| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 1482/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | 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. |
| Package: OmnipathR |
| Version: 3.19.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.0.tar.gz |
| StartedAt: 2025-11-01 01:52:47 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 02:27:53 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 2106.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-11-01 01:53:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-01 01:53:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:30] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 01:53:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-01 01:53:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-31
[2025-11-01 01:53:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-10-31 19:16:53 UTC; unix
[2025-11-01 01:53:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-01 01:53:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-01 01:53:30] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-01 01:53:31] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-01 01:53:31] [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 2.3.3(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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-10-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-01 01:53:31] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-01 01:53:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-01 01:53:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-01 01:53:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-01 01:53:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-01 01:53:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:31] [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
[2025-11-01 01:53:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-01 01:53:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 01:53:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-01 01:53:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-31
[2025-11-01 01:53:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-10-31 19:16:53 UTC; unix
[2025-11-01 01:53:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-01 01:53:55] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-01 01:53:58] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-01 01:53:58] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-01 01:53:58] [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); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-10-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-01 01:53:58] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-01 01:53:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-01 01:53:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 01:53:58] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-01 01:53:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-01 01:53:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-01 01:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 01:53:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-01 01:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-01 01:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-01 01:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-01 01:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-01 01:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 01:53:59] [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_compartments: no visible global function definition for
‘.slow_dowtest’
recon3d_genes: no visible global function definition for
‘.slow_dowtest’
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 global function definition for
‘.slow_dowtest’
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 binding for global variable ‘hmdb’
recon3d_metabolites: no visible binding for global variable ‘metHMDBID’
recon3d_raw: no visible global function definition for ‘.slow_dowtest’
recon3d_raw_vmh: no visible global function definition for
‘.slow_dowtest’
recon3d_reactions: no visible global function definition for
‘.slow_dowtest’
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’
recon3d_table: no visible global function definition for
‘.slow_dowtest’
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:
.slow_dowtest annotation 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 ... 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: recon3d_metabolites
> ### Title: Metabolites from Recon-3D
> ### Aliases: recon3d_metabolites recon3d_reactions recon3d_genes
> ### recon3d_compartments
>
> ### ** Examples
>
> recon3d_metabolites()
Error in .slow_dowtest() : could not find function ".slow_dowtest"
Calls: recon3d_metabolites
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 79.211 0.190 80.733
curated_ligrec_stats 43.930 4.387 113.589
filter_extra_attrs 41.242 6.168 56.214
omnipath-interactions 36.168 3.393 65.908
extra_attrs_to_cols 28.296 2.139 34.922
all_uniprots 22.274 1.743 38.137
giant_component 22.025 1.477 30.898
nichenet_gr_network_omnipath 21.606 1.521 25.990
has_extra_attrs 15.842 1.843 24.148
nichenet_signaling_network_omnipath 16.328 0.942 20.788
filter_by_resource 16.359 0.518 23.984
go_annot_download 15.112 1.518 16.706
extra_attr_values 12.830 1.638 16.910
pivot_annotations 12.943 1.310 23.623
extra_attrs 10.944 1.422 15.535
print_interactions 10.794 0.704 16.257
omnipath_for_cosmos 10.015 0.609 40.743
curated_ligand_receptor_interactions 6.856 1.002 16.921
pubmed_open 6.258 0.988 8.384
hpo_download 6.467 0.490 7.167
filter_intercell 6.436 0.491 10.944
find_all_paths 6.475 0.129 7.201
print_path_vs 4.788 0.958 9.123
kegg_conv 3.395 0.127 16.436
ensembl_id_mapping_table 2.629 0.188 27.208
kinasephos 1.977 0.753 21.597
intercell_consensus_filter 2.489 0.153 5.151
kegg_picture 2.310 0.122 8.346
metalinksdb_sqlite 1.288 0.318 10.994
kegg_rm_prefix 1.318 0.088 7.052
kegg_link 1.076 0.066 6.049
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-10-31 15:17:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-31 15:17:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:06] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-31 15:17:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-31 15:17:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-31 [2025-10-31 15:17:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-10-31 19:16:53 UTC; unix [2025-10-31 15:17:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-10-31 15:17:06] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-10-31 15:17:07] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-31; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-10-31 15:17:07] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-10-31 15:17:07] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-10-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-31 15:17:07] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-10-31 15:17:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-31 15:17:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-31 15:17:07] [TRACE] [OmnipathR] Contains 9 files. [2025-10-31 15:17:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-31 15:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-31 15:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-31 15:17:07] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-31 15:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-31 15:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-31 15:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-31 15:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-31 15:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:07] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-31 15:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-31 15:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-31 15:17:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-31 15:17:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-31 [2025-10-31 15:17:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-10-31 19:16:53 UTC; unix [2025-10-31 15:17:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-10-31 15:17:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-10-31 15:17:10] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-31; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-10-31 15:17:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-10-31 15:17:10] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-10-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-31 15:17:10] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-10-31 15:17:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-31 15:17:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-31 15:17:10] [TRACE] [OmnipathR] Contains 1 files. [2025-10-31 15:17:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-31 15:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-31 15:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-31 15:17:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-10-31 15:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-31 15:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-31 15:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-31 15:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-31 15:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-31 15:17:10] [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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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> #!/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)
[2025-11-01 02:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-01 02:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 02:09:37] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 02:09:37] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-01 02:09:37] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-31
[2025-11-01 02:09:37] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-10-31 19:16:53 UTC; unix
[2025-11-01 02:09:37] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-01 02:09:37] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-01 02:09:38] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-01 02:09:38] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-01 02:09:38] [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 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); 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 3.19.0(2025-10-31); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-01 02:09:38] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Contains 11 files.
