Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-04 12:07 -0400 (Sat, 04 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1490/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.17.6 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 3.17.6 |
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_3.17.6.tar.gz |
StartedAt: 2025-10-03 09:49:54 -0000 (Fri, 03 Oct 2025) |
EndedAt: 2025-10-03 10:11:13 -0000 (Fri, 03 Oct 2025) |
EllapsedTime: 1278.6 seconds |
RetCode: 1 |
Status: ERROR |
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_3.17.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.17.6’ * 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 [2025-10-03 09:50:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 09:50:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:50:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 09:50:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-03 09:50:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-02 [2025-10-03 09:50:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-02 20:26:56 UTC; unix [2025-10-03 09:50:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-03 09:50:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-03 09:50:43] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-03; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-03 09:50:43] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-10-03 09:50:43] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-02); pillar 1.11.1(2025-09-17); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-03 09:50:43] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-10-03 09:50:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-03 09:50:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 09:50:43] [TRACE] [OmnipathR] Contains 1 files. [2025-10-03 09:50:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-03 09:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 09:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:50:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 09:50:43] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-03 09:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-03 09:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-03 09:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-03 09:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-03 09:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:50:43] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-10-03 09:51:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 09:51:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:51:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 09:51:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-03 09:51:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-02 [2025-10-03 09:51:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-02 20:26:56 UTC; unix [2025-10-03 09:51:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-03 09:51:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-03 09:51:10] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-03; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-03 09:51:10] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-10-03 09:51:11] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-02); pillar 1.11.1(2025-09-17); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-03 09:51:11] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-10-03 09:51:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-03 09:51:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 09:51:11] [TRACE] [OmnipathR] Contains 1 files. [2025-10-03 09:51:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-03 09:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 09:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:51:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 09:51:11] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-03 09:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-03 09:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-03 09:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-03 09:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-03 09:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 09:51:11] [TRACE] [OmnipathR] Cache locked: FALSE .cosmos_pkn: no visible global function definition for ‘metabolite_idsc’ cosmos_ksn: no visible binding for global variable ‘substrate_genesymbol’ cosmos_ksn: no visible binding for global variable ‘residue_type’ cosmos_ksn: no visible binding for global variable ‘residue_offset’ cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ cosmos_ksn: no visible binding for global variable ‘mor’ recon3d_genes: no visible binding for global variable ‘notes’ recon3d_genes: no visible binding for global variable ‘annotation’ recon3d_genes: no visible binding for global variable ‘original_bigg_ids’ recon3d_metabolites: no visible binding for global variable ‘notes’ recon3d_metabolites: no visible binding for global variable ‘original_bigg_ids’ recon3d_metabolites: no visible binding for global variable ‘annotation’ recon3d_metabolites: no visible global function definition for ‘chalmers_gem_matlab_tibble’ recon3d_metabolites: no visible binding for global variable ‘hmdb’ recon3d_metabolites: no visible binding for global variable ‘metHMDBID’ recon3d_reactions: no visible binding for global variable ‘notes’ recon3d_reactions: no visible binding for global variable ‘metabolites’ recon3d_reactions: no visible binding for global variable ‘original_bigg_ids’ taxon_names_table: no visible binding for global variable ‘latin_name_uniprot’ taxon_names_table: no visible binding for global variable ‘latin_name_ensembl’ taxon_names_table: no visible binding for global variable ‘latin_name_oma’ taxon_names_table: no visible binding for global variable ‘common_name_ensembl’ taxon_names_table: no visible binding for global variable ‘common_name_uniprot’ Undefined global functions or variables: annotation chalmers_gem_matlab_tibble common_name_ensembl common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc metabolites mor notes original_bigg_ids residue_offset residue_type substrate_genesymbol * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘recon3d_raw’ ‘recon3d_raw_vmh’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'recon3d.Rd' ‘extra_hmdb’ Undocumented arguments in Rd file 'translate_ids_multi.Rd' ‘ramp’ ‘expand’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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: recon3d_metabolites > ### Title: Metabolites from Recon-3D > ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes > ### recon3d_compartments > > ### ** Examples > > recon3d_metabolites() Warning in readLines(con = path, encoding = encoding) : incomplete final line found on '/home/biocbuild/.cache/OmnipathR/be81cd1c9a119b749e4206f26272806591e8fb4c-1.gz' Error in chalmers_gem_matlab_tibble(., "mets", "metHMDBID") : could not find function "chalmers_gem_matlab_tibble" Calls: recon3d_metabolites ... same_src.data.frame -> is.data.frame -> %>% -> unnest -> unnest Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 107.128 0.008 120.693 curated_ligrec_stats 43.781 2.935 187.016 filter_extra_attrs 36.566 6.387 50.163 omnipath-interactions 36.687 2.818 73.992 all_uniprots 32.372 2.273 52.692 extra_attrs_to_cols 21.859 1.318 37.649 nichenet_gr_network_omnipath 20.297 0.791 22.710 extra_attr_values 18.484 1.493 37.869 nichenet_signaling_network_omnipath 14.587 1.231 18.833 giant_component 13.296 1.014 21.582 omnipath_for_cosmos 12.534 1.145 32.740 go_annot_download 12.741 0.803 24.838 extra_attrs 11.150 1.206 21.631 filter_by_resource 11.209 0.480 16.894 has_extra_attrs 9.735 1.450 11.211 pivot_annotations 9.620 0.511 20.797 curated_ligand_receptor_interactions 7.777 0.553 24.560 find_all_paths 7.674 0.355 13.047 print_interactions 7.530 0.432 11.989 filter_intercell 7.296 0.436 15.915 pubmed_open 5.273 0.320 5.606 omnipath_query 4.795 0.381 5.232 hpo_download 3.094 0.670 24.030 print_path_vs 2.776 0.349 6.254 enzsub_graph 2.676 0.109 5.792 ensembl_id_mapping_table 2.456 0.136 20.471 annotated_network 1.444 0.068 5.985 metalinksdb_sqlite 0.986 0.174 12.073 * 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 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.17.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-10-02 20:27:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-02 20:27:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:16] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-02 20:27:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-02 20:27:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-02 [2025-10-02 20:27:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-02 20:26:56 UTC; unix [2025-10-02 20:27:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-02 20:27:16] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-02 20:27:16] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-02; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-02 20:27:16] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-10-02 20:27:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-02); pillar 1.11.1(2025-09-17); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-02 20:27:16] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-10-02 20:27:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-02 