Denes Turei
| Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_21 |
| git_last_commit: 08e98a0 |
| git_last_commit_date: 2025-04-15 11:51:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1484/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.16.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 3.16.0 |
| 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_3.16.0.tar.gz |
| StartedAt: 2025-04-21 20:43:38 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 20:56:07 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 748.8 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_3.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.16.0’
* 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
[2025-04-21 20:43:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-21 20:43:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:43:51] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:43:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-21 20:43:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-21
[2025-04-21 20:43:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-21 19:04:52 UTC; unix
[2025-04-21 20:43:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-21 20:43:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-21 20:43:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-04-21 20:43:52] [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=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; 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/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-21 20:43:52] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-21); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-21 20:43:52] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (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
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-21 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:43:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-21 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-21 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-21 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-21 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:43:52] [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
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-21 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:44:00] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:44:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-21 20:44:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-21
[2025-04-21 20:44:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-21 19:04:52 UTC; unix
[2025-04-21 20:44:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-21 20:44:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-21 20:44:00] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-04-21 20:44:00] [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=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; 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/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-21 20:44:00] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-21); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-21 20:44:00] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (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
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-21 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:44:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-21 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-21 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-21 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-21 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:44:00] [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 35.365 0.038 36.963
curated_ligrec_stats 12.576 1.856 82.696
omnipath-interactions 10.176 1.214 36.586
filter_extra_attrs 7.322 3.654 12.206
go_annot_download 5.689 0.447 7.629
nichenet_gr_network_omnipath 5.106 0.738 8.458
extra_attr_values 4.297 1.067 10.685
extra_attrs_to_cols 4.423 0.845 5.808
with_extra_attrs 4.012 0.795 7.790
pivot_annotations 4.431 0.333 14.189
nichenet_signaling_network_omnipath 3.716 0.460 7.206
giant_component 3.578 0.424 7.468
omnipath_for_cosmos 3.051 0.252 13.937
filter_by_resource 2.721 0.250 6.215
translate_ids_multi 2.452 0.241 14.799
curated_ligand_receptor_interactions 2.089 0.388 12.020
filter_intercell 2.298 0.174 7.155
print_interactions 2.072 0.183 6.511
ensembl_id_mapping_table 0.944 0.187 13.184
kegg_conv 0.790 0.150 13.249
all_uniprots 0.593 0.102 20.090
uniprot_full_id_mapping_table 0.417 0.112 196.472
translate_ids 0.376 0.082 18.144
metalinksdb_sqlite 0.313 0.124 12.128
kegg_picture 0.384 0.025 5.549
kegg_link 0.284 0.054 5.915
kegg_rm_prefix 0.257 0.035 5.447
* 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-3.21-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/4.5-arm64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.16.0’ ** 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 [2025-04-21 15:04:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-21 15:04:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:58] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-21 15:04:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-21 15:04:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-21 [2025-04-21 15:04:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-21 19:04:52 UTC; unix [2025-04-21 15:04:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-21 15:04:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-21 15:04:58] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto] [2025-04-21 15:04:58] [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=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; 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/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-04-21 15:04:58] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-21); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-21 15:04:58] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (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 [2025-04-21 15:04:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-21 15:04:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-21 15:04:58] [TRACE] [OmnipathR] Contains 1 files. [2025-04-21 15:04:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-21 15:04:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-21 15:04:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-21 15:04:58] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-04-21 15:04:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-21 15:04:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-21 15:04:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-21 15:04:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-21 15:04:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-21 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-21 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:04:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-21 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-21 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-21 [2025-04-21 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-21 19:04:52 UTC; unix [2025-04-21 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-21 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-21 15:04:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto] [2025-04-21 15:04:59] [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=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; 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/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-04-21 15:05:00] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-21); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-04-21 15:05:00] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (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 [2025-04-21 15:05:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-21 15:05:00] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-21 15:05:00] [TRACE] [OmnipathR] Contains 1 files. [2025-04-21 15:05:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-21 15:05:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-21 15:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:05:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-21 15:05:00] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-04-21 15:05:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-21 15:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:05:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-21 15:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:05:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-21 15:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:05:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-21 15:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-21 15:05:00] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-04-21 20:55:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-21 20:55:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:55:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:55:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-21 20:55:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-21
[2025-04-21 20:55:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-21 19:04:52 UTC; unix
[2025-04-21 20:55:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-21 20:55:25] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-21 20:55:25] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-21; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-04-21 20:55:26] [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=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; 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/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-21 20:55:26] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-21); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-21 20:55:26] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (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
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Contains 21 files.