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-01 02:09:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 02:09:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-01 02:09:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-01 02:09:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-01 02:09:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 02:09:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-01 02:09:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-01 02:09:38] [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
46.052 3.189 79.154
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.015 | 0.002 | 0.017 | |
| all_uniprots | 22.274 | 1.743 | 38.137 | |
| ancestors | 0.006 | 0.002 | 0.009 | |
| annotated_network | 1.731 | 0.312 | 4.976 | |
| annotation_categories | 79.211 | 0.190 | 80.733 | |
| annotation_resources | 0.134 | 0.027 | 0.829 | |
| annotations | 0.759 | 0.103 | 1.681 | |
| biomart_query | 1.184 | 0.105 | 4.003 | |
| bioplex1 | 0.008 | 0.001 | 0.009 | |
| bioplex2 | 0.007 | 0.002 | 0.008 | |
| bioplex3 | 0.008 | 0.000 | 0.008 | |
| bioplex_all | 0.008 | 0.000 | 0.008 | |
| bioplex_hct116_1 | 0.008 | 0.000 | 0.008 | |
| bma_motif_es | 0.879 | 0.269 | 1.865 | |
| bma_motif_vs | 0.276 | 0.017 | 0.911 | |
| chalmers_gem | 0.009 | 0.001 | 0.010 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.009 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_network | 0.009 | 0.001 | 0.011 | |
| chalmers_gem_raw | 0.007 | 0.003 | 0.011 | |
| chalmers_gem_reactions | 0.007 | 0.003 | 0.010 | |
| common_name | 0.150 | 0.016 | 0.165 | |
| complex_genes | 0.886 | 0.239 | 2.939 | |
| complex_resources | 0.172 | 0.007 | 0.801 | |
| complexes | 0.324 | 0.016 | 0.962 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.027 | 0.001 | 0.027 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.856 | 1.002 | 16.921 | |
| curated_ligrec_stats | 43.930 | 4.387 | 113.589 | |
| database_summary | 1.713 | 0.085 | 3.234 | |
| descendants | 0.01 | 0.00 | 0.01 | |
| ensembl_dataset | 0.047 | 0.002 | 0.048 | |
| ensembl_id_mapping_table | 2.629 | 0.188 | 27.208 | |
| ensembl_id_type | 0.001 | 0.001 | 0.002 | |
| ensembl_name | 0.303 | 0.007 | 0.310 | |
| ensembl_organisms | 0.113 | 0.006 | 0.119 | |
| ensembl_organisms_raw | 0.104 | 0.011 | 0.115 | |
| ensembl_orthology | 0.001 | 0.000 | 0.000 | |
| enzsub_graph | 2.432 | 0.105 | 4.446 | |
| enzsub_resources | 0.181 | 0.010 | 0.922 | |
| enzyme_substrate | 1.222 | 0.032 | 1.875 | |
| evex_download | 0.008 | 0.001 | 0.010 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 12.830 | 1.638 | 16.910 | |
| extra_attrs | 10.944 | 1.422 | 15.535 | |
| extra_attrs_to_cols | 28.296 | 2.139 | 34.922 | |
| filter_by_resource | 16.359 | 0.518 | 23.984 | |
| filter_extra_attrs | 41.242 | 6.168 | 56.214 | |
| filter_intercell | 6.436 | 0.491 | 10.944 | |
| filter_intercell_network | 0.020 | 0.000 | 0.021 | |
| find_all_paths | 6.475 | 0.129 | 7.201 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.015 | 0.001 | 0.016 | |
| giant_component | 22.025 | 1.477 | 30.898 | |
| go_annot_download | 15.112 | 1.518 | 16.706 | |
| go_annot_slim | 0.001 | 0.000 | 0.001 | |
| go_ontology_download | 0.015 | 0.002 | 0.017 | |
| guide2pharma_download | 0.016 | 0.001 | 0.017 | |
| harmonizome_download | 0.017 | 0.001 | 0.017 | |