20:27:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-02 20:27:16] [TRACE] [OmnipathR] Contains 7 files. [2025-10-02 20:27:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-02 20:27:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-02 20:27:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-02 20:27:16] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-02 20:27:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-02 20:27:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-02 20:27:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-02 20:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-02 20:27:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:17] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-02 20:27:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-02 20:27:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-02 20:27:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-02 20:27:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-02 [2025-10-02 20:27:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-02 20:26:56 UTC; unix [2025-10-02 20:27:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-02 20:27:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-02 20:27:20] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-02; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-02 20:27:20] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-10-02 20:27:20] [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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-02); pillar 1.11.1(2025-09-17); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-02 20:27:20] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-10-02 20:27:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-02 20:27:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-02 20:27:20] [TRACE] [OmnipathR] Contains 1 files. [2025-10-02 20:27:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-02 20:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-02 20:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-02 20:27:20] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-02 20:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-02 20:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-02 20:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-02 20:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-02 20:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-02 20:27:20] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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) [2025-10-03 10:09:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 10:09:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 10:09:16] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 10:09:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-03 10:09:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-02 [2025-10-03 10:09:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-02 20:26:56 UTC; unix [2025-10-03 10:09:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-03 10:09:16] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-10-03 10:09:17] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-03; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-03 10:09:17] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-10-03 10:09:17] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.17.6(2025-10-02); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-03 10:09:17] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-10-03 10:09:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-03 10:09:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 10:09:18] [TRACE] [OmnipathR] Contains 12 files. [2025-10-03 10:09:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-03 10:09:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-03 10:09:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 10:09:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-03 10:09:18] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-03 10:09:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-03 10:09:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 10:09:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-03 10:09:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 10:09:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-03 10:09:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 10:09:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-03 10:09:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-03 10:09:18] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 59.210 4.881 106.105
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.024 | 0.000 | 0.024 | |
all_uniprots | 32.372 | 2.273 | 52.692 | |
ancestors | 0.012 | 0.000 | 0.012 | |
annotated_network | 1.444 | 0.068 | 5.985 | |
annotation_categories | 107.128 | 0.008 | 120.693 | |
annotation_resources | 0.085 | 0.009 | 1.174 | |
annotations | 0.702 | 0.058 | 2.741 | |
biomart_query | 1.294 | 0.073 | 4.860 | |
bioplex1 | 0.009 | 0.004 | 0.013 | |
bioplex2 | 0.012 | 0.000 | 0.013 | |
bioplex3 | 0.012 | 0.000 | 0.013 | |
bioplex_all | 0.013 | 0.000 | 0.013 | |
bioplex_hct116_1 | 0.013 | 0.000 | 0.013 | |
bma_motif_es | 0.769 | 0.028 | 2.865 | |
bma_motif_vs | 0.263 | 0.005 | 1.442 | |
chalmers_gem | 0.014 | 0.000 | 0.028 | |
chalmers_gem_id_mapping_table | 0.010 | 0.004 | 0.014 | |
chalmers_gem_id_type | 0.003 | 0.000 | 0.003 | |
chalmers_gem_metabolites | 0.010 | 0.004 | 0.032 | |
chalmers_gem_network | 0.014 | 0.000 | 0.055 | |
chalmers_gem_raw | 0.012 | 0.000 | 0.019 | |
chalmers_gem_reactions | 0.013 | 0.000 | 0.021 | |
common_name | 0.185 | 0.000 | 0.216 | |
complex_genes | 0.791 | 0.034 | 3.528 | |
complex_resources | 0.084 | 0.000 | 1.062 | |
complexes | 0.211 | 0.021 | 1.491 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.048 | 0.000 | 0.048 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 7.777 | 0.553 | 24.560 | |
curated_ligrec_stats | 43.781 | 2.935 | 187.016 | |
database_summary | 1.880 | 0.140 | 3.415 | |
descendants | 0.012 | 0.000 | 0.019 | |
ensembl_dataset | 0.048 | 0.008 | 0.057 | |
ensembl_id_mapping_table | 2.456 | 0.136 | 20.471 | |
ensembl_id_type | 0.003 | 0.000 | 0.003 | |
ensembl_name | 0.332 | 0.021 | 0.354 | |
ensembl_organisms | 0.151 | 0.012 | 0.164 | |
ensembl_organisms_raw | 0.141 | 0.016 | 0.158 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 2.676 | 0.109 | 5.792 | |
enzsub_resources | 0.076 | 0.009 | 1.024 | |
enzyme_substrate | 1.422 | 0.120 | 2.772 | |
evex_download | 0.013 | 0.000 | 0.013 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 18.484 | 1.493 | 37.869 | |
extra_attrs | 11.150 | 1.206 | 21.631 | |
extra_attrs_to_cols | 21.859 | 1.318 | 37.649 | |
filter_by_resource | 11.209 | 0.480 | 16.894 | |
filter_extra_attrs | 36.566 | 6.387 | 50.163 | |
filter_intercell | 7.296 | 0.436 | 15.915 | |
filter_intercell_network | 0.022 | 0.004 | 0.027 | |
find_all_paths | 7.674 | 0.355 | 13.047 | |
from_evidences | 0.001 | 0.000 | 0.000 | |
get_db | 0 | 0 | 0 | |
get_ontology_db | 0.014 | 0.000 | 0.014 | |
giant_component | 13.296 | 1.014 | 21.582 | |
go_annot_download | 12.741 | 0.803 | 24.838 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.013 | 0.000 | 0.014 | |
guide2pharma_download | 0.010 | 0.004 | 0.014 | |
harmonizome_download | 0.014 | 0.000 | 0.014 | |
has_extra_attrs | 9.735 | 1.450 | 11.211 | |
hmdb_id_mapping_table | 0.012 | 0.000 | 0.012 | |
hmdb_id_type | 0.003 | 0.000 | 0.003 | |
hmdb_metabolite_fields | 0.000 | 0.001 | 0.000 | |
hmdb_protein_fields | 0 | 0 | 0 | |
hmdb_table | 0.010 | 0.002 | 0.013 | |
homologene_download | 0.013 | 0.000 | 0.013 | |
homologene_raw | 0.064 | 0.004 | 0.068 | |
homologene_uniprot_orthology | 0.012 | 0.000 | 0.012 | |
hpo_download | 3.094 | 0.670 | 24.030 | |
htridb_download | 0.012 | 0.000 | 0.013 | |
id_translation_resources | 0 | 0 | 0 | |
id_types | 0.044 | 0.021 | 0.066 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.826 | 0.085 | 1.423 | |
interaction_graph | 0.503 | 0.003 | 1.537 | |
interaction_resources | 0.089 | 0.000 | 0.907 | |
interaction_types | 0.102 | 0.000 | 0.103 | |
intercell | 0.940 | 0.066 | 1.984 | |
intercell_categories | 0.736 | 0.056 | 1.331 | |
intercell_consensus_filter | 1.619 | 0.069 | 3.152 | |
intercell_generic_categories | 0.097 | 0.008 | 0.105 | |
intercell_network | 0.015 | 0.000 | 0.015 | |
intercell_resources | 0.074 | 0.008 | 1.094 | |
intercell_summary | 0.094 | 0.008 | 0.103 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.078 | 0.000 | 0.078 | |
is_trembl | 0.072 | 0.008 | 0.080 | |
is_uniprot | 0.011 | 0.005 | 0.017 | |
kegg_api_templates | 0.000 | 0.001 | 0.002 | |
kegg_conv | 1.528 | 0.154 | 4.460 | |
kegg_databases | 0.000 | 0.001 | 0.001 | |
kegg_ddi | 0.661 | 0.039 | 1.728 | |
kegg_find | 0.668 | 0.040 | 1.782 | |
kegg_info | 0.013 | 0.000 | 0.013 | |
kegg_link | 0.761 | 0.044 | 2.373 | |
kegg_list | 0.668 | 0.026 | 1.067 | |
kegg_open | 0.013 | 0.000 | 0.013 | |
kegg_operations | 0 | 0 | 0 | |
kegg_organism_codes | 0.014 | 0.013 | 0.026 | |
kegg_organisms | 0.028 | 0.004 | 0.032 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.013 | 0.000 | 0.013 | |
kegg_pathway_list | 0.013 | 0.000 | 0.013 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.991 | 0.029 | 1.846 | |
kegg_process | 0.023 | 0.000 | 0.023 | |
kegg_query | 0.01 | 0.00 | 0.01 | |
kegg_request | 0.074 | 0.004 | 0.079 | |
kegg_rm_prefix | 0.794 | 0.047 | 2.078 | |
kinasephos | 1.004 | 0.099 | 4.813 | |
latin_name | 0.291 | 0.008 | 0.301 | |
load_db | 0.097 | 0.012 | 0.109 | |
metalinksdb_sqlite | 0.986 | 0.174 | 12.073 | |
metalinksdb_table | 0.287 | 0.012 | 0.298 | |
metalinksdb_tables | 0.025 | 0.000 | 0.025 | |
ncbi_taxid | 0.296 | 0.011 | 0.308 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.014 | 0.000 | 0.013 | |
nichenet_gr_network | 0.034 | 0.005 | 0.039 | |
nichenet_gr_network_evex | 0.012 | 0.000 | 0.013 | |
nichenet_gr_network_harmonizome | 0.013 | 0.000 | 0.013 | |
nichenet_gr_network_htridb | 0.013 | 0.000 | 0.013 | |
nichenet_gr_network_omnipath | 20.297 | 0.791 | 22.710 | |
nichenet_gr_network_pathwaycommons | 0.013 | 0.000 | 0.013 | |
nichenet_gr_network_regnetwork | 0.013 | 0.000 | 0.013 | |
nichenet_gr_network_remap | 0.012 | 0.000 | 0.013 | |
nichenet_gr_network_trrust | 0.012 | 0.000 | 0.012 | |
nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.033 | 0.004 | 0.037 | |
nichenet_lr_network_guide2pharma | 0.013 | 0.000 | 0.014 | |
nichenet_lr_network_omnipath | 0.036 | 0.000 | 0.037 | |
nichenet_lr_network_ramilowski | 0.009 | 0.004 | 0.013 | |
nichenet_main | 0.001 | 0.000 | 0.001 | |
nichenet_networks | 0.053 | 0.008 | 0.062 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.038 | 0.000 | 0.037 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.032 | 0.008 | 0.039 | |
nichenet_signaling_network_cpdb | 0.014 | 0.000 | 0.014 | |
nichenet_signaling_network_evex | 0.012 | 0.000 | 0.013 | |
nichenet_signaling_network_harmonizome | 0.013 | 0.000 | 0.012 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 14.587 | 1.231 | 18.833 | |
nichenet_signaling_network_pathwaycommons | 0.355 | 0.007 | 0.364 | |
nichenet_signaling_network_vinayagam | 0.007 | 0.004 | 0.011 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0.001 | 0.000 | 0.000 | |
obo_parser | 0.097 | 0.017 | 0.834 | |
oma_code | 0.150 | 0.000 | 0.152 | |
oma_organisms | 0.070 | 0.011 | 0.085 | |
oma_pairwise | 0.008 | 0.004 | 0.013 | |
oma_pairwise_genesymbols | 0.012 | 0.000 | 0.013 | |
oma_pairwise_translated | 0.009 | 0.005 | 0.014 | |
omnipath-interactions | 36.687 | 2.818 | 73.992 | |
omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
omnipath_cache_clean | 0.014 | 0.000 | 0.014 | |
omnipath_cache_clean_db | 0.135 | 0.012 | 0.149 | |
omnipath_cache_download_ready | 0.645 | 0.113 | 0.774 | |
omnipath_cache_filter_versions | 0.136 | 0.017 | 0.159 | |
omnipath_cache_get | 0.103 | 0.019 | 0.126 | |
omnipath_cache_key | 0.002 | 0.000 | 0.002 | |
omnipath_cache_latest_or_new | 0.085 | 0.004 | 0.092 | |
omnipath_cache_load | 0.551 | 0.081 | 4.117 | |
omnipath_cache_move_in | 0.184 | 0.041 | 0.233 | |
omnipath_cache_remove | 0.116 | 0.016 | 0.138 | |
omnipath_cache_save | 0.173 | 0.033 | 0.312 | |
omnipath_cache_search | 0 | 0 | 0 | |
omnipath_cache_set_ext | 0.092 | 0.012 | 0.112 | |
omnipath_cache_update_status | 0.185 | 0.004 | 0.190 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_config_path | 0.000 | 0.000 | 0.001 | |
omnipath_for_cosmos | 12.534 | 1.145 | 32.740 | |
omnipath_load_config | 0.001 | 0.000 | 0.000 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.001 | 0.000 | 0.002 | |
omnipath_msg | 0.003 | 0.004 | 0.007 | |
omnipath_query | 4.795 | 0.381 | 5.232 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0.000 | 0.000 | 0.001 | |
omnipath_set_cachedir | 0.025 | 0.009 | 0.034 | |
omnipath_set_console_loglevel | 0.005 | 0.000 | 0.005 | |
omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.004 | |
omnipath_set_loglevel | 0.002 | 0.000 | 0.002 | |
omnipath_show_db | 0.084 | 0.007 | 0.093 | |
omnipath_unlock_cache_db | 0 | 0 | 0 | |
only_from | 0 | 0 | 0 | |
ontology_ensure_id | 0.001 | 0.001 | 0.001 | |
ontology_ensure_name | 0 | 0 | 0 | |
ontology_name_id | 0.001 | 0.000 | 0.001 | |
organism_for | 0.198 | 0.003 | 0.203 | |
pathwaycommons_download | 0.001 | 0.000 | 0.000 | |
pivot_annotations | 9.620 | 0.511 | 20.797 | |
preppi_download | 0.001 | 0.000 | 0.001 | |
preppi_filter | 0.001 | 0.000 | 0.001 | |
print_bma_motif_es | 0.480 | 0.073 | 2.077 | |
print_bma_motif_vs | 0.192 | 0.000 | 1.266 | |
print_interactions | 7.530 | 0.432 | 11.989 | |
print_path_es | 0.912 | 0.087 | 2.925 | |
print_path_vs | 2.776 | 0.349 | 6.254 | |
pubmed_open | 5.273 | 0.320 | 5.606 | |
query_info | 0.409 | 0.015 | 0.931 | |
ramilowski_download | 0 | 0 | 0 | |
ramp_id_mapping_table | 0.000 | 0.000 | 0.001 | |
ramp_id_type | 0.002 | 0.000 | 0.003 | |
ramp_sqlite | 0.000 | 0.000 | 0.001 | |
ramp_table | 0.000 | 0.000 | 0.001 | |
ramp_tables | 0.000 | 0.000 | 0.001 | |