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-21 20:55:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:55:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-21 20:55:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-21 20:55:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-21 20:55:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-21 20:55:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-21 20:55:26] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
5.423 0.755 35.209
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.005 | 0.001 | 0.006 | |
| all_uniprots | 0.593 | 0.102 | 20.090 | |
| ancestors | 0.003 | 0.001 | 0.003 | |
| annotated_network | 0.448 | 0.062 | 3.836 | |
| annotation_categories | 35.365 | 0.038 | 36.963 | |
| annotation_resources | 0.019 | 0.003 | 0.586 | |
| annotations | 0.184 | 0.018 | 1.090 | |
| biomart_query | 0.514 | 0.071 | 3.017 | |
| bioplex1 | 0.002 | 0.001 | 0.002 | |
| bioplex2 | 0.002 | 0.000 | 0.002 | |
| bioplex3 | 0.003 | 0.001 | 0.002 | |
| bioplex_all | 0.002 | 0.000 | 0.003 | |
| bioplex_hct116_1 | 0.003 | 0.000 | 0.003 | |
| bma_motif_es | 0.205 | 0.027 | 1.082 | |
| bma_motif_vs | 0.058 | 0.011 | 0.599 | |
| chalmers_gem | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_id_mapping_table | 0.002 | 0.001 | 0.003 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.001 | |
| chalmers_gem_metabolites | 0.002 | 0.001 | 0.003 | |
| chalmers_gem_network | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_raw | 0.002 | 0.001 | 0.003 | |
| chalmers_gem_reactions | 0.003 | 0.001 | 0.003 | |
| common_name | 0.009 | 0.001 | 0.011 | |
| complex_genes | 0.238 | 0.028 | 2.278 | |
| complex_resources | 0.021 | 0.003 | 0.669 | |
| complexes | 0.055 | 0.006 | 0.643 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.003 | 0.001 | 0.002 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 2.089 | 0.388 | 12.020 | |
| curated_ligrec_stats | 12.576 | 1.856 | 82.696 | |
| database_summary | 1.023 | 0.145 | 3.890 | |
| descendants | 0.008 | 0.001 | 0.018 | |
| ensembl_dataset | 0.010 | 0.001 | 0.021 | |
| ensembl_id_mapping_table | 0.944 | 0.187 | 13.184 | |
| ensembl_id_type | 0.001 | 0.000 | 0.015 | |
| ensembl_name | 0.055 | 0.006 | 0.149 | |
| ensembl_organisms | 0.128 | 0.022 | 0.378 | |
| ensembl_organisms_raw | 0.099 | 0.018 | 0.340 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 0.849 | 0.081 | 3.331 | |
| enzsub_resources | 0.019 | 0.003 | 0.550 | |
| enzyme_substrate | 0.334 | 0.016 | 1.012 | |
| evex_download | 0.002 | 0.000 | 0.003 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 4.297 | 1.067 | 10.685 | |
| extra_attrs | 2.161 | 0.708 | 3.013 | |
| extra_attrs_to_cols | 4.423 | 0.845 | 5.808 | |
| filter_by_resource | 2.721 | 0.250 | 6.215 | |
| filter_extra_attrs | 7.322 | 3.654 | 12.206 | |
| filter_intercell | 2.298 | 0.174 | 7.155 | |
| filter_intercell_network | 0.007 | 0.002 | 0.008 | |
| find_all_paths | 2.117 | 0.146 | 2.260 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.002 | 0.000 | 0.003 | |
| giant_component | 3.578 | 0.424 | 7.468 | |
| go_annot_download | 5.689 | 0.447 | 7.629 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.002 | 0.000 | 0.003 | |
| guide2pharma_download | 0.002 | 0.001 | 0.003 | |
| harmonizome_download | 0.002 | 0.001 | 0.003 | |
| has_extra_attrs | 2.266 | 0.725 | 3.101 | |
| hmdb_id_mapping_table | 0.002 | 0.001 | 0.002 | |
| hmdb_id_type | 0.001 | 0.000 | 0.001 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.000 | |
| hmdb_table | 0.002 | 0.000 | 0.003 | |
| homologene_download | 0.002 | 0.001 | 0.003 | |
| homologene_raw | 0.006 | 0.001 | 0.007 | |
| homologene_uniprot_orthology | 0.002 | 0.001 | 0.003 | |
