Denes Turei
| Snapshot Date: 2025-04-28 17:48 -0400 (Mon, 28 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 2025-05-01 11:42 -0400 (Thu, 01 May 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" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4553 |
| 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 | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.16.0 |
| 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: 2025-04-29 10:43:29 -0400 (Tue, 29 Apr 2025) |
| EndedAt: 2025-04-29 11:11:30 -0400 (Tue, 29 Apr 2025) |
| EllapsedTime: 1680.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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###
### Running 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
###
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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: x86_64-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 Monterey 12.7.6
* 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
[2025-04-29 10:44:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-29 10:44:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:44:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 10:44:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-29 10:44:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-28
[2025-04-29 10:44:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-28 22:47:07 UTC; unix
[2025-04-29 10:44:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-29 10:44:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-29 10:44:32] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-29; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-04-29 10:44:33] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-29 10:44:33] [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 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); 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(2025-04-28); 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)
[2025-04-29 10:44:33] [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: x86_64-apple-darwin22.6.0; 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
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-29 10:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:44:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-29 10:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-29 10:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-29 10:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:44:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-29 10:44:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:44:33] [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
[2025-04-29 10:45:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-29 10:45:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:45:15] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 10:45:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-29 10:45:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-28
[2025-04-29 10:45:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-28 22:47:07 UTC; unix
[2025-04-29 10:45:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-29 10:45:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-29 10:45:16] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-29; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-04-29 10:45:16] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-29 10:45:17] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); 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(2025-04-28); 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)
[2025-04-29 10:45:17] [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: x86_64-apple-darwin22.6.0; 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
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-29 10:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:45:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-29 10:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-29 10:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-29 10:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-29 10:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 10:45:17] [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 91.790 0.379 95.176
filter_extra_attrs 65.781 17.865 118.172
curated_ligrec_stats 67.014 6.806 137.502
omnipath-interactions 58.406 4.735 87.519
extra_attrs_to_cols 35.744 5.617 50.758
extra_attr_values 33.208 5.841 45.124
with_extra_attrs 30.437 6.056 37.376
nichenet_gr_network_omnipath 33.645 2.591 45.807
nichenet_signaling_network_omnipath 23.747 1.753 28.242
giant_component 22.076 1.909 40.841
extra_attrs 19.189 4.636 29.200
go_annot_download 21.343 2.360 22.418
has_extra_attrs 18.988 4.578 26.872
filter_by_resource 19.735 1.043 22.236
omnipath_for_cosmos 17.498 1.191 28.061
pivot_annotations 16.451 1.877 27.405
find_all_paths 13.404 0.748 23.223
print_interactions 12.958 0.853 17.530
curated_ligand_receptor_interactions 11.813 1.961 22.349
translate_ids_multi 12.861 0.792 32.362
signed_ptms 11.077 0.483 12.066
static_table 9.537 0.829 10.896
filter_intercell 9.064 1.002 20.327
pubmed_open 9.052 0.428 9.562
omnipath_query 8.911 0.411 9.379
resources_in 8.781 0.386 9.314
print_path_vs 4.468 0.486 6.748
enzsub_graph 4.380 0.298 6.034
all_uniprots 2.482 0.367 21.663
kegg_conv 2.221 0.345 61.134
ensembl_id_mapping_table 2.191 0.297 11.200
uniprot_full_id_mapping_table 1.631 0.244 23.775
translate_ids 1.499 0.220 22.991
kegg_rm_prefix 1.215 0.178 41.120
kegg_link 1.142 0.186 59.764
kegg_picture 1.154 0.088 17.856
tfcensus_download 0.742 0.110 7.096
obo_parser 0.188 0.045 6.445
* 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-x86_64/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 [2025-04-28 18:47:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-28 18:47:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:27] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-28 18:47:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-28 18:47:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-28 [2025-04-28 18:47:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-28 22:47:07 UTC; unix [2025-04-28 18:47:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-28 18:47:27] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-28 18:47:28] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-28; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-04-28 18:47:28] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-04-28 18:47:29] [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 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); 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(2025-04-28); 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) [2025-04-28 18:47:29] [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: x86_64-apple-darwin22.6.0; 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 [2025-04-28 18:47:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-28 18:47:29] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-28 18:47:29] [TRACE] [OmnipathR] Contains 1 files. [2025-04-28 18:47:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-28 18:47:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-28 18:47:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-28 18:47:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-28 18:47:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-28 18:47:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-28 18:47:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-28 18:47:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-28 18:47:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:29] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-28 18:47:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-28 18:47:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:32] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-28 18:47:32] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-28 18:47:32] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-28 [2025-04-28 18:47:32] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-28 22:47:07 UTC; unix [2025-04-28 18:47:32] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-28 18:47:32] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-28 18:47:32] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-28; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-04-28 18:47:33] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-04-28 18:47:33] [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 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); 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(2025-04-28); 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) [2025-04-28 18:47:33] [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: x86_64-apple-darwin22.6.0; 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 [2025-04-28 18:47:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-28 18:47:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-28 18:47:33] [TRACE] [OmnipathR] Contains 1 files. [2025-04-28 18:47:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-28 18:47:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-28 18:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-28 18:47:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-28 18:47:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-28 18:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-28 18:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-28 18:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-28 18:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-28 18:47:33] [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: x86_64-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)
[2025-04-29 11:10:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-29 11:10:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 11:10:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 11:10:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-29 11:10:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-28
[2025-04-29 11:10:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-28 22:47:07 UTC; unix
[2025-04-29 11:10:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-29 11:10:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-29 11:10:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-29; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-04-29 11:10:07] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-29 11:10:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); 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(2025-04-28); 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)
[2025-04-29 11:10:07] [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: x86_64-apple-darwin22.6.0; 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
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Contains 21 files.
