| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-12-04 12:01 -0500 (Thu, 04 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4878 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4624 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4669 |
| 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 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.18.2 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.18.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.18.2.tar.gz |
| StartedAt: 2025-12-02 02:40:27 -0500 (Tue, 02 Dec 2025) |
| EndedAt: 2025-12-02 03:20:27 -0500 (Tue, 02 Dec 2025) |
| EllapsedTime: 2400.5 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.18.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘3.18.2’
* 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
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-02 02:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:40:57] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 02:40:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-02 02:40:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-01
[2025-12-02 02:40:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-01 20:25:52 UTC; unix
[2025-12-02 02:40:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-02 02:40:57] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-02 02:40:57] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2025-12-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-02 02:40:57] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-02 02:40:57] [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 0.6.39(2025-11-19); 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 3.18.2(2025-12-01); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-02 02:40:57] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-02 02:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:40:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-02 02:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-02 02:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:40:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-02 02:40:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:40:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-02 02:40:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:40:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-02 02:40:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:40:58] [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
[2025-12-02 02:41:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-02 02:41:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:41:14] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 02:41:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-02 02:41:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-01
[2025-12-02 02:41:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-01 20:25:52 UTC; unix
[2025-12-02 02:41:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-02 02:41:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-02 02:41:14] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2025-12-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-02 02:41:14] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-02 02:41:15] [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 0.6.39(2025-11-19); 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 3.18.2(2025-12-01); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-02 02:41:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-02 02:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:41:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-02 02:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-02 02:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-02 02:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-02 02:41:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 02:41:15] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
Undefined global functions or variables:
enzyme_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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 91.019 0.069 99.399
curated_ligrec_stats 43.867 4.808 165.650
filter_extra_attrs 38.655 5.656 49.587
omnipath-interactions 35.090 2.308 90.470
extra_attr_values 24.166 2.250 36.358
nichenet_gr_network_omnipath 23.434 1.311 45.038
all_uniprots 22.715 1.479 40.617
extra_attrs_to_cols 22.289 1.856 26.181
uniprot_organisms 20.248 1.013 24.655
go_annot_download 17.466 1.304 21.773
nichenet_signaling_network_omnipath 17.428 1.089 24.205
filter_by_resource 17.168 0.593 43.680
extra_attrs 14.722 1.566 20.976
has_extra_attrs 12.572 1.475 15.405
with_extra_attrs 12.402 1.421 18.093
giant_component 11.162 0.813 38.497
find_all_paths 11.393 0.421 15.268
filter_intercell 10.096 0.897 37.288
omnipath_for_cosmos 10.249 0.642 59.219
pivot_annotations 9.811 0.675 24.942
translate_ids_multi 8.465 0.258 29.215
curated_ligand_receptor_interactions 7.085 1.067 28.624
print_interactions 6.302 0.214 15.231
static_table 5.518 0.245 6.658
ensembl_id_mapping_table 5.087 0.249 33.673
signed_ptms 4.742 0.104 5.842
hpo_download 4.387 0.206 6.792
enzsub_graph 3.440 0.242 9.620
intercell_consensus_filter 2.544 0.311 7.821
print_path_vs 2.583 0.176 10.772
kegg_conv 1.795 0.203 37.616
metalinksdb_sqlite 1.584 0.231 16.498
annotated_network 1.643 0.155 6.709
biomart_query 1.185 0.116 8.387
kegg_picture 1.209 0.020 6.047
kinasephos 1.121 0.082 17.479
translate_ids 1.048 0.035 13.378
uniprot_full_id_mapping_table 1.014 0.026 15.150
print_path_es 0.943 0.061 5.026
kegg_rm_prefix 0.894 0.109 5.490
omnipath_cache_load 0.892 0.050 18.617
complex_genes 0.824 0.067 5.175
kegg_link 0.764 0.052 5.665
* 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 ...