| has_extra_attrs | 15.842 | 1.843 | 24.148 | |
| hmdb_id_mapping_table | 0.033 | 0.001 | 0.034 | |
| hmdb_id_type | 0.009 | 0.000 | 0.009 | |
| hmdb_metabolite_fields | 0.001 | 0.001 | 0.002 | |
| hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_table | 0.031 | 0.006 | 0.037 | |
| homologene_download | 0.029 | 0.002 | 0.032 | |
| homologene_raw | 0.164 | 0.047 | 0.211 | |
| homologene_uniprot_orthology | 0.033 | 0.003 | 0.036 | |
| hpo_download | 6.467 | 0.490 | 7.167 | |
| htridb_download | 0.021 | 0.002 | 0.023 | |
| id_translation_resources | 0.000 | 0.001 | 0.001 | |
| id_types | 0.094 | 0.010 | 0.105 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0.001 | 0.000 | 0.000 | |
| interaction_datasets | 1.267 | 0.045 | 1.515 | |
| interaction_graph | 0.509 | 0.018 | 1.147 | |
| interaction_resources | 0.146 | 0.010 | 0.813 | |
| interaction_types | 0.122 | 0.003 | 0.124 | |
| intercell | 1.011 | 0.124 | 2.022 | |
| intercell_categories | 0.700 | 0.041 | 0.971 | |
| intercell_consensus_filter | 2.489 | 0.153 | 5.151 | |
| intercell_generic_categories | 0.171 | 0.006 | 0.285 | |
| intercell_network | 0.024 | 0.000 | 0.048 | |
| intercell_resources | 0.178 | 0.012 | 1.131 | |
| intercell_summary | 0.160 | 0.025 | 0.358 | |
| is_ontology_id | 0.000 | 0.001 | 0.000 | |
| is_swissprot | 0.105 | 0.003 | 0.109 | |
| is_trembl | 0.110 | 0.006 | 0.237 | |
| is_uniprot | 0.025 | 0.005 | 0.093 | |
| kegg_api_templates | 0.003 | 0.004 | 0.021 | |
| kegg_conv | 3.395 | 0.127 | 16.436 | |
| kegg_databases | 0.000 | 0.001 | 0.001 | |
| kegg_ddi | 1.813 | 0.074 | 3.727 | |
| kegg_find | 2.349 | 0.194 | 4.482 | |
| kegg_info | 0.035 | 0.005 | 0.040 | |
| kegg_link | 1.076 | 0.066 | 6.049 | |
| kegg_list | 0.755 | 0.042 | 2.120 | |
| kegg_open | 0.017 | 0.000 | 0.035 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.033 | 0.116 | 0.295 | |
| kegg_organisms | 0.037 | 0.003 | 0.074 | |
| kegg_pathway_annotations | 0.001 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.013 | 0.003 | 0.016 | |
| kegg_pathway_list | 0.012 | 0.000 | 0.014 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.000 | |
| kegg_picture | 2.310 | 0.122 | 8.346 | |
| kegg_process | 0.039 | 0.002 | 0.062 | |
| kegg_query | 0.017 | 0.002 | 0.030 | |
| kegg_request | 0.133 | 0.008 | 0.236 | |
| kegg_rm_prefix | 1.318 | 0.088 | 7.052 | |
| kinasephos | 1.977 | 0.753 | 21.597 | |
| latin_name | 0.502 | 0.049 | 0.575 | |
| load_db | 0.106 | 0.015 | 0.121 | |
| metalinksdb_sqlite | 1.288 | 0.318 | 10.994 | |
| metalinksdb_table | 0.400 | 0.049 | 0.448 | |
| metalinksdb_tables | 0.032 | 0.005 | 0.036 | |
| ncbi_taxid | 0.450 | 0.019 | 0.468 | |
| nichenet_build_model | 0.000 | 0.000 | 0.001 | |
| nichenet_expression_data | 0.017 | 0.002 | 0.018 | |
| nichenet_gr_network | 0.041 | 0.004 | 0.045 | |
| nichenet_gr_network_evex | 0.014 | 0.000 | 0.014 | |
| nichenet_gr_network_harmonizome | 0.016 | 0.001 | 0.016 | |
| nichenet_gr_network_htridb | 0.016 | 0.019 | 0.035 | |
| nichenet_gr_network_omnipath | 21.606 | 1.521 | 25.990 | |
| nichenet_gr_network_pathwaycommons | 0.015 | 0.001 | 0.017 | |
| nichenet_gr_network_regnetwork | 0.014 | 0.000 | 0.015 | |
| nichenet_gr_network_remap | 0.014 | 0.001 | 0.014 | |
| nichenet_gr_network_trrust | 0.013 | 0.002 | 0.015 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.043 | 0.002 | 0.046 | |
| nichenet_lr_network_guide2pharma | 0.014 | 0.000 | 0.015 | |
| nichenet_lr_network_omnipath | 0.044 | 0.001 | 0.044 | |
| nichenet_lr_network_ramilowski | 0.013 | 0.003 | 0.016 | |
| nichenet_main | 0.001 | 0.000 | 0.000 | |
| nichenet_networks | 0.075 | 0.003 | 0.078 | |
| nichenet_optimization | 0.000 | 0.000 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.044 | 0.002 | 0.046 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.027 | 0.007 | 0.034 | |
| nichenet_signaling_network_cpdb | 0.006 | 0.003 | 0.009 | |
| nichenet_signaling_network_evex | 0.009 | 0.000 | 0.009 | |
| nichenet_signaling_network_harmonizome | 0.007 | 0.002 | 0.010 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 16.328 | 0.942 | 20.788 | |
| nichenet_signaling_network_pathwaycommons | 0.286 | 0.012 | 0.313 | |
| nichenet_signaling_network_vinayagam | 0.021 | 0.000 | 0.021 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.171 | 0.020 | 2.330 | |
| oma_code | 0.166 | 0.002 | 0.168 | |
| oma_organisms | 0.064 | 0.011 | 0.075 | |
| oma_pairwise | 0.011 | 0.000 | 0.011 | |
| oma_pairwise_genesymbols | 0.008 | 0.001 | 0.009 | |
| oma_pairwise_translated | 0.004 | 0.004 | 0.008 | |
| omnipath-interactions | 36.168 | 3.393 | 65.908 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.007 | 0.001 | 0.008 | |
| omnipath_cache_clean_db | 0.085 | 0.019 | 0.105 | |
| omnipath_cache_download_ready | 0.469 | 0.094 | 0.576 | |
| omnipath_cache_filter_versions | 0.077 | 0.010 | 0.090 | |
| omnipath_cache_get | 0.064 | 0.008 | 0.072 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.051 | 0.003 | 0.053 | |
| omnipath_cache_load | 0.595 | 0.040 | 2.855 | |
| omnipath_cache_move_in | 0.127 | 0.031 | 0.164 | |
| omnipath_cache_remove | 0.087 | 0.014 | 0.105 | |
| omnipath_cache_save | 0.186 | 0.018 | 0.314 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.066 | 0.015 | 0.086 | |
| omnipath_cache_update_status | 0.170 | 0.018 | 0.188 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 10.015 | 0.609 | 40.743 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.002 | 0.000 | 0.001 | |
| omnipath_msg | 0.003 | 0.003 | 0.005 | |
| omnipath_query | 3.616 | 0.129 | 3.740 | |
| omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.023 | 0.003 | 0.026 | |
| omnipath_set_console_loglevel | 0.004 | 0.000 | 0.004 | |
| omnipath_set_logfile_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_set_loglevel | 0.002 | 0.000 | 0.002 | |
| omnipath_show_db | 0.064 | 0.008 | 0.072 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.000 | 0.001 | 0.000 | |
| ontology_name_id | 0.000 | 0.002 | 0.001 | |
| organism_for | 0.196 | 0.005 | 0.199 | |
| pathwaycommons_download | 0.000 | 0.001 | 0.001 | |
| pivot_annotations | 12.943 | 1.310 | 23.623 | |
| preppi_download | 0.001 | 0.001 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.680 | 0.070 | 1.441 | |
| print_bma_motif_vs | 0.269 | 0.007 | 0.901 | |
| print_interactions | 10.794 | 0.704 | 16.257 | |
| print_path_es | 0.921 | 0.097 | 2.488 | |
| print_path_vs | 4.788 | 0.958 | 9.123 | |
| pubmed_open | 6.258 | 0.988 | 8.384 | |
| query_info | 0.937 | 0.175 | 2.203 | |
| ramilowski_download | 0.002 | 0.000 | 0.002 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.003 | 0.001 | 0.004 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |