| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1530/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.12 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | TIMEOUT | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.19.12 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.19.12.tar.gz |
| StartedAt: 2026-04-17 05:16:15 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 05:56:16 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 2400.5 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.19.12.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.12’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-04-17 05:16:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:16:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:16:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:16:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 05:16:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 05:16:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 05:16:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 05:16:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 05:16:59] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 05:16:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 05:16:59] [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 3.19.12(2026-04-16); 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)
[2026-04-17 05:16:59] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:16:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 05:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 05:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 05:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:16:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 05:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:16:59] [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 ... WARNING
'::' or ':::' import not declared from: ‘SBMLR’
'loadNamespace' or 'requireNamespace' call not declared from: ‘SBMLR’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-04-17 05:17:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:17:22] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:17:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 05:17:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 05:17:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 05:17:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 05:17:22] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 05:17:23] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 05:17:23] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 05:17:23] [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 3.19.12(2026-04-16); 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)
[2026-04-17 05:17:23] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:17:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 05:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 05:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 05:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 05:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:17:23] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
macdb_metabolite_cancer_associations: no visible binding for global
variable ‘case_control_p-value’
macdb_metabolite_cancer_associations: no visible binding for global
variable ‘log2FC’
macdb_metabolite_cancer_associations: no visible binding for global
variable ‘case_concentration’
macdb_metabolite_cancer_associations: no visible binding for global
variable ‘control_concentration’
metabolic_atlas_list_gems: no visible binding for global variable
‘git_repo’
metabolic_atlas_list_gems: no visible binding for global variable
‘git_host’
metabolic_atlas_list_gems: no visible binding for global variable
‘gem_info’
metabolic_atlas_list_gems: no visible binding for global variable
‘latest_version’
metabolic_atlas_model: no visible binding for global variable ‘path’
metabolic_atlas_model : silent_sbml: no visible binding for global
variable ‘result’
metabolic_atlas_models: no visible binding for global variable ‘id’
patch_httr2_keep_handle: no visible binding for global variable
‘handle’
patch_httr2_keep_handle: no visible global function definition for
‘ORIGINAL’
wikipathways_pathways: no visible binding for global variable
‘pathway_id’
wikipathways_pathways: no visible binding for global variable
‘pathway_name’
wikipathways_pathways: no visible binding for global variable
‘pathway_url’
Undefined global functions or variables:
ORIGINAL case_concentration case_control_p-value
control_concentration enzyme_genesymbol gem_info git_host git_repo
handle id latest_version log2FC path pathway_id pathway_name
pathway_url result
* 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: metabolic_atlas_models
> ### Title: Download and load one or more SBML models from Metabolic Atlas
> ### Aliases: metabolic_atlas_models
>
> ### ** Examples
>
> # Load model by ID
> model <- metabolic_atlas_model(1)
Error in metabolic_atlas_model(1) :
could not find function "metabolic_atlas_model"
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
metabolic_atlas_list_models 977.991 73.935 1413.062
annotation_categories 108.225 0.251 109.936
curated_ligrec_stats 47.987 7.148 160.464
metabolic_atlas_list_gems 43.681 5.315 134.110
filter_extra_attrs 37.553 5.797 45.131
all_uniprots 36.932 3.066 52.952
extra_attrs_to_cols 20.295 1.642 22.242
extra_attr_values 17.003 1.605 20.240
go_annot_download 14.296 0.508 24.708
giant_component 13.313 1.089 17.408