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.18.2’ ** 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 [2025-12-01 15:26:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-01 15:26:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-01 15:26:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-01 15:26:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-01 [2025-12-01 15:26:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-01 20:25:52 UTC; unix [2025-12-01 15:26:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2 [2025-12-01 15:26:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-12-01 15:26:05] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2025-12-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-12-01 15:26:06] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-01 15:26:06] [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 0.6.39(2025-11-19); 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 3.18.2(2025-12-01); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-01 15:26:06] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-12-01 15:26:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-01 15:26:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-01 15:26:06] [TRACE] [OmnipathR] Contains 9 files. [2025-12-01 15:26:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-01 15:26:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-01 15:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-01 15:26:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-01 15:26:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-01 15:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-01 15:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-01 15:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-01 15:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-12-01 15:26:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-01 15:26:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-01 15:26:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-01 15:26:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-01 [2025-12-01 15:26:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-01 20:25:52 UTC; unix [2025-12-01 15:26:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2 [2025-12-01 15:26:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-12-01 15:26:08] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2025-12-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-12-01 15:26:08] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-01 15:26:08] [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 0.6.39(2025-11-19); 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 3.18.2(2025-12-01); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-01 15:26:09] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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 [2025-12-01 15:26:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-01 15:26:09] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-01 15:26:09] [TRACE] [OmnipathR] Contains 1 files. [2025-12-01 15:26:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-01 15:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-01 15:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-01 15:26:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-01 15:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-01 15:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-01 15:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-01 15:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-01 15:26:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-01 15:26:09] [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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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)
[2025-12-02 03:03:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-02 03:03:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 03:03:33] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 03:03:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-02 03:03:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-01
[2025-12-02 03:03:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-01 20:25:52 UTC; unix
[2025-12-02 03:03:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-02 03:03:33] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-02 03:03:33] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); 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=2025-12-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-02 03:03:33] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-02 03:03:34] [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 0.6.39(2025-11-19); 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 3.18.2(2025-12-01); 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 1.2.0(2025-11-04); 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 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.1(2025-11-25); 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 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-02 03:03:34] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; 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
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Contains 22 files.
