0.478 | 7.213 | |
| go_annot_download | 4.970 | 0.467 | 5.473 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.003 | 0.002 | 0.005 | |
| guide2pharma_download | 0.003 | 0.000 | 0.003 | |
| harmonizome_download | 0.002 | 0.000 | 0.003 | |
| has_extra_attrs | 2.912 | 1.034 | 4.447 | |
| hmdb_id_mapping_table | 0.006 | 0.001 | 0.007 | |
| hmdb_id_type | 0.001 | 0.000 | 0.000 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_table | 0.005 | 0.002 | 0.007 | |
| homologene_download | 0.005 | 0.002 | 0.007 | |
| homologene_raw | 0.023 | 0.003 | 0.025 | |
| homologene_uniprot_orthology | 0.005 | 0.002 | 0.007 | |
| hpo_download | 0.004 | 0.002 | 0.005 | |
| htridb_download | 0.004 | 0.001 | 0.005 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.054 | 0.007 | 0.067 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.393 | 0.128 | 0.748 | |
| interaction_graph | 0.166 | 0.022 | 1.034 | |
| interaction_resources | 0.027 | 0.006 | 0.662 | |
| interaction_types | 0.036 | 0.008 | 0.047 | |
| intercell | 0.383 | 0.146 | 1.419 | |
| intercell_categories | 0.317 | 0.140 | 0.682 | |
| intercell_consensus_filter | 0.643 | 0.188 | 2.407 | |
| intercell_generic_categories | 0.035 | 0.006 | 0.042 | |
| intercell_network | 0.003 | 0.001 | 0.004 | |
| intercell_resources | 0.023 | 0.006 | 0.726 | |
| intercell_summary | 0.049 | 0.010 | 0.060 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.138 | 0.143 | 0.287 | |
| is_trembl | 0.155 | 0.147 | 0.308 | |
| is_uniprot | 0.003 | 0.001 | 0.005 | |
| kegg_api_templates | 0.000 | 0.001 | 0.001 | |
| kegg_conv | 0.840 | 0.472 | 12.204 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.315 | 0.167 | 1.791 | |
| kegg_find | 0.299 | 0.153 | 2.047 | |
| kegg_info | 0.003 | 0.001 | 0.004 | |
| kegg_link | 0.350 | 0.187 | 6.359 | |
| kegg_list | 0.311 | 0.170 | 1.442 | |
| kegg_open | 0.003 | 0.001 | 0.004 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.008 | 0.024 | 0.032 | |
| kegg_organisms | 0.007 | 0.002 | 0.010 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.003 | 0.001 | 0.004 | |
| kegg_pathway_list | 0.003 | 0.001 | 0.004 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.568 | 0.036 | 4.900 | |
| kegg_process | 0.008 | 0.002 | 0.010 | |
| kegg_query | 0.003 | 0.000 | 0.004 | |
| kegg_request | 0.030 | 0.006 | 0.038 | |
| kegg_rm_prefix | 0.404 | 0.192 | 5.004 | |
| kinasephos | 0.670 | 0.626 | 198.889 | |
| latin_name | 0.091 | 0.005 | 0.101 | |
| load_db | 0.195 | 0.201 | 0.395 | |
| macdb_metabolite_cancer_associations | 0.004 | 0.001 | 0.005 | |
| metabolic_atlas_list_gems | 0 | 0 | 0 | |
| metabolic_atlas_list_models | 0 | 0 | 0 | |
| metabolic_atlas_models | 0 | 0 | 0 | |
| metalinksdb_sqlite | 0.565 | 0.479 | 10.309 | |
| metalinksdb_table | 0.091 | 0.018 | 0.108 | |
| metalinksdb_tables | 0.007 | 0.003 | 0.009 | |
| metatlas_gem_genes | 0.003 | 0.001 | 0.003 | |
| metatlas_gem_metabolites | 0.003 | 0.001 | 0.004 | |
| metatlas_gem_reactions | 0.003 | 0.001 | 0.004 | |
| metatlas_gem_sbml | 0.003 | 0.001 | 0.004 | |
| metatlas_gem_tsv | 0.005 | 0.002 | 0.008 | |
| ncbi_taxid | 0.085 | 0.004 | 0.089 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network | 0.009 | 0.003 | 0.011 | |
| nichenet_gr_network_evex | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network_harmonizome | 0.024 | 0.001 | 0.025 | |
| nichenet_gr_network_htridb | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network_omnipath | 6.971 | 0.742 | 10.042 | |
| nichenet_gr_network_pathwaycommons | 0.004 | 0.001 | 0.005 | |
| nichenet_gr_network_regnetwork | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network_remap | 0.003 | 0.001 | 0.004 | |
| nichenet_gr_network_trrust | 0.002 | 0.001 | 0.003 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.081 | 0.004 | 0.085 | |
| nichenet_lr_network_guide2pharma | 0.004 | 0.002 | 0.005 | |
| nichenet_lr_network_omnipath | 0.013 | 0.004 | 0.018 | |
| nichenet_lr_network_ramilowski | 0.005 | 0.001 | 0.007 | |
| nichenet_main | 0.000 | 0.001 | 0.000 | |
| nichenet_networks | 0.020 | 0.006 | 0.027 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.012 | 0.004 | 0.017 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network | 0.010 | 0.004 | 0.014 | |
| nichenet_signaling_network_cpdb | 0.004 | 0.001 | 0.004 | |
| nichenet_signaling_network_evex | 0.003 | 0.001 | 0.004 | |
| nichenet_signaling_network_harmonizome | 0.003 | 0.002 | 0.004 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 7.129 | 0.744 | 11.300 | |
| nichenet_signaling_network_pathwaycommons | 0.003 | 0.001 | 0.005 | |