| hpo_download | 1.457 | 0.159 | 2.873 | |
| htridb_download | 0.008 | 0.002 | 0.019 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.040 | 0.006 | 0.079 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.405 | 0.055 | 1.090 | |
| interaction_graph | 0.225 | 0.029 | 1.032 | |
| interaction_resources | 0.029 | 0.007 | 0.577 | |
| interaction_types | 0.014 | 0.001 | 0.017 | |
| intercell | 0.279 | 0.046 | 0.946 | |
| intercell_categories | 0.243 | 0.043 | 0.911 | |
| intercell_consensus_filter | 0.872 | 0.105 | 3.212 | |
| intercell_generic_categories | 0.042 | 0.008 | 0.162 | |
| intercell_network | 0.009 | 0.002 | 0.022 | |
| intercell_resources | 0.041 | 0.009 | 0.783 | |
| intercell_summary | 0.044 | 0.016 | 0.141 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.024 | 0.004 | 0.051 | |
| is_trembl | 0.025 | 0.004 | 0.060 | |
| is_uniprot | 0.010 | 0.002 | 0.043 | |
| kegg_api_templates | 0.001 | 0.002 | 0.003 | |
| kegg_conv | 0.790 | 0.150 | 13.249 | |
| kegg_databases | 0.000 | 0.001 | 0.000 | |
| kegg_ddi | 0.222 | 0.025 | 1.606 | |
| kegg_find | 0.245 | 0.038 | 1.762 | |
| kegg_info | 0.005 | 0.002 | 0.015 | |
| kegg_link | 0.284 | 0.054 | 5.915 | |
| kegg_list | 0.213 | 0.034 | 1.400 | |
| kegg_open | 0.004 | 0.001 | 0.016 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.007 | 0.017 | 0.052 | |
| kegg_organisms | 0.008 | 0.004 | 0.019 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.003 | 0.001 | 0.003 | |
| kegg_pathway_list | 0.002 | 0.001 | 0.003 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.384 | 0.025 | 5.549 | |
| kegg_process | 0.005 | 0.000 | 0.005 | |
| kegg_query | 0.002 | 0.001 | 0.002 | |
| kegg_request | 0.022 | 0.003 | 0.057 | |
| kegg_rm_prefix | 0.257 | 0.035 | 5.447 | |
| latin_name | 0.020 | 0.003 | 0.026 | |
| load_db | 0.027 | 0.009 | 0.044 | |
| metalinksdb_sqlite | 0.313 | 0.124 | 12.128 | |
| metalinksdb_table | 0.082 | 0.017 | 0.100 | |
| metalinksdb_tables | 0.006 | 0.002 | 0.008 | |
| ncbi_taxid | 0.017 | 0.003 | 0.019 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network | 0.006 | 0.001 | 0.011 | |
| nichenet_gr_network_evex | 0.002 | 0.000 | 0.003 | |
| nichenet_gr_network_harmonizome | 0.002 | 0.000 | 0.003 | |
| nichenet_gr_network_htridb | 0.002 | 0.001 | 0.002 | |
| nichenet_gr_network_omnipath | 5.106 | 0.738 | 8.458 | |
| nichenet_gr_network_pathwaycommons | 0.016 | 0.001 | 0.017 | |
| nichenet_gr_network_regnetwork | 0.002 | 0.001 | 0.003 | |
| nichenet_gr_network_remap | 0.002 | 0.001 | 0.004 | |
| nichenet_gr_network_trrust | 0.003 | 0.000 | 0.004 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.006 | 0.001 | 0.008 | |
| nichenet_lr_network_guide2pharma | 0.003 | 0.000 | 0.009 | |
| nichenet_lr_network_omnipath | 0.007 | 0.002 | 0.015 | |
| nichenet_lr_network_ramilowski | 0.003 | 0.001 | 0.004 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.011 | 0.003 | 0.027 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.007 | 0.001 | 0.012 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.007 | 0.001 | 0.019 | |
| nichenet_signaling_network_cpdb | 0.002 | 0.000 | 0.003 | |
| nichenet_signaling_network_evex | 0.002 | 0.000 | 0.004 | |
| nichenet_signaling_network_harmonizome | 0.003 | 0.000 | 0.006 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 3.716 | 0.460 | 7.206 | |
| nichenet_signaling_network_pathwaycommons | 0.002 | 0.001 | 0.003 | |
| nichenet_signaling_network_vinayagam | 0.003 | 0.001 | 0.004 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.026 | 0.006 | 0.149 | |
| oma_code | 0.010 | 0.002 | 0.011 | |
| oma_organisms | 0.023 | 0.004 | 0.038 | |
| oma_pairwise | 0.003 | 0.000 | 0.003 | |
| oma_pairwise_genesymbols | 0.002 | 0.001 | 0.002 | |