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-02 03:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 03:03:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-02 03:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-02 03:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-02 03:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 03:03:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-02 03:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-02 03:03:34] [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
45.793 3.889 97.840
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.017 | 0.000 | 0.018 | |
| all_uniprots | 22.715 | 1.479 | 40.617 | |
| ancestors | 0.008 | 0.000 | 0.008 | |
| annotated_network | 1.643 | 0.155 | 6.709 | |
| annotation_categories | 91.019 | 0.069 | 99.399 | |
| annotation_resources | 0.169 | 0.022 | 1.072 | |
| annotations | 0.775 | 0.059 | 2.067 | |
| biomart_query | 1.185 | 0.116 | 8.387 | |
| bioplex1 | 0.008 | 0.001 | 0.009 | |
| bioplex2 | 0.007 | 0.001 | 0.008 | |
| bioplex3 | 0.008 | 0.000 | 0.008 | |
| bioplex_all | 0.008 | 0.000 | 0.008 | |
| bioplex_hct116_1 | 0.007 | 0.001 | 0.008 | |
| bma_motif_es | 0.809 | 0.114 | 3.299 | |
| bma_motif_vs | 0.337 | 0.045 | 1.977 | |
| chalmers_gem | 0.009 | 0.001 | 0.010 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_id_type | 0.001 | 0.001 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.002 | 0.009 | |
| chalmers_gem_network | 0.007 | 0.002 | 0.009 | |
| chalmers_gem_raw | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_reactions | 0.009 | 0.000 | 0.009 | |
| common_name | 0.118 | 0.011 | 0.129 | |
| complex_genes | 0.824 | 0.067 | 5.175 | |
| complex_resources | 0.153 | 0.011 | 1.255 | |
| complexes | 0.224 | 0.006 | 1.413 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.007 | 0.001 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.085 | 1.067 | 28.624 | |
| curated_ligrec_stats | 43.867 | 4.808 | 165.650 | |
| database_summary | 1.796 | 0.149 | 4.205 | |
| descendants | 0.01 | 0.00 | 0.01 | |
| ensembl_dataset | 0.056 | 0.002 | 0.058 | |
| ensembl_id_mapping_table | 5.087 | 0.249 | 33.673 | |
| ensembl_id_type | 0.005 | 0.000 | 0.006 | |
| ensembl_name | 0.807 | 0.006 | 0.814 | |
| ensembl_organisms | 0.289 | 0.022 | 0.311 | |
| ensembl_organisms_raw | 0.293 | 0.011 | 0.303 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 3.440 | 0.242 | 9.620 | |
| enzsub_resources | 0.172 | 0.010 | 1.184 | |
| enzyme_substrate | 2.193 | 0.066 | 4.216 | |
| evex_download | 0.019 | 0.000 | 0.019 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 24.166 | 2.250 | 36.358 | |
| extra_attrs | 14.722 | 1.566 | 20.976 | |
| extra_attrs_to_cols | 22.289 | 1.856 | 26.181 | |
| filter_by_resource | 17.168 | 0.593 | 43.680 | |
| filter_extra_attrs | 38.655 | 5.656 | 49.587 | |
| filter_intercell | 10.096 | 0.897 | 37.288 | |
| filter_intercell_network | 0.018 | 0.000 | 0.018 | |
| find_all_paths | 11.393 | 0.421 | 15.268 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.021 | 0.002 | 0.024 | |
| giant_component | 11.162 | 0.813 | 38.497 | |
| go_annot_download | 17.466 | 1.304 | 21.773 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.009 | 0.000 | 0.009 | |
| guide2pharma_download | 0.007 | 0.001 | 0.009 | |
| harmonizome_download | 0.007 | 0.001 | 0.008 | |
| has_extra_attrs | 12.572 | 1.475 | 15.405 | |
| hmdb_id_mapping_table | 0.017 | 0.000 | 0.017 | |
| hmdb_id_type | 0.004 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.014 | 0.001 | 0.015 | |
| homologene_download | 0.014 | 0.000 | 0.014 | |
| homologene_raw | 0.091 | 0.002 | 0.093 | |
| homologene_uniprot_orthology | 0.015 | 0.001 | 0.017 | |
| hpo_download | 4.387 | 0.206 | 6.792 | |
| htridb_download | 0.008 | 0.001 | 0.009 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.035 | 0.006 | 0.041 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.787 | 0.034 | 1.423 | |
| interaction_graph | 0.855 | 0.040 | 3.855 | |
| interaction_resources | 0.198 | 0.010 | 1.242 | |
| interaction_types | 0.150 | 0.006 | 0.386 | |
| intercell | 1.743 | 0.095 | 3.967 | |
| intercell_categories | 1.380 | 0.155 | 2.192 | |
| intercell_consensus_filter | 2.544 | 0.311 | 7.821 | |
| intercell_generic_categories | 0.174 | 0.006 | 0.289 | |
| intercell_network | 0.022 | 0.002 | 0.042 | |
| intercell_resources | 0.196 | 0.021 | 1.228 | |
| intercell_summary | 0.165 | 0.014 | 0.413 | |
| is_ontology_id | 0.001 | 0.000 | 0.004 | |
| is_swissprot | 0.124 | 0.004 | 0.258 | |
| is_trembl | 0.228 | 0.008 | 0.470 | |
| is_uniprot | 0.022 | 0.002 | 0.048 | |
| kegg_api_templates | 0.002 | 0.001 | 0.008 | |
| kegg_conv | 1.795 | 0.203 | 37.616 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.649 | 0.040 | 1.974 | |
| kegg_find | 0.648 | 0.032 | 2.709 | |
| kegg_info | 0.009 | 0.000 | 0.009 | |
| kegg_link | 0.764 | 0.052 | 5.665 | |
| kegg_list | 0.679 | 0.033 | 1.817 | |
| kegg_open | 0.009 | 0.000 | 0.009 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.014 | 0.006 | 0.021 | |
| kegg_organisms | 0.024 | 0.000 | 0.023 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.008 | 0.001 | 0.009 | |
| kegg_pathway_list | 0.008 | 0.000 | 0.008 | |
| kegg_pathways_download | 0.001 | 0.000 | 0.000 | |
| kegg_picture | 1.209 | 0.020 | 6.047 | |
| kegg_process | 0.017 | 0.001 | 0.018 | |
| kegg_query | 0.008 | 0.000 | 0.008 | |
| kegg_request | 0.075 | 0.005 | 0.080 | |
| kegg_rm_prefix | 0.894 | 0.109 | 5.490 | |
| kinasephos | 1.121 | 0.082 | 17.479 | |
| latin_name | 0.279 | 0.001 | 0.280 | |
| load_db | 0.072 | 0.008 | 0.079 | |
| metalinksdb_sqlite | 1.584 | 0.231 | 16.498 | |
| metalinksdb_table | 0.400 | 0.025 | 0.425 | |
| metalinksdb_tables | 0.036 | 0.004 | 0.040 | |
| ncbi_taxid | 0.465 | 0.009 | 0.594 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.019 | 0.001 | 0.020 | |
| nichenet_gr_network | 0.057 | 0.001 | 0.098 | |
| nichenet_gr_network_evex | 0.018 | 0.002 | 0.039 | |
| nichenet_gr_network_harmonizome | 0.016 | 0.001 | 0.017 | |
| nichenet_gr_network_htridb | 0.016 | 0.001 | 0.017 | |
| nichenet_gr_network_omnipath | 23.434 | 1.311 | 45.038 | |
| nichenet_gr_network_pathwaycommons | 0.008 | 0.001 | 0.009 | |
| nichenet_gr_network_regnetwork | 0.007 | 0.001 | 0.008 | |
| nichenet_gr_network_remap | 0.007 | 0.001 | 0.008 | |
| nichenet_gr_network_trrust | 0.008 | 0.000 | 0.008 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0.001 | 0.000 | 0.000 | |
| nichenet_lr_network | 0.021 | 0.003 | 0.024 | |
| nichenet_lr_network_guide2pharma | 0.008 | 0.000 | 0.008 | |
| nichenet_lr_network_omnipath | 0.022 | 0.001 | 0.023 | |
| nichenet_lr_network_ramilowski | 0.045 | 0.003 | 0.048 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.037 | 0.003 | 0.039 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.022 | 0.001 | 0.023 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.025 | 0.000 | 0.025 | |
| nichenet_signaling_network_cpdb | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_evex | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.000 | 0.007 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 17.428 | 1.089 | 24.205 | |
| nichenet_signaling_network_pathwaycommons | 0.019 | 0.001 | 0.020 | |
| nichenet_signaling_network_vinayagam | 0.017 | 0.001 | 0.017 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.312 | 0.024 | 1.349 | |
| oma_code | 0.230 | 0.002 | 0.300 | |
| oma_organisms | 0.126 | 0.010 | 0.202 | |
| oma_pairwise | 0.021 | 0.001 | 0.033 | |
| oma_pairwise_genesymbols | 0.020 | 0.003 | 0.046 | |
| oma_pairwise_translated | 0.020 | 0.002 | 0.043 | |
| omnipath-interactions | 35.090 | 2.308 | 90.470 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.008 | 0.000 | 0.008 | |
| omnipath_cache_clean_db | 0.088 | 0.006 | 0.094 | |
| omnipath_cache_download_ready | 0.522 | 0.072 | 1.678 | |
| omnipath_cache_filter_versions | 0.103 | 0.007 | 0.126 | |
| omnipath_cache_get | 0.067 | 0.001 | 0.069 | |
| omnipath_cache_key | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.044 | 0.005 | 0.050 | |
| omnipath_cache_load | 0.892 | 0.050 | 18.617 | |
| omnipath_cache_move_in | 0.144 | 0.011 | 0.174 | |
| omnipath_cache_remove | 0.103 | 0.004 | 0.121 | |
| omnipath_cache_save | 0.253 | 0.017 | 0.450 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_set_ext | 0.086 | 0.017 | 0.118 | |
| omnipath_cache_update_status | 0.075 | 0.007 | 0.082 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 10.249 | 0.642 | 59.219 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.000 | 0.002 | |
| omnipath_msg | 0.006 | 0.000 | 0.006 | |
| omnipath_query | 3.563 | 0.136 | 3.694 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.022 | 0.001 | 0.022 | |
| omnipath_set_console_loglevel | 0.004 | 0.000 | 0.003 | |
| omnipath_set_logfile_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.002 | |
| omnipath_show_db | 0.054 | 0.005 | 0.059 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.186 | 0.001 | 0.186 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 9.811 | 0.675 | 24.942 | |
| preppi_download | 0.000 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.695 | 0.071 | 1.966 | |
| print_bma_motif_vs | 0.270 | 0.020 | 1.473 | |
| print_interactions | 6.302 | 0.214 | 15.231 | |
| print_path_es | 0.943 | 0.061 | 5.026 | |
| print_path_vs | 2.583 | 0.176 | 10.772 | |
| pubmed_open | 3.718 | 0.099 | 3.819 | |
| query_info | 0.506 | 0.005 | 0.855 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0.002 | 0.000 | 0.002 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0 | 0 | 0 | |
| recon3d | 0.001 | 0.000 | 0.001 | |
| recon3d_raw | 0 | 0 | 0 | |
| recon3d_raw_vmh | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.245 | 0.020 | 0.981 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.060 | 0.005 | 0.191 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.000 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.566 | 0.019 | 0.930 | |
| resources | 0.147 | 0.010 | 1.151 | |
| resources_colname | 1.135 | 0.043 | 4.976 | |
| resources_in | 3.440 | 0.093 | 3.537 | |
| show_network | 0.001 | 0.000 | 0.000 | |
| signed_ptms | 4.742 | 0.104 | 5.842 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 5.518 | 0.245 | 6.658 | |
| static_tables | 0.047 | 0.005 | 0.061 | |
| stitch_actions | 0.000 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.007 | 0.000 | 0.007 | |
| swap_relations | 0.116 | 0.005 | 0.501 | |
| swissprots_only | 0.145 | 0.002 | 0.147 | |
| tfcensus_download | 0.575 | 0.017 | 1.227 | |
| translate_ids | 1.048 | 0.035 | 13.378 | |
| translate_ids_multi | 8.465 | 0.258 | 29.215 | |
| trembls_only | 0.133 | 0.001 | 0.135 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 1.014 | 0.026 | 15.150 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.000 | 0.001 | 0.000 | |
| uniprot_id_type | 0.002 | 0.000 | 0.002 | |
| uniprot_idmapping_id_types | 0.558 | 0.016 | 1.515 | |
| uniprot_organisms | 20.248 | 1.013 | 24.655 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.002 | 0.000 | 0.002 | |
| vinayagam_download | 0.000 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.000 | 0.001 | 0.002 | |
| with_extra_attrs | 12.402 | 1.421 | 18.093 | |
| with_references | 1.041 | 0.086 | 4.258 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |