| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-26 11:36 -0400 (Tue, 26 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4938 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4640 |
| 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 1516/2379 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 4.1.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | ||||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 4.1.0 |
| 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_4.1.0.tar.gz |
| StartedAt: 2026-05-25 20:52:45 -0400 (Mon, 25 May 2026) |
| EndedAt: 2026-05-25 21:03:44 -0400 (Mon, 25 May 2026) |
| EllapsedTime: 659.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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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_4.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/OmnipathR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-26 00:52:45 UTC
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘4.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-05-25 20:52:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 20:52:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:52:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 20:52:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-25 20:52:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-25
[2026-05-25 20:52:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-25 19:05:23 UTC; unix
[2026-05-25 20:52:59] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-25 20:52:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-25 20:53:00] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-25; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-25 20:53:00] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-05-25 20:53:00] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-05-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-25 20:53:00] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 20:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`.
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-25 20:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-25 20:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-25 20:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-25 20:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:00] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 20:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:08] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 20:53:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-25 20:53:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-25
[2026-05-25 20:53:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-25 19:05:23 UTC; unix
[2026-05-25 20:53:08] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-25 20:53:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-25 20:53:08] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-25; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-25 20:53:08] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-05-25 20:53:08] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-05-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-25 20:53:08] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 20:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`.
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-25 20:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-25 20:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-25 20:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-25 20:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:53:08] [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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kinasephos
> ### Title: Kinase-PTM relationships from KinasePhos 3.0
> ### Aliases: kinasephos
>
> ### ** Examples
>
> kinasephos()
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Looking up in cache: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`.
[2026-05-25 20:58:41] [INFO] [OmnipathR] Cache record does not exist: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`.
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 20:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 20:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 20:58:41] [INFO] [OmnipathR] Cache item `332c57703a2a947f42ea25504bcc6401dc01fb00` version 1: status changed from `unknown` to `started`.
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/332c57703a2a947f42ea25504bcc6401dc01fb00-1.rds`.
[2026-05-25 20:58:41] [INFO] [OmnipathR] Retrieving URL: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Attempt 1/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2026-05-25 20:58:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-25 20:58:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-25 21:00:00] [TRACE] [OmnipathR] HTTP vNA GET: status 0.
[2026-05-25 21:00:00] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 19.061538s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.972741s, Connection: 0.973576s, Pretransfer: 3.835661s, First byte at: 0s
[2026-05-25 21:00:00] [TRACE] [OmnipathR] HTTP headers:
[2026-05-25 21:00:00] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2026-05-25 21:00:00] [WARN] [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 1/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2026-05-25 21:00:05] [TRACE] [OmnipathR] Attempt 2/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2026-05-25 21:00:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-25 21:00:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-25 21:01:22] [TRACE] [OmnipathR] HTTP vNA GET: status 0.
[2026-05-25 21:01:22] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 17.069463s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.00144s, Connection: 0.002484s, Pretransfer: 1.836326s, First byte at: 0s
[2026-05-25 21:01:22] [TRACE] [OmnipathR] HTTP headers:
[2026-05-25 21:01:22] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2026-05-25 21:01:22] [WARN] [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 2/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2026-05-25 21:01:27] [TRACE] [OmnipathR] Attempt 3/3: `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv`
[2026-05-25 21:01:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-25 21:01:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-25 21:02:43] [TRACE] [OmnipathR] HTTP vNA GET: status 0.
[2026-05-25 21:02:43] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 16.13221s from awi.cuhk.edu.cn (0 bytes/s); Redirect: 0s, DNS look up: 0.001782s, Connection: 0.002566s, Pretransfer: 0.908657s, First byte at: 0s
[2026-05-25 21:02:43] [TRACE] [OmnipathR] HTTP headers:
[2026-05-25 21:02:43] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2026-05-25 21:02:43] [ERROR] [OmnipathR] Failed to download `https://awi.cuhk.edu.cn/KinasePhos/dataset.csv` (attempt 3/3); error: Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
[2026-05-25 21:02:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-25 21:02:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-25
[2026-05-25 21:02:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-25 19:05:23 UTC; unix
[2026-05-25 21:02:43] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-25 21:02:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-25 21:02:44] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-25; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-25 21:02:44] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-05-25 21:02:44] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-05-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.3(2026-04-11); vroom 1.7.1(2026-03-31); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-25 21:02:44] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
Error in (function (url, curlopt = list(), callback = NULL, compr = NULL, :
Failed to open 'https://awi.cuhk.edu.cn/KinasePhos/dataset.csv': Empty reply from server
Calls: kinasephos ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 37.233 0.075 38.782
curated_ligrec_stats 14.627 4.775 93.919
filter_extra_attrs 9.046 4.489 14.905
extra_attrs_to_cols 8.907 2.043 16.559
all_uniprots 7.642 1.264 22.651
filter_by_resource 5.768 0.691 11.210
extra_attr_values 4.246 1.529 8.325
go_annot_download 4.797 0.448 5.170
giant_component 3.630 0.527 6.634
curated_ligand_receptor_interactions 2.578 0.762 13.219
filter_intercell 2.642 0.252 6.871
kegg_conv 1.357 0.960 13.221
kegg_link 0.503 0.326 6.505
* 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: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.24-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘4.1.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-05-25 15:05:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-25 15:05:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:28] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-25 15:05:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-25 15:05:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-25 [2026-05-25 15:05:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-25 19:05:23 UTC; unix [2026-05-25 15:05:28] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-25 15:05:28] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-25 15:05:29] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-25; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-05-25 15:05:29] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-05-25 15:05:29] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-05-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-25 15:05:29] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-05-25 15:05:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-25 15:05:29] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-25 15:05:29] [TRACE] [OmnipathR] Contains 1 files. [2026-05-25 15:05:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-25 15:05:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-25 15:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-25 15:05:29] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`. [2026-05-25 15:05:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-25 15:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-25 15:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-25 15:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-25 15:05:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:29] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-05-25 15:05:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-25 15:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-25 15:05:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-25 15:05:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-25 [2026-05-25 15:05:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-25 19:05:23 UTC; unix [2026-05-25 15:05:30] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-25 15:05:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-25 15:05:30] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-25; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-05-25 15:05:30] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-05-25 15:05:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-05-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-25 15:05:30] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-05-25 15:05:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-25 15:05:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-25 15:05:30] [TRACE] [OmnipathR] Contains 1 files. [2026-05-25 15:05:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-25 15:05:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-25 15:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-05-25 15:05:30] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`. [2026-05-25 15:05:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-25 15:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-25 15:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-25 15:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-25 15:05:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-25 15:05:30] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2026-05-25 21:02:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 21:02:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 21:02:45] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 21:02:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-25 21:02:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-25
[2026-05-25 21:02:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-25 19:05:23 UTC; unix
[2026-05-25 21:02:45] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-25 21:02:45] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-25 21:02:45] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-25; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-25 21:02:45] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-05-25 21:02:45] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 4.1.0(2026-05-25); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-25 21:02:45] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-05-25 21:02:45] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-25 21:02:45] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 21:02:45] [TRACE] [OmnipathR] Contains 58 files.
[2026-05-25 21:02:45] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-25 21:02:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-25 21:02:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 21:02:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-25 21:02:46] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`.
[2026-05-25 21:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-25 21:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 21:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-25 21:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 21:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-25 21:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 21:02:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-25 21:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-25 21:02:46] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
>
> proc.time()
user system elapsed
17.277 2.777 52.960
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.006 | 0.003 | 0.009 | |
| all_uniprots | 7.642 | 1.264 | 22.651 | |
| ancestors | 0.003 | 0.001 | 0.004 | |
| annotated_network | 0.510 | 0.107 | 3.685 | |
| annotation_categories | 37.233 | 0.075 | 38.782 | |
| annotation_resources | 0.027 | 0.012 | 0.939 | |
| annotations | 0.245 | 0.056 | 1.305 | |
| biomart_query | 0.287 | 0.111 | 0.637 | |
| bioplex1 | 0.003 | 0.001 | 0.004 | |
| bioplex2 | 0.003 | 0.002 | 0.006 | |
| bioplex3 | 0.003 | 0.001 | 0.004 | |
| bioplex_all | 0.003 | 0.001 | 0.004 | |
| bioplex_hct116_1 | 0.003 | 0.002 | 0.004 | |
| bma_motif_es | 0.253 | 0.058 | 1.280 | |
| bma_motif_vs | 0.076 | 0.014 | 0.860 | |
| chalmers_gem | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_id_mapping_table | 0.003 | 0.001 | 0.003 | |
| chalmers_gem_id_type | 0.000 | 0.000 | 0.001 | |
| chalmers_gem_metabolites | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_network | 0.003 | 0.002 | 0.004 | |
| chalmers_gem_raw | 0.003 | 0.001 | 0.004 | |
| chalmers_gem_reactions | 0.003 | 0.001 | 0.005 | |
| common_name | 0.038 | 0.002 | 0.039 | |
| complex_genes | 0.307 | 0.066 | 2.295 | |
| complex_resources | 0.024 | 0.004 | 0.879 | |
| complexes | 0.070 | 0.011 | 0.928 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.003 | 0.001 | 0.004 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 2.578 | 0.762 | 13.219 | |
| curated_ligrec_stats | 14.627 | 4.775 | 93.919 | |
| database_summary | 0.642 | 0.196 | 2.141 | |
| descendants | 0.004 | 0.002 | 0.006 | |
| ensembl_dataset | 0.019 | 0.001 | 0.020 | |
| ensembl_id_mapping_table | 0.473 | 0.263 | 1.016 | |
| ensembl_id_type | 0.001 | 0.000 | 0.000 | |
| ensembl_name | 0.081 | 0.003 | 0.083 | |
| ensembl_organisms | 0.037 | 0.008 | 0.045 | |
| ensembl_organisms_raw | 0.050 | 0.011 | 0.060 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 0.767 | 0.181 | 3.000 | |
| enzsub_resources | 0.025 | 0.007 | 0.835 | |
| enzyme_substrate | 0.335 | 0.037 | 1.142 | |
| evex_download | 0.003 | 0.001 | 0.004 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 4.246 | 1.529 | 8.325 | |
| extra_attrs | 2.647 | 1.207 | 4.092 | |
| extra_attrs_to_cols | 8.907 | 2.043 | 16.559 | |
| filter_by_resource | 5.768 | 0.691 | 11.210 | |
| filter_extra_attrs | 9.046 | 4.489 | 14.905 | |
| filter_intercell | 2.642 | 0.252 | 6.871 | |
| filter_intercell_network | 0.008 | 0.002 | 0.010 | |
| find_all_paths | 2.209 | 0.151 | 2.372 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_ontology_db | 0.004 | 0.002 | 0.005 | |
| giant_component | 3.630 | 0.527 | 6.634 | |
| go_annot_download | 4.797 | 0.448 | 5.170 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.003 | 0.001 | 0.004 | |
| guide2pharma_download | 0.003 | 0.001 | 0.003 | |
| harmonizome_download | 0.003 | 0.002 | 0.004 | |
| has_extra_attrs | 2.596 | 0.729 | 3.351 | |
| hmdb_id_mapping_table | 0.003 | 0.001 | 0.004 | |
| hmdb_id_type | 0 | 0 | 0 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.002 | 0.001 | 0.004 | |
| homologene_download | 0.002 | 0.001 | 0.004 | |
| homologene_raw | 0.020 | 0.001 | 0.021 | |
| homologene_uniprot_orthology | 0.003 | 0.001 | 0.004 | |
| hpo_download | 0.002 | 0.001 | 0.003 | |
| htridb_download | 0.003 | 0.001 | 0.003 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.034 | 0.003 | 0.037 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.363 | 0.142 | 0.877 | |
| interaction_graph | 0.166 | 0.016 | 0.915 | |
| interaction_resources | 0.024 | 0.007 | 0.762 | |
| interaction_types | 0.035 | 0.007 | 0.044 | |
| intercell | 0.381 | 0.158 | 1.408 | |
| intercell_categories | 0.318 | 0.147 | 0.695 | |
| intercell_consensus_filter | 0.627 | 0.184 | 2.117 | |
| intercell_generic_categories | 0.033 | 0.006 | 0.039 | |
| intercell_network | 0.004 | 0.002 | 0.006 | |
| intercell_resources | 0.023 | 0.004 | 0.652 | |
| intercell_summary | 0.035 | 0.010 | 0.045 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.158 | 0.151 | 0.307 | |
| is_trembl | 0.151 | 0.144 | 0.310 | |
| is_uniprot | 0.003 | 0.001 | 0.004 | |
| kegg_api_templates | 0.000 | 0.001 | 0.002 | |
| kegg_conv | 1.357 | 0.960 | 13.221 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.571 | 0.382 | 2.611 | |
| kegg_find | 0.431 | 0.278 | 2.345 | |
| kegg_info | 0.007 | 0.003 | 0.010 | |
| kegg_link | 0.503 | 0.326 | 6.505 | |
| kegg_list | 0.374 | 0.242 | 1.674 | |
| kegg_open | 0.003 | 0.002 | 0.005 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.007 | 0.021 | 0.029 | |
| kegg_organisms | 0.006 | 0.003 | 0.011 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.003 | 0.001 | 0.004 | |
| kegg_pathway_list | 0.003 | 0.001 | 0.004 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.462 | 0.030 | 4.270 | |
| kegg_process | 0.005 | 0.001 | 0.007 | |
| kegg_query | 0.003 | 0.000 | 0.003 | |
| kegg_request | 0.022 | 0.005 | 0.027 | |
| kegg_rm_prefix | 0.336 | 0.164 | 4.872 | |