filter_by_resource 12.018 0.361 13.925
has_extra_attrs 10.574 1.586 12.440
extra_attrs 9.751 1.380 11.336
curated_ligand_receptor_interactions 8.440 1.646 21.941
find_all_paths 8.056 0.461 8.565
filter_intercell 8.055 0.252 10.977
hpo_download 2.966 0.500 21.076
ensembl_id_mapping_table 2.940 0.209 22.477
kegg_conv 2.159 0.353 5.148
annotated_network 1.679 0.314 5.527
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.12’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-04-16 20:22:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:22:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:30] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:22:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-16 20:22:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16 [2026-04-16 20:22:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix [2026-04-16 20:22:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-16 20:22:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-16 20:22:30] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-04-16 20:22:30] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2026-04-16 20:22:31] [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 3.19.12(2026-04-16); 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) [2026-04-16 20:22:31] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-04-16 20:22:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-16 20:22:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:22:31] [TRACE] [OmnipathR] Contains 8 files. [2026-04-16 20:22:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-16 20:22:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:22:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:22:31] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-04-16 20:22:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-16 20:22:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-16 20:22:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-16 20:22:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-16 20:22:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:31] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-04-16 20:22:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:22:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:34] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:22:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-16 20:22:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16 [2026-04-16 20:22:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix [2026-04-16 20:22:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-16 20:22:34] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-16 20:22:34] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-04-16 20:22:34] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2026-04-16 20:22:35] [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 3.19.12(2026-04-16); 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) [2026-04-16 20:22:35] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-04-16 20:22:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-16 20:22:35] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:22:35] [TRACE] [OmnipathR] Contains 1 files. [2026-04-16 20:22:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-16 20:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:22:35] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-04-16 20:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-16 20:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-16 20:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-16 20:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-16 20:22:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:22:35] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2026-04-17 05:54:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:54:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:54:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:54:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 05:54:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 05:54:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 05:54:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 05:54:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 05:54:58] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 05:54:58] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 05:54:58] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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); 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 3.19.12(2026-04-16); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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); 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)
[2026-04-17 05:54:58] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 05:54:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 05:54:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:54:58] [TRACE] [OmnipathR] Contains 453 files.
[2026-04-17 05:54:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 05:54:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:54:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:54:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:54:59] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 05:54:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 05:54:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:54:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 05:54:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:54:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 05:54:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:54:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 05:54:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:54:59] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.026 | 0.000 | 0.026 | |
| all_uniprots | 36.932 | 3.066 | 52.952 | |
| ancestors | 0.013 | 0.000 | 0.013 | |
| annotated_network | 1.679 | 0.314 | 5.527 | |
| annotation_categories | 108.225 | 0.251 | 109.936 | |
| annotation_resources | 0.075 | 0.028 | 1.027 | |
| annotations | 0.698 | 0.060 | 2.140 | |
| biomart_query | 0.914 | 0.036 | 1.552 | |
| bioplex1 | 0.012 | 0.000 | 0.013 | |
| bioplex2 | 0.008 | 0.004 | 0.013 | |
| bioplex3 | 0.009 | 0.004 | 0.012 | |
| bioplex_all | 0.013 | 0.000 | 0.013 | |
| bioplex_hct116_1 | 0.012 | 0.000 | 0.013 | |
| bma_motif_es | 0.750 | 0.059 | 2.258 | |
| bma_motif_vs | 0.280 | 0.032 | 1.236 | |
| chalmers_gem | 0.015 | 0.000 | 0.015 | |
| chalmers_gem_id_mapping_table | 0.015 | 0.000 | 0.014 | |
| chalmers_gem_id_type | 0.003 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.009 | 0.004 | 0.014 | |
| chalmers_gem_network | 0.014 | 0.000 | 0.014 | |
| chalmers_gem_raw | 0.014 | 0.000 | 0.014 | |
| chalmers_gem_reactions | 0.010 | 0.004 | 0.014 | |
| common_name | 0.145 | 0.020 | 0.166 | |
| complex_genes | 0.870 | 0.131 | 2.994 | |
| complex_resources | 0.082 | 0.008 | 0.972 | |
| complexes | 0.254 | 0.008 | 1.157 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.016 | 0.008 | 0.025 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 8.440 | 1.646 | 21.941 | |
| curated_ligrec_stats | 47.987 | 7.148 | 160.464 | |
| database_summary | 2.136 | 0.219 | 3.602 | |
| descendants | 0.012 | 0.000 | 0.012 | |
| ensembl_dataset | 0.059 | 0.000 | 0.059 | |
| ensembl_id_mapping_table | 2.940 | 0.209 | 22.477 | |
| ensembl_id_type | 0.003 | 0.000 | 0.003 | |
| ensembl_name | 0.381 | 0.015 | 0.397 | |
| ensembl_organisms | 0.154 | 0.024 | 0.180 | |
| ensembl_organisms_raw | 0.172 | 0.008 | 0.183 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 2.517 | 0.196 | 4.750 | |
| enzsub_resources | 0.090 | 0.011 | 1.054 | |
| enzyme_substrate | 1.287 | 0.076 | 2.254 | |
| evex_download | 0.014 | 0.000 | 0.014 | |
| evidences | 0.001 | 0.000 | 0.000 | |
| extra_attr_values | 17.003 | 1.605 | 20.240 | |
| extra_attrs | 9.751 | 1.380 | 11.336 | |
| extra_attrs_to_cols | 20.295 | 1.642 | 22.242 | |
| filter_by_resource | 12.018 | 0.361 | 13.925 | |
| filter_extra_attrs | 37.553 | 5.797 | 45.131 | |
| filter_intercell | 8.055 | 0.252 | 10.977 | |
| filter_intercell_network | 0.029 | 0.000 | 0.029 | |
| find_all_paths | 8.056 | 0.461 | 8.565 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.006 | 0.008 | 0.015 | |
| giant_component | 13.313 | 1.089 | 17.408 | |
| go_annot_download | 14.296 | 0.508 | 24.708 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.009 | 0.003 | 0.013 | |
| guide2pharma_download | 0.014 | 0.000 | 0.015 | |
| harmonizome_download | 0.014 | 0.000 | 0.013 | |
| has_extra_attrs | 10.574 | 1.586 | 12.440 | |
| hmdb_id_mapping_table | 0.012 | 0.000 | 0.012 | |
| hmdb_id_type | 0.003 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.013 | 0.000 | 0.013 | |
| homologene_download | 0.013 | 0.000 | 0.013 | |
| homologene_raw | 0.060 | 0.011 | 0.073 | |
| homologene_uniprot_orthology | 0.013 | 0.000 | 0.013 | |
| hpo_download | 2.966 | 0.500 | 21.076 | |
| htridb_download | 0.010 | 0.004 | 0.014 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.058 | 0.008 | 0.068 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.887 | 0.092 | 1.460 | |
| interaction_graph | 0.522 | 0.044 | 1.505 | |
| interaction_resources | 0.110 | 0.040 | 1.044 | |
| interaction_types | 0.119 | 0.040 | 0.159 | |
| intercell | 0.997 | 0.432 | 2.356 | |
| intercell_categories | 0.830 | 0.124 | 1.435 | |
| intercell_consensus_filter | 1.733 | 0.381 | 3.283 | |
| intercell_generic_categories | 0.113 | 0.020 | 0.133 | |
| intercell_network | 0.010 | 0.004 | 0.014 | |
| intercell_resources | 0.091 | 0.004 | 0.985 | |
| intercell_summary | 0.125 | 0.012 | 0.137 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.476 | 0.044 | 0.525 | |
| is_trembl | 0.441 | 0.035 | 0.482 | |
| is_uniprot | 0.010 | 0.004 | 0.015 | |
| kegg_api_templates | 0.002 | 0.000 | 0.002 | |
| kegg_conv | 2.159 | 0.353 | 5.148 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.780 | 0.084 | 1.749 | |
| kegg_find | 0.732 | 0.101 | 1.949 | |
| kegg_info | 0.013 | 0.000 | 0.013 | |
| kegg_link | 0.786 | 0.166 | 2.452 | |
| kegg_list | 0.768 | 0.040 | 1.188 | |
| kegg_open | 0.014 | 0.000 | 0.014 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.024 | 0.004 | 0.030 | |
| kegg_organisms | 0.034 | 0.000 | 0.035 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.016 | 0.000 | 0.015 | |
| kegg_pathway_list | 0.015 | 0.000 | 0.015 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.166 | 0.366 | 2.475 | |
| kegg_process | 0.025 | 0.000 | 0.026 | |
| kegg_query | 0.012 | 0.000 | 0.013 | |
| kegg_request | 0.080 | 0.004 | 0.084 | |
| kegg_rm_prefix | 0.856 | 0.167 | 2.281 | |
| kinasephos | 1.172 | 0.174 | 4.410 | |
| latin_name | 0.316 | 0.016 | 0.336 | |
| load_db | 0.492 | 0.072 | 0.567 | |
| macdb_metabolite_cancer_associations | 0.013 | 0.000 | 0.013 | |
| metabolic_atlas_list_gems | 43.681 | 5.315 | 134.110 | |
| metabolic_atlas_list_models | 977.991 | 73.935 | 1413.062 | |