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-29 11:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 11:10:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-29 11:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-29 11:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-29 11:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 11:10:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-29 11:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-29 11:10:08] [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
26.638 3.459 60.452
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.001 | 0.002 | |
| all_uniprot_acs | 0.041 | 0.005 | 0.046 | |
| all_uniprots | 2.482 | 0.367 | 21.663 | |
| ancestors | 0.020 | 0.003 | 0.022 | |
| annotated_network | 1.983 | 0.205 | 4.490 | |
| annotation_categories | 91.790 | 0.379 | 95.176 | |
| annotation_resources | 0.130 | 0.017 | 0.775 | |
| annotations | 0.808 | 0.077 | 1.729 | |
| biomart_query | 1.843 | 0.269 | 3.023 | |
| bioplex1 | 0.018 | 0.003 | 0.022 | |
| bioplex2 | 0.019 | 0.002 | 0.021 | |
| bioplex3 | 0.019 | 0.003 | 0.021 | |
| bioplex_all | 0.019 | 0.003 | 0.021 | |
| bioplex_hct116_1 | 0.019 | 0.003 | 0.022 | |
| bma_motif_es | 0.973 | 0.100 | 2.001 | |
| bma_motif_vs | 0.365 | 0.041 | 1.006 | |
| chalmers_gem | 0.020 | 0.003 | 0.024 | |
| chalmers_gem_id_mapping_table | 0.019 | 0.002 | 0.023 | |
| chalmers_gem_id_type | 0.004 | 0.001 | 0.005 | |
| chalmers_gem_metabolites | 0.019 | 0.002 | 0.023 | |
| chalmers_gem_network | 0.020 | 0.003 | 0.022 | |
| chalmers_gem_raw | 0.018 | 0.003 | 0.021 | |
| chalmers_gem_reactions | 0.019 | 0.003 | 0.022 | |
| common_name | 0.058 | 0.005 | 0.062 | |
| complex_genes | 1.057 | 0.092 | 2.345 | |
| complex_resources | 0.127 | 0.013 | 0.738 | |
| complexes | 0.296 | 0.026 | 0.918 | |
| consensuspathdb_download | 0.001 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.018 | 0.002 | 0.021 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 11.813 | 1.961 | 22.349 | |
| curated_ligrec_stats | 67.014 | 6.806 | 137.502 | |
| database_summary | 3.110 | 0.328 | 4.137 | |
| descendants | 0.020 | 0.003 | 0.023 | |
| ensembl_dataset | 0.022 | 0.002 | 0.024 | |
| ensembl_id_mapping_table | 2.191 | 0.297 | 11.200 | |
| ensembl_id_type | 0.004 | 0.001 | 0.005 | |
| ensembl_name | 0.117 | 0.013 | 0.130 | |
| ensembl_organisms | 0.317 | 0.048 | 0.371 | |
| ensembl_organisms_raw | 0.285 | 0.046 | 0.333 | |
| ensembl_orthology | 0.001 | 0.001 | 0.002 | |
| enzsub_graph | 4.380 | 0.298 | 6.034 | |
| enzsub_resources | 0.123 | 0.012 | 0.734 | |
| enzyme_substrate | 2.497 | 0.106 | 3.294 | |
| evex_download | 0.019 | 0.003 | 0.024 | |
| evidences | 0.001 | 0.000 | 0.000 | |
| extra_attr_values | 33.208 | 5.841 | 45.124 | |
| extra_attrs | 19.189 | 4.636 | 29.200 | |
| extra_attrs_to_cols | 35.744 | 5.617 | 50.758 | |
| filter_by_resource | 19.735 | 1.043 | 22.236 | |
| filter_extra_attrs | 65.781 | 17.865 | 118.172 | |
| filter_intercell | 9.064 | 1.002 | 20.327 | |
| filter_intercell_network | 0.042 | 0.007 | 0.106 | |
| find_all_paths | 13.404 | 0.748 | 23.223 | |
| from_evidences | 0.001 | 0.001 | 0.001 | |