| nichenet_signaling_network_vinayagam | 0.002 | 0.001 | 0.004 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.055 | 0.012 | 0.213 | |
| oma_code | 0.044 | 0.002 | 0.046 | |
| oma_organisms | 0.024 | 0.005 | 0.032 | |
| oma_pairwise | 0.003 | 0.001 | 0.004 | |
| oma_pairwise_genesymbols | 0.003 | 0.001 | 0.004 | |
| oma_pairwise_translated | 0.003 | 0.001 | 0.004 | |
| omnipath-interactions | 13.305 | 4.132 | 42.491 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.003 | 0.002 | 0.004 | |
| omnipath_cache_clean_db | 0.057 | 0.081 | 0.141 | |
| omnipath_cache_download_ready | 0.431 | 0.514 | 1.001 | |
| omnipath_cache_filter_versions | 0.396 | 0.440 | 0.866 | |
| omnipath_cache_get | 0.416 | 0.461 | 0.906 | |
| omnipath_cache_key | 0 | 0 | 0 | |
| omnipath_cache_latest_or_new | 0.263 | 0.308 | 0.585 | |
| omnipath_cache_load | 0.537 | 0.445 | 3.422 | |
| omnipath_cache_move_in | 0.532 | 0.634 | 1.212 | |
| omnipath_cache_remove | 0.404 | 0.474 | 0.926 | |
| omnipath_cache_save | 0.400 | 0.466 | 0.927 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.308 | 0.336 | 0.660 | |
| omnipath_cache_update_status | 0.429 | 0.479 | 0.904 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 3.967 | 1.061 | 25.522 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.001 | 0.001 | |
| omnipath_msg | 0.001 | 0.000 | 0.002 | |
| omnipath_query | 1.461 | 0.081 | 1.568 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0.000 | 0.001 | 0.000 | |
| omnipath_set_cachedir | 0.039 | 0.068 | 0.109 | |
| omnipath_set_console_loglevel | 0.002 | 0.000 | 0.002 | |
| omnipath_set_logfile_loglevel | 0.002 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_show_db | 0.028 | 0.009 | 0.041 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.001 | 0.000 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.065 | 0.005 | 0.074 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.000 | |
| pivot_annotations | 5.160 | 0.936 | 15.721 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.059 | 0.009 | 0.653 | |
| print_bma_motif_vs | 0.053 | 0.008 | 0.728 | |
| print_interactions | 3.279 | 0.975 | 8.796 | |
| print_path_es | 0.189 | 0.017 | 0.836 | |
| print_path_vs | 0.984 | 0.181 | 2.600 | |
| pubmed_open | 1.882 | 0.185 | 2.189 | |
| query_info | 0.023 | 0.002 | 0.035 | |
| ramilowski_download | 0.000 | 0.001 | 0.000 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0.000 | 0.000 | 0.001 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0 | 0 | 0 | |
| reactome_chebi | 0 | 0 | 0 | |
| reactome_chebi_pathways | 0.001 | 0.000 | 0.000 | |
| reactome_pathway_relations | 0 | 0 | 0 | |
| reactome_pathways | 0.000 | 0.000 | 0.001 | |
| recon3d | 0.000 | 0.000 | 0.001 | |
| recon3d_raw | 0 | 0 | 0 | |
| recon3d_raw_vmh | 0.000 | 0.001 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.000 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.040 | 0.014 | 0.257 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.032 | 0.014 | 0.100 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.000 | |
| remap_filtered | 0.000 | 0.000 | 0.001 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.526 | 0.396 | 1.170 | |
| resources | 0.028 | 0.006 | 0.701 | |
| resources_colname | 0.857 | 0.360 | 2.985 | |
| resources_in | 1.813 | 0.169 | 2.166 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 2.103 | 0.161 | 3.057 | |
| simplify_intercell_network | 0.000 | 0.000 | 0.001 | |
| static_table | 3.306 | 0.537 | 10.800 | |
| static_tables | 0.024 | 0.008 | 0.036 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.003 | 0.001 | 0.004 | |
| swap_relations | 0.033 | 0.015 | 0.245 | |
| swissprots_only | 0.058 | 0.005 | 0.068 | |
| tfcensus_download | 0.504 | 0.260 | 0.955 | |
| translate_ids | 0.667 | 0.361 | 141.103 | |
| translate_ids_multi | 2.954 | 1.169 | 4.757 | |
| trembls_only | 0.044 | 0.002 | 0.049 | |
| trrust_download | 0.000 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 0.594 | 0.272 | 12.712 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| uniprot_id_type | 0.001 | 0.000 | 0.000 | |
| uniprot_idmapping_id_types | 0.426 | 0.258 | 1.108 | |
| uniprot_organisms | 0.048 | 0.007 | 0.058 | |
| unique_intercell_network | 0.000 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.000 | 0.000 | 0.001 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0.000 | 0.001 | 0.000 | |
| wikipathways_metabolites | 0 | 0 | 0 | |
| wikipathways_metabolites_sparql | 0 | 0 | 0 | |
| wikipathways_pathways | 0 | 0 | 0 | |
| with_extra_attrs | 4.694 | 1.289 | 6.284 | |
| with_references | 0.148 | 0.026 | 1.046 | |
| zenodo_download | 0.000 | 0.001 | 0.001 | |