| oma_pairwise_translated | 0.018 | 0.000 | 0.019 | |
| omnipath-interactions | 10.176 | 1.214 | 36.586 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.003 | 0.001 | 0.004 | |
| omnipath_cache_clean_db | 0.040 | 0.009 | 0.052 | |
| omnipath_cache_download_ready | 0.152 | 0.048 | 0.303 | |
| omnipath_cache_filter_versions | 0.027 | 0.011 | 0.055 | |
| omnipath_cache_get | 0.022 | 0.007 | 0.034 | |
| omnipath_cache_key | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.016 | 0.006 | 0.030 | |
| omnipath_cache_load | 0.207 | 0.023 | 2.977 | |
| omnipath_cache_move_in | 0.042 | 0.015 | 0.088 | |
| omnipath_cache_remove | 0.034 | 0.008 | 0.058 | |
| omnipath_cache_save | 0.039 | 0.008 | 0.109 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.019 | 0.005 | 0.031 | |
| omnipath_cache_update_status | 0.021 | 0.005 | 0.026 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 3.051 | 0.252 | 13.937 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.000 | 0.001 | |
| omnipath_msg | 0.001 | 0.000 | 0.002 | |
| omnipath_query | 1.101 | 0.057 | 1.216 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.007 | 0.002 | 0.008 | |
| omnipath_set_console_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_loglevel | 0 | 0 | 0 | |
| omnipath_show_db | 0.017 | 0.007 | 0.022 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0 | 0 | 0 | |
| organism_for | 0.015 | 0.002 | 0.017 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 4.431 | 0.333 | 14.189 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0.000 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.180 | 0.036 | 1.257 | |
| print_bma_motif_vs | 0.038 | 0.009 | 0.612 | |
| print_interactions | 2.072 | 0.183 | 6.511 | |
| print_path_es | 0.306 | 0.030 | 1.957 | |
| print_path_vs | 0.840 | 0.116 | 3.666 | |
| pubmed_open | 1.248 | 0.067 | 1.317 | |
| query_info | 0.147 | 0.023 | 0.400 | |
| ramilowski_download | 0.000 | 0.001 | 0.000 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| ramp_id_type | 0.000 | 0.000 | 0.001 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0.000 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.000 | |
| relations_list_to_table | 0.024 | 0.005 | 0.046 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.020 | 0.004 | 0.036 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.001 | 0.000 | 0.000 | |
| resource_info | 0.140 | 0.020 | 0.394 | |
| resources | 0.017 | 0.004 | 0.547 | |
| resources_colname | 0.371 | 0.026 | 2.426 | |
| resources_in | 1.168 | 0.069 | 1.236 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 1.553 | 0.090 | 2.211 | |
| simplify_intercell_network | 0 | 0 | 0 | |
| static_table | 3.014 | 0.172 | 4.382 | |
| static_tables | 0.019 | 0.006 | 0.030 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0.001 | 0.000 | 0.000 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0.003 | 0.000 | 0.003 | |
| swap_relations | 0.051 | 0.008 | 0.071 | |
| swissprots_only | 0.012 | 0.001 | 0.013 | |
| tfcensus_download | 0.231 | 0.028 | 0.385 | |
| translate_ids | 0.376 | 0.082 | 18.144 | |
| translate_ids_multi | 2.452 | 0.241 | 14.799 | |
| trembls_only | 0.011 | 0.002 | 0.012 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 0.417 | 0.112 | 196.472 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| uniprot_id_type | 0.001 | 0.000 | 0.001 | |
| uniprot_idmapping_id_types | 0.197 | 0.027 | 1.053 | |
| unique_intercell_network | 0.000 | 0.000 | 0.001 | |
| unnest_evidences | 0.001 | 0.000 | 0.000 | |
| uploadlists_id_type | 0.000 | 0.000 | 0.001 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0.000 | 0.000 | 0.001 | |
| with_extra_attrs | 4.012 | 0.795 | 7.790 | |
| with_references | 0.318 | 0.042 | 1.774 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |