Denes Turei
| Snapshot Date: 2025-04-17 13:40 -0400 (Thu, 17 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 2025-04-18 11:44 -0400 (Fri, 18 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 | OK | | ||||||||
| 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 | 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: 2025-04-17 22:23:14 -0400 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 22:43:46 -0400 (Thu, 17 Apr 2025) |
| EllapsedTime: 1232.2 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
[2025-04-17 22:23:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 22:23:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:23:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:23:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-17 22:23:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-17
[2025-04-17 22:23:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 19:09:17 UTC; unix
[2025-04-17 22:23:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-17 22:23:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-17 22:23:50] [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=2025-04-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-17 22:23:51] [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]
[2025-04-17 22:23:51] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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(2025-04-17); 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)
[2025-04-17 22:23:51] [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
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 22:23:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:23:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-17 22:23:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-17 22:23:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-17 22:23:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:23:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-17 22:23:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:23:51] [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
[2025-04-17 22:24:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 22:24:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:24:15] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:24:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-17 22:24:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-17
[2025-04-17 22:24:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 19:09:17 UTC; unix
[2025-04-17 22:24:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-17 22:24:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-17 22:24:15] [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=2025-04-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-17 22:24:15] [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]
[2025-04-17 22:24:16] [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(2025-04-17); 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)
[2025-04-17 22:24:16] [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
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 22:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:24:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-17 22:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-17 22:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-17 22:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:24:16] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-17 22:24:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:24:16] [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
curated_ligrec_stats 38.595 18.978 131.619
annotation_categories 55.933 0.334 58.208
filter_extra_attrs 38.683 12.034 62.743
omnipath-interactions 29.034 2.969 55.513
extra_attr_values 16.995 4.443 32.587
nichenet_gr_network_omnipath 16.382 1.659 20.848
extra_attrs_to_cols 14.996 2.847 21.226
with_extra_attrs 14.072 3.173 19.615
go_annot_download 13.483 1.684 13.737
extra_attrs 10.924 2.348 19.397
nichenet_signaling_network_omnipath 11.983 1.149 15.802
has_extra_attrs 9.852 3.086 13.006
giant_component 11.130 1.253 16.349
filter_by_resource 10.692 0.755 19.325
pivot_annotations 10.262 1.030 20.738
omnipath_for_cosmos 8.933 0.970 22.592
find_all_paths 7.310 0.541 10.257
curated_ligand_receptor_interactions 6.603 1.130 17.095
filter_intercell 7.058 0.623 15.646
translate_ids_multi 7.084 0.550 17.598
static_table 6.781 0.633 7.800
print_interactions 6.185 0.522 10.958
signed_ptms 5.154 0.299 6.107
enzsub_graph 2.502 0.843 7.157
hpo_download 2.608 0.448 9.430
print_path_vs 2.530 0.299 5.655
ensembl_id_mapping_table 1.884 0.213 18.185
all_uniprots 1.707 0.250 25.664
kegg_conv 1.345 0.190 10.693
metalinksdb_sqlite 0.990 0.359 12.326
translate_ids 1.068 0.168 18.377
uniprot_full_id_mapping_table 0.934 0.178 21.163
kegg_picture 0.891 0.059 5.213
kegg_rm_prefix 0.757 0.088 5.500
kegg_link 0.703 0.098 5.843
* 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 [2025-04-17 15:09:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-17 15:09:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-17 15:09:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-17 15:09:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-17 [2025-04-17 15:09:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 19:09:17 UTC; unix [2025-04-17 15:09:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-17 15:09:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-17 15:09:31] [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=2025-04-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA] [2025-04-17 15:09:32] [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] [2025-04-17 15:09:32] [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(2025-04-17); 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) [2025-04-17 15:09:32] [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 [2025-04-17 15:09:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-17 15:09:32] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-17 15:09:32] [TRACE] [OmnipathR] Contains 1 files. [2025-04-17 15:09:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-17 15:09:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-17 15:09:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-17 15:09:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-17 15:09:32] [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). [2025-04-17 15:09:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:32] [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). [2025-04-17 15:09:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:32] [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). [2025-04-17 15:09:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:32] [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). [2025-04-17 15:09:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:32] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-17 15:09:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-17 15:09:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:34] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-17 15:09:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-17 15:09:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-17 [2025-04-17 15:09:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 19:09:17 UTC; unix [2025-04-17 15:09:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-17 15:09:34] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-17 15:09:35] [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=2025-04-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA] [2025-04-17 15:09:35] [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] [2025-04-17 15:09:35] [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(2025-04-17); 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) [2025-04-17 15:09:35] [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 [2025-04-17 15:09:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-17 15:09:35] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-17 15:09:35] [TRACE] [OmnipathR] Contains 1 files. [2025-04-17 15:09:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-17 15:09:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-04-17 15:09:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-04-17 15:09:35] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-17 15:09:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-17 15:09:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-17 15:09:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-17 15:09:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-17 15:09:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-17 15:09:35] [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)
[2025-04-17 22:39:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 22:39:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:39:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:39:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-17 22:39:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-17
[2025-04-17 22:39:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-17 19:09:17 UTC; unix
[2025-04-17 22:39:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-17 22:39:26] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-17 22:39:27] [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=2025-04-17; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-17 22:39:27] [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]
[2025-04-17 22:39:27] [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(2025-04-17); 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)
[2025-04-17 22:39:27] [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
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Contains 21 files.
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-17 22:39:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:39:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-17 22:39:27] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-17 22:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:39:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-17 22:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:39:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-17 22:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:39:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-17 22:39:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-17 22:39:28] [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
15.705 2.450 243.710
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.022 | 0.003 | 0.026 | |
| all_uniprots | 1.707 | 0.250 | 25.664 | |
| ancestors | 0.011 | 0.002 | 0.012 | |
| annotated_network | 1.266 | 0.134 | 4.411 | |
| annotation_categories | 55.933 | 0.334 | 58.208 | |
| annotation_resources | 0.061 | 0.008 | 0.677 | |
| annotations | 0.524 | 0.050 | 1.334 | |
| biomart_query | 1.235 | 0.184 | 2.346 | |
| bioplex1 | 0.011 | 0.002 | 0.013 | |
| bioplex2 | 0.010 | 0.002 | 0.012 | |
| bioplex3 | 0.010 | 0.002 | 0.012 | |
| bioplex_all | 0.011 | 0.002 | 0.012 | |
| bioplex_hct116_1 | 0.009 | 0.001 | 0.011 | |
| bma_motif_es | 0.627 | 0.073 | 1.573 | |
| bma_motif_vs | 0.191 | 0.028 | 0.857 | |
| chalmers_gem | 0.011 | 0.002 | 0.013 | |
| chalmers_gem_id_mapping_table | 0.010 | 0.002 | 0.012 | |
| chalmers_gem_id_type | 0.001 | 0.001 | 0.002 | |
| chalmers_gem_metabolites | 0.011 | 0.002 | 0.013 | |
| chalmers_gem_network | 0.011 | 0.002 | 0.012 | |
| chalmers_gem_raw | 0.011 | 0.002 | 0.012 | |
| chalmers_gem_reactions | 0.010 | 0.002 | 0.013 | |
| common_name | 0.032 | 0.003 | 0.035 | |
| complex_genes | 0.652 | 0.062 | 2.396 | |
| complex_resources | 0.061 | 0.007 | 0.705 | |
| complexes | 0.164 | 0.015 | 0.783 | |
| consensuspathdb_download | 0.001 | 0.000 | 0.000 | |
| consensuspathdb_raw_table | 0.011 | 0.001 | 0.013 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.603 | 1.130 | 17.095 | |
| curated_ligrec_stats | 38.595 | 18.978 | 131.619 | |
| database_summary | 1.579 | 0.195 | 3.296 | |
| descendants | 0.011 | 0.002 | 0.012 | |
| ensembl_dataset | 0.013 | 0.002 | 0.015 | |
| ensembl_id_mapping_table | 1.884 | 0.213 | 18.185 | |
| ensembl_id_type | 0.002 | 0.000 | 0.002 | |
| ensembl_name | 0.058 | 0.005 | 0.073 | |
| ensembl_organisms | 0.217 | 0.033 | 0.446 | |
| ensembl_organisms_raw | 0.188 | 0.030 | 0.352 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 2.502 | 0.843 | 7.157 | |
| enzsub_resources | 0.075 | 0.011 | 0.851 | |
| enzyme_substrate | 1.470 | 0.079 | 3.889 | |
| evex_download | 0.019 | 0.003 | 0.113 | |
| evidences | 0.000 | 0.001 | 0.000 | |
| extra_attr_values | 16.995 | 4.443 | 32.587 | |
| extra_attrs | 10.924 | 2.348 | 19.397 | |
| extra_attrs_to_cols | 14.996 | 2.847 | 21.226 | |
| filter_by_resource | 10.692 | 0.755 | 19.325 | |
| filter_extra_attrs | 38.683 | 12.034 | 62.743 | |
| filter_intercell | 7.058 | 0.623 | 15.646 | |
| filter_intercell_network | 0.030 | 0.004 | 0.036 | |
| find_all_paths | 7.310 | 0.541 | 10.257 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.014 | 0.002 | 0.015 | |
| giant_component | 11.130 | 1.253 | 16.349 | |
| go_annot_download | 13.483 | 1.684 | 13.737 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.012 | 0.002 | 0.015 | |
| guide2pharma_download | 0.010 | 0.003 | 0.013 | |
| harmonizome_download | 0.011 | 0.002 | 0.013 | |
| has_extra_attrs | 9.852 | 3.086 | 13.006 | |
| hmdb_id_mapping_table | 0.011 | 0.002 | 0.013 | |
| hmdb_id_type | 0.003 | 0.001 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0.001 | 0.001 | 0.001 | |
| hmdb_table | 0.011 | 0.002 | 0.012 | |
| homologene_download | 0.011 | 0.002 | 0.013 | |
| homologene_raw | 0.024 | 0.004 | 0.027 | |
| homologene_uniprot_orthology | 0.013 | 0.003 | 0.015 | |
| hpo_download | 2.608 | 0.448 | 9.430 | |
| htridb_download | 0.011 | 0.002 | 0.013 | |
| id_translation_resources | 0.001 | 0.001 | 0.000 | |
| id_types | 0.059 | 0.012 | 0.070 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0.000 | 0.001 | 0.000 | |
| interaction_datasets | 0.665 | 0.085 | 0.995 | |
| interaction_graph | 0.395 | 0.029 | 1.001 | |
| interaction_resources | 0.088 | 0.010 | 0.691 | |
| interaction_types | 0.051 | 0.007 | 0.058 | |
| intercell | 0.686 | 0.094 | 1.216 | |
| intercell_categories | 0.607 | 0.088 | 0.921 | |
| intercell_consensus_filter | 1.334 | 0.179 | 2.886 | |
| intercell_generic_categories | 0.055 | 0.010 | 0.070 | |
| intercell_network | 0.012 | 0.002 | 0.014 | |
| intercell_resources | 0.063 | 0.008 | 0.602 | |
| intercell_summary | 0.061 | 0.017 | 0.078 | |
| is_ontology_id | 0.001 | 0.000 | 0.001 | |
| is_swissprot | 0.036 | 0.004 | 0.041 | |
| is_trembl | 0.035 | 0.005 | 0.040 | |
| is_uniprot | 0.012 | 0.002 | 0.015 | |
| kegg_api_templates | 0.002 | 0.003 | 0.004 | |
| kegg_conv | 1.345 | 0.190 | 10.693 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.611 | 0.078 | 1.969 | |
| kegg_find | 0.612 | 0.078 | 2.138 | |
| kegg_info | 0.010 | 0.002 | 0.012 | |
| kegg_link | 0.703 | 0.098 | 5.843 | |
| kegg_list | 0.688 | 0.089 | 1.714 | |
| kegg_open | 0.011 | 0.002 | 0.013 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.023 | 0.062 | 0.087 | |
| kegg_organisms | 0.030 | 0.008 | 0.038 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.010 | 0.002 | 0.012 | |
| kegg_pathway_list | 0.011 | 0.002 | 0.013 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.891 | 0.059 | 5.213 | |
| kegg_process | 0.020 | 0.003 | 0.023 | |
| kegg_query | 0.010 | 0.001 | 0.010 | |
| kegg_request | 0.072 | 0.009 | 0.081 | |
| kegg_rm_prefix | 0.757 | 0.088 | 5.500 | |
| latin_name | 0.074 | 0.006 | 0.079 | |
| load_db | 0.107 | 0.021 | 0.127 | |
| metalinksdb_sqlite | 0.990 | 0.359 | 12.326 | |
| metalinksdb_table | 0.269 | 0.044 | 0.315 | |
| metalinksdb_tables | 0.023 | 0.005 | 0.028 | |
| ncbi_taxid | 0.075 | 0.007 | 0.083 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.012 | 0.002 | 0.015 | |
| nichenet_gr_network | 0.028 | 0.004 | 0.032 | |
| nichenet_gr_network_evex | 0.009 | 0.001 | 0.011 | |
| nichenet_gr_network_harmonizome | 0.011 | 0.002 | 0.013 | |
| nichenet_gr_network_htridb | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_omnipath | 16.382 | 1.659 | 20.848 | |
| nichenet_gr_network_pathwaycommons | 0.010 | 0.002 | 0.012 | |
| nichenet_gr_network_regnetwork | 0.009 | 0.002 | 0.010 | |
| nichenet_gr_network_remap | 0.011 | 0.002 | 0.012 | |
| nichenet_gr_network_trrust | 0.013 | 0.002 | 0.014 | |
| nichenet_ligand_activities | 0.001 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.034 | 0.005 | 0.039 | |
| nichenet_lr_network_guide2pharma | 0.011 | 0.002 | 0.013 | |
| nichenet_lr_network_omnipath | 0.029 | 0.005 | 0.035 | |
| nichenet_lr_network_ramilowski | 0.011 | 0.001 | 0.012 | |
| nichenet_main | 0.001 | 0.000 | 0.001 | |
| nichenet_networks | 0.089 | 0.011 | 0.101 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.032 | 0.005 | 0.036 | |
| nichenet_results_dir | 0.000 | 0.001 | 0.001 | |
| nichenet_signaling_network | 0.033 | 0.005 | 0.039 | |
| nichenet_signaling_network_cpdb | 0.008 | 0.001 | 0.010 | |
| nichenet_signaling_network_evex | 0.009 | 0.001 | 0.010 | |
| nichenet_signaling_network_harmonizome | 0.010 | 0.001 | 0.011 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 11.983 | 1.149 | 15.802 | |
| nichenet_signaling_network_pathwaycommons | 0.011 | 0.002 | 0.014 | |
| nichenet_signaling_network_vinayagam | 0.010 | 0.002 | 0.013 | |
| nichenet_test | 0.000 | 0.001 | 0.000 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.101 | 0.024 | 0.295 | |
| oma_code | 0.032 | 0.003 | 0.036 | |
| oma_organisms | 0.124 | 0.021 | 0.146 | |
| oma_pairwise | 0.010 | 0.002 | 0.011 | |
| oma_pairwise_genesymbols | 0.010 | 0.002 | 0.011 | |
| oma_pairwise_translated | 0.010 | 0.001 | 0.012 | |
| omnipath-interactions | 29.034 | 2.969 | 55.513 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.000 | |
| omnipath_cache_clean | 0.014 | 0.005 | 0.019 | |
| omnipath_cache_clean_db | 0.192 | 0.030 | 0.223 | |
| omnipath_cache_download_ready | 0.592 | 0.144 | 0.795 | |
| omnipath_cache_filter_versions | 0.112 | 0.031 | 0.152 | |
| omnipath_cache_get | 0.096 | 0.022 | 0.120 | |
| omnipath_cache_key | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_latest_or_new | 0.071 | 0.016 | 0.088 | |
| omnipath_cache_load | 0.562 | 0.051 | 3.509 | |
| omnipath_cache_move_in | 0.219 | 0.102 | 0.399 | |
| omnipath_cache_remove | 0.113 | 0.034 | 0.154 | |
| omnipath_cache_save | 0.196 | 0.034 | 0.281 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.111 | 0.034 | 0.156 | |
| omnipath_cache_update_status | 0.131 | 0.029 | 0.164 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 8.933 | 0.970 | 22.592 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0.000 | 0.001 | 0.001 | |
| omnipath_logfile | 0.002 | 0.001 | 0.002 | |
| omnipath_msg | 0.007 | 0.002 | 0.009 | |
| omnipath_query | 3.884 | 0.233 | 4.136 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.033 | 0.006 | 0.039 | |
| omnipath_set_console_loglevel | 0.005 | 0.000 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.004 | 0.001 | 0.004 | |
| omnipath_set_loglevel | 0.002 | 0.000 | 0.003 | |
| omnipath_show_db | 0.073 | 0.017 | 0.091 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |
| organism_for | 0.048 | 0.006 | 0.054 | |
| pathwaycommons_download | 0.000 | 0.001 | 0.001 | |
| pivot_annotations | 10.262 | 1.030 | 20.738 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.001 | 0.001 | |
| print_bma_motif_es | 0.476 | 0.089 | 1.539 | |
| print_bma_motif_vs | 0.134 | 0.020 | 0.731 | |
| print_interactions | 6.185 | 0.522 | 10.958 | |
| print_path_es | 0.765 | 0.079 | 2.250 | |
| print_path_vs | 2.530 | 0.299 | 5.655 | |
| pubmed_open | 4.130 | 0.258 | 4.459 | |
| query_info | 0.344 | 0.033 | 0.749 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.000 | 0.001 | 0.001 | |
| ramp_id_type | 0.002 | 0.001 | 0.003 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0.000 | 0.001 | 0.001 | |
| relations_list_to_table | 0.105 | 0.021 | 0.210 | |
| relations_table_to_graph | 0.001 | 0.000 | 0.000 | |
| relations_table_to_list | 0.080 | 0.016 | 0.110 | |
| remap_dorothea_download | 0.000 | 0.000 | 0.001 | |
| remap_filtered | 0.000 | 0.001 | 0.000 | |
| remap_tf_target_download | 0.000 | 0.000 | 0.001 | |
| resource_info | 0.396 | 0.077 | 0.723 | |
| resources | 0.051 | 0.008 | 0.589 | |
| resources_colname | 0.832 | 0.071 | 2.937 | |
| resources_in | 3.827 | 0.231 | 4.100 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 5.154 | 0.299 | 6.107 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 6.781 | 0.633 | 7.800 | |
| static_tables | 0.063 | 0.015 | 0.156 | |
| stitch_actions | 0.000 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.009 | 0.002 | 0.010 | |
| swap_relations | 0.087 | 0.019 | 0.120 | |
| swissprots_only | 0.103 | 0.006 | 0.111 | |
| tfcensus_download | 0.514 | 0.068 | 0.748 | |
| translate_ids | 1.068 | 0.168 | 18.377 | |
| translate_ids_multi | 7.084 | 0.550 | 17.598 | |
| trembls_only | 0.039 | 0.004 | 0.042 | |
| trrust_download | 0.001 | 0.001 | 0.001 | |
| uniprot_full_id_mapping_table | 0.934 | 0.178 | 21.163 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.001 | |
| uniprot_id_type | 0.002 | 0.001 | 0.003 | |
| uniprot_idmapping_id_types | 0.466 | 0.057 | 0.923 | |
| unique_intercell_network | 0.001 | 0.001 | 0.002 | |
| unnest_evidences | 0.000 | 0.001 | 0.000 | |
| uploadlists_id_type | 0.003 | 0.001 | 0.004 | |
| vinayagam_download | 0.000 | 0.001 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.001 | 0.002 | |
| with_extra_attrs | 14.072 | 3.173 | 19.615 | |
| with_references | 0.789 | 0.110 | 2.413 | |
| zenodo_download | 0.001 | 0.001 | 0.002 | |