| get_db | 0.000 | 0.001 | 0.001 | |
| get_ontology_db | 0.019 | 0.002 | 0.021 | |
| giant_component | 22.076 | 1.909 | 40.841 | |
| go_annot_download | 21.343 | 2.360 | 22.418 | |
| go_annot_slim | 0.000 | 0.001 | 0.002 | |
| go_ontology_download | 0.020 | 0.003 | 0.022 | |
| guide2pharma_download | 0.020 | 0.003 | 0.023 | |
| harmonizome_download | 0.021 | 0.004 | 0.024 | |
| has_extra_attrs | 18.988 | 4.578 | 26.872 | |
| hmdb_id_mapping_table | 0.020 | 0.003 | 0.022 | |
| hmdb_id_type | 0.004 | 0.001 | 0.005 | |
| hmdb_metabolite_fields | 0.000 | 0.002 | 0.003 | |
| hmdb_protein_fields | 0.002 | 0.001 | 0.003 | |
| hmdb_table | 0.019 | 0.002 | 0.022 | |
| homologene_download | 0.020 | 0.003 | 0.023 | |
| homologene_raw | 0.039 | 0.006 | 0.045 | |
| homologene_uniprot_orthology | 0.020 | 0.003 | 0.023 | |
| hpo_download | 4.216 | 0.593 | 4.894 | |
| htridb_download | 0.021 | 0.004 | 0.025 | |
| id_translation_resources | 0.001 | 0.000 | 0.001 | |
| id_types | 0.094 | 0.017 | 0.109 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0.000 | 0.001 | 0.001 | |
| interaction_datasets | 1.019 | 0.113 | 1.437 | |
| interaction_graph | 0.761 | 0.044 | 1.441 | |
| interaction_resources | 0.180 | 0.024 | 0.825 | |
| interaction_types | 0.085 | 0.010 | 0.094 | |
| intercell | 1.105 | 0.145 | 1.651 | |
| intercell_categories | 1.003 | 0.151 | 1.428 | |
| intercell_consensus_filter | 2.277 | 0.263 | 3.554 | |
| intercell_generic_categories | 0.095 | 0.012 | 0.109 | |
| intercell_network | 0.021 | 0.003 | 0.023 | |
| intercell_resources | 0.128 | 0.012 | 0.732 | |
| intercell_summary | 0.103 | 0.045 | 0.146 | |
| is_ontology_id | 0.001 | 0.001 | 0.001 | |
| is_swissprot | 0.056 | 0.006 | 0.062 | |
| is_trembl | 0.057 | 0.007 | 0.064 | |
| is_uniprot | 0.022 | 0.004 | 0.024 | |
| kegg_api_templates | 0.003 | 0.009 | 0.011 | |
| kegg_conv | 2.221 | 0.345 | 61.134 | |
| kegg_databases | 0.001 | 0.001 | 0.002 | |
| kegg_ddi | 0.987 | 0.116 | 2.583 | |
| kegg_find | 0.965 | 0.115 | 3.301 | |
| kegg_info | 0.018 | 0.003 | 0.021 | |
| kegg_link | 1.142 | 0.186 | 59.764 | |
| kegg_list | 0.965 | 0.115 | 4.140 | |
| kegg_open | 0.017 | 0.003 | 0.020 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.069 | 0.247 | 0.570 | |
| kegg_organisms | 0.045 | 0.012 | 0.057 | |
| kegg_pathway_annotations | 0.001 | 0.001 | 0.033 | |
| kegg_pathway_download | 0.019 | 0.003 | 0.026 | |
| kegg_pathway_list | 0.018 | 0.003 | 0.021 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.001 | |
| kegg_picture | 1.154 | 0.088 | 17.856 | |
| kegg_process | 0.037 | 0.006 | 0.042 | |
| kegg_query | 0.015 | 0.001 | 0.017 | |
| kegg_request | 0.128 | 0.016 | 0.144 | |
| kegg_rm_prefix | 1.215 | 0.178 | 41.120 | |
| latin_name | 0.112 | 0.011 | 0.193 | |
| load_db | 0.166 | 0.031 | 0.320 | |
| metalinksdb_sqlite | 1.625 | 0.444 | 4.542 | |
| metalinksdb_table | 0.475 | 0.086 | 0.618 | |
| metalinksdb_tables | 0.036 | 0.009 | 0.073 | |
| ncbi_taxid | 0.116 | 0.011 | 0.154 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.020 | 0.003 | 0.023 | |
| nichenet_gr_network | 0.058 | 0.008 | 0.080 | |
| nichenet_gr_network_evex | 0.020 | 0.003 | 0.023 | |
| nichenet_gr_network_harmonizome | 0.020 | 0.003 | 0.024 | |
| nichenet_gr_network_htridb | 0.019 | 0.003 | 0.022 | |
| nichenet_gr_network_omnipath | 33.645 | 2.591 | 45.807 | |
| nichenet_gr_network_pathwaycommons | 0.059 | 0.005 | 0.065 | |
| nichenet_gr_network_regnetwork | 0.018 | 0.003 | 0.021 | |
| nichenet_gr_network_remap | 0.019 | 0.003 | 0.022 | |
| nichenet_gr_network_trrust | 0.019 | 0.003 | 0.022 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.002 | |
| nichenet_ligand_target_links | 0.001 | 0.002 | 0.002 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.002 | |
| nichenet_lr_network | 0.057 | 0.008 | 0.069 | |
| nichenet_lr_network_guide2pharma | 0.019 | 0.003 | 0.022 | |
| nichenet_lr_network_omnipath | 0.057 | 0.007 | 0.065 | |
| nichenet_lr_network_ramilowski | 0.021 | 0.004 | 0.024 | |
| nichenet_main | 0.001 | 0.001 | 0.001 | |
| nichenet_networks | 0.097 | 0.016 | 0.115 | |
| nichenet_optimization | 0.000 | 0.001 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.060 | 0.009 | 0.068 | |
| nichenet_results_dir | 0.000 | 0.001 | 0.001 | |
| nichenet_signaling_network | 0.065 | 0.010 | 0.077 | |
| nichenet_signaling_network_cpdb | 0.020 | 0.003 | 0.024 | |
| nichenet_signaling_network_evex | 0.020 | 0.003 | 0.026 | |
| nichenet_signaling_network_harmonizome | 0.019 | 0.003 | 0.023 | |
| nichenet_signaling_network_inbiomap | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 23.747 | 1.753 | 28.242 | |
| nichenet_signaling_network_pathwaycommons | 0.020 | 0.003 | 0.023 | |
| nichenet_signaling_network_vinayagam | 0.021 | 0.004 | 0.024 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.188 | 0.045 | 6.445 | |
| oma_code | 0.059 | 0.006 | 0.064 | |
| oma_organisms | 0.189 | 0.028 | 0.217 | |
| oma_pairwise | 0.021 | 0.003 | 0.023 | |
| oma_pairwise_genesymbols | 0.020 | 0.003 | 0.023 | |
| oma_pairwise_translated | 0.019 | 0.003 | 0.021 | |
| omnipath-interactions | 58.406 | 4.735 | 87.519 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.022 | 0.006 | 0.033 | |
| omnipath_cache_clean_db | 0.281 | 0.043 | 0.325 | |
| omnipath_cache_download_ready | 1.092 | 0.227 | 1.415 | |
| omnipath_cache_filter_versions | 0.183 | 0.038 | 0.230 | |
| omnipath_cache_get | 0.165 | 0.028 | 0.193 | |
| omnipath_cache_key | 0.002 | 0.001 | 0.003 | |
| omnipath_cache_latest_or_new | 0.122 | 0.021 | 0.146 | |
| omnipath_cache_load | 0.956 | 0.070 | 2.313 | |
| omnipath_cache_move_in | 0.305 | 0.069 | 0.391 | |
| omnipath_cache_remove | 0.222 | 0.050 | 0.276 | |
| omnipath_cache_save | 0.277 | 0.045 | 0.462 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.002 | |
| omnipath_cache_set_ext | 0.152 | 0.042 | 0.196 | |
| omnipath_cache_update_status | 0.182 | 0.030 | 0.213 | |
| omnipath_cache_wipe | 0.000 | 0.001 | 0.001 | |
| omnipath_config_path | 0.001 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 17.498 | 1.191 | 28.061 | |
| omnipath_load_config | 0.000 | 0.001 | 0.001 | |
| omnipath_log | 0.000 | 0.001 | 0.000 | |
| omnipath_logfile | 0.003 | 0.000 | 0.003 | |
| omnipath_msg | 0.011 | 0.002 | 0.012 | |
| omnipath_query | 8.911 | 0.411 | 9.379 | |
| omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
| omnipath_save_config | 0.000 | 0.001 | 0.001 | |
| omnipath_set_cachedir | 0.081 | 0.008 | 0.089 | |
| omnipath_set_console_loglevel | 0.008 | 0.001 | 0.009 | |
| omnipath_set_logfile_loglevel | 0.006 | 0.001 | 0.008 | |
| omnipath_set_loglevel | 0.004 | 0.000 | 0.004 | |
| omnipath_show_db | 0.123 | 0.029 | 0.152 | |
| omnipath_unlock_cache_db | 0.001 | 0.001 | 0.001 | |
| only_from | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_id | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.001 | 0.001 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |
| organism_for | 0.074 | 0.007 | 0.080 | |
| pathwaycommons_download | 0.000 | 0.001 | 0.002 | |
| pivot_annotations | 16.451 | 1.877 | 27.405 | |
| preppi_download | 0.001 | 0.001 | 0.002 | |
| preppi_filter | 0.001 | 0.000 | 0.002 | |
| print_bma_motif_es | 0.655 | 0.123 | 1.542 | |
| print_bma_motif_vs | 0.239 | 0.034 | 0.909 | |
| print_interactions | 12.958 | 0.853 | 17.530 | |
| print_path_es | 1.206 | 0.103 | 2.329 | |
| print_path_vs | 4.468 | 0.486 | 6.748 | |
| pubmed_open | 9.052 | 0.428 | 9.562 | |
| query_info | 0.442 | 0.045 | 0.774 | |
| ramilowski_download | 0.001 | 0.002 | 0.002 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.005 | 0.001 | 0.005 | |
| ramp_sqlite | 0.000 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.001 | 0.002 | |
| regnetwork_download | 0.001 | 0.000 | 0.002 | |
| relations_list_to_table | 0.161 | 0.031 | 0.201 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.129 | 0.027 | 0.158 | |
| remap_dorothea_download | 0.001 | 0.001 | 0.002 | |
| remap_filtered | 0.000 | 0.000 | 0.002 | |
| remap_tf_target_download | 0.001 | 0.001 | 0.001 | |
| resource_info | 0.595 | 0.174 | 1.046 | |
| resources | 0.107 | 0.014 | 0.755 | |
| resources_colname | 1.217 | 0.130 | 2.617 | |
| resources_in | 8.781 | 0.386 | 9.314 | |
| show_network | 0.000 | 0.000 | 0.001 | |
| signed_ptms | 11.077 | 0.483 | 12.066 | |
| simplify_intercell_network | 0.001 | 0.001 | 0.002 | |
| static_table | 9.537 | 0.829 | 10.896 | |
| static_tables | 0.106 | 0.025 | 0.237 | |
| stitch_actions | 0.001 | 0.001 | 0.002 | |
| stitch_links | 0.001 | 0.000 | 0.002 | |
| stitch_network | 0.001 | 0.001 | 0.002 | |
| stitch_remove_prefixes | 0.013 | 0.002 | 0.015 | |
| swap_relations | 0.149 | 0.029 | 0.178 | |
| swissprots_only | 0.060 | 0.007 | 0.066 | |
| tfcensus_download | 0.742 | 0.110 | 7.096 | |
| translate_ids | 1.499 | 0.220 | 22.991 | |
| translate_ids_multi | 12.861 | 0.792 | 32.362 | |
| trembls_only | 0.062 | 0.006 | 0.069 | |
| trrust_download | 0.001 | 0.001 | 0.002 | |
| uniprot_full_id_mapping_table | 1.631 | 0.244 | 23.775 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.002 | |
| uniprot_id_type | 0.004 | 0.000 | 0.004 | |
| uniprot_idmapping_id_types | 0.599 | 0.072 | 1.234 | |
| unique_intercell_network | 0.002 | 0.000 | 0.002 | |
| unnest_evidences | 0.000 | 0.001 | 0.001 | |
| uploadlists_id_type | 0.004 | 0.001 | 0.008 | |
| vinayagam_download | 0.001 | 0.001 | 0.002 | |
| walk_ontology_tree | 0.003 | 0.001 | 0.003 | |
| with_extra_attrs | 30.437 | 6.056 | 37.376 | |
| with_references | 1.166 | 0.145 | 2.362 | |
| zenodo_download | 0.003 | 0.001 | 0.004 | |