| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-15 11:58 -0500 (Sat, 15 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4903 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 3.18.1 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| 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: 3.18.1 |
| 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_3.18.1.tar.gz |
| StartedAt: 2025-11-15 02:34:38 -0500 (Sat, 15 Nov 2025) |
| EndedAt: 2025-11-15 03:14:39 -0500 (Sat, 15 Nov 2025) |
| EllapsedTime: 2400.6 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_3.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘3.18.1’
* 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
[2025-11-15 02:35:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-15 02:35:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 02:35:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-15 02:35:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-15 02:35:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-15 02:35:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-15 02:35:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-15 02:35:08] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-11-15; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-15 02:35:08] [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]
[2025-11-15 02:35:09] [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 0.6.38(2025-11-12); 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 3.18.1(2025-11-14); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); 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 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-15 02:35:09] [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
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-15 02:35:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-15 02:35:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-15 02:35:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-15 02:35:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-15 02:35:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:09] [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
[2025-11-15 02:35:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-15 02:35:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 02:35:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-15 02:35:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-15 02:35:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-15 02:35:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-15 02:35:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-15 02:35:25] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-11-15; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-15 02:35:25] [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]
[2025-11-15 02:35:25] [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 0.6.38(2025-11-12); 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 3.18.1(2025-11-14); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); 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 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-15 02:35:25] [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
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-15 02:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-15 02:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-15 02:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-15 02:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-15 02:35:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 02:35:25] [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 81.742 0.063 83.284
curated_ligrec_stats 66.692 4.592 176.676
omnipath-interactions 29.669 1.667 59.788
filter_extra_attrs 23.231 4.546 28.584
all_uniprots 25.159 1.573 293.626
uniprot_organisms 18.795 1.027 22.997
extra_attrs_to_cols 13.248 1.365 14.626
nichenet_gr_network_omnipath 14.053 0.491 17.068
curated_ligand_receptor_interactions 12.559 1.059 29.289
with_extra_attrs 11.962 1.147 15.789
extra_attr_values 11.288 1.291 15.421
go_annot_download 11.865 0.690 13.495
nichenet_signaling_network_omnipath 10.267 0.326 13.432
omnipath_for_cosmos 9.754 0.347 26.770
pivot_annotations 9.293 0.458 19.216
giant_component 9.116 0.496 12.878
translate_ids_multi 8.004 0.301 26.278
has_extra_attrs 7.126 1.104 8.239
filter_by_resource 7.728 0.334 10.639
extra_attrs 6.503 1.133 7.667
filter_intercell 6.452 0.394 11.659
print_interactions 5.982 0.210 11.256
static_table 5.475 0.175 6.518
find_all_paths 5.130 0.177 5.302
signed_ptms 4.755 0.070 5.579
ensembl_id_mapping_table 4.031 0.267 19.942
database_summary 2.985 0.204 6.490
ensembl_organisms 2.511 0.415 284.447
print_path_vs 2.608 0.132 6.144
ensembl_organisms_raw 1.887 0.404 223.687
kegg_conv 1.406 0.081 10.750
biomart_query 1.297 0.170 5.762
kegg_picture 1.175 0.027 5.767
translate_ids 1.085 0.045 10.720
metalinksdb_sqlite 0.925 0.158 11.346
kinasephos 1.003 0.071 17.647
uniprot_full_id_mapping_table 0.941 0.043 12.122
kegg_rm_prefix 0.745 0.050 5.902
kegg_link 0.735 0.040 6.017
* 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 ‘3.18.1’ ** 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 [2025-11-14 15:10:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-14 15:10:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-11-14 15:10:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-14 15:10:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14 [2025-11-14 15:10:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix [2025-11-14 15:10:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1 [2025-11-14 15:10:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-11-14 15:10:24] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-11-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-14 15:10:24] [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] [2025-11-14 15:10:25] [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 0.6.38(2025-11-12); 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 3.18.1(2025-11-14); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); 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 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-14 15:10:25] [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 [2025-11-14 15:10:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-14 15:10:25] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-11-14 15:10:25] [TRACE] [OmnipathR] Contains 10 files. [2025-11-14 15:10:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-14 15:10:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-14 15:10:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-11-14 15:10:25] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-11-14 15:10:25] [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). [2025-11-14 15:10:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:25] [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). [2025-11-14 15:10:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-14 15:10:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:25] [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). [2025-11-14 15:10:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:25] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-11-14 15:10:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-14 15:10:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:27] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-11-14 15:10:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-14 15:10:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14 [2025-11-14 15:10:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix [2025-11-14 15:10:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1 [2025-11-14 15:10:27] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-11-14 15:10:27] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-11-14; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-14 15:10:27] [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] [2025-11-14 15:10:27] [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 0.6.38(2025-11-12); 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 3.18.1(2025-11-14); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); 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 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-14 15:10:27] [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 [2025-11-14 15:10:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-14 15:10:27] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-11-14 15:10:27] [TRACE] [OmnipathR] Contains 1 files. [2025-11-14 15:10:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-14 15:10:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-14 15:10:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-11-14 15:10:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-11-14 15:10:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-14 15:10:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-14 15:10:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-14 15:10:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-14 15:10:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-14 15:10:27] [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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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)
[2025-11-15 03:03:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-15 03:03:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 03:03:30] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 03:03:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-15 03:03:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-14
[2025-11-15 03:03:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-14 20:10:11 UTC; unix
[2025-11-15 03:03:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.1
[2025-11-15 03:03:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-15 03:03:30] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); 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=2025-11-15; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-15 03:03:30] [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]
[2025-11-15 03:03:31] [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); 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 0.6.38(2025-11-12); 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 3.18.1(2025-11-14); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); 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 3.3.0(2025-11-13); 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 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-15 03:03:31] [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
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Contains 22 files.
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-15 03:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 03:03:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-15 03:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-15 03:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-15 03:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 03:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-15 03:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-15 03:03:31] [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
46.036 2.877 366.087
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.014 | 0.003 | 0.018 | |
| all_uniprots | 25.159 | 1.573 | 293.626 | |
| ancestors | 0.008 | 0.000 | 0.009 | |
| annotated_network | 1.397 | 0.118 | 4.811 | |
| annotation_categories | 81.742 | 0.063 | 83.284 | |
| annotation_resources | 0.174 | 0.017 | 1.090 | |
| annotations | 0.825 | 0.094 | 1.851 | |
| biomart_query | 1.297 | 0.170 | 5.762 | |
| bioplex1 | 0.01 | 0.00 | 0.01 | |
| bioplex2 | 0.009 | 0.000 | 0.010 | |
| bioplex3 | 0.009 | 0.000 | 0.008 | |
| bioplex_all | 0.007 | 0.001 | 0.008 | |
| bioplex_hct116_1 | 0.007 | 0.000 | 0.008 | |
| bma_motif_es | 0.871 | 0.082 | 1.981 | |
| bma_motif_vs | 0.352 | 0.017 | 1.112 | |
| chalmers_gem | 0.008 | 0.003 | 0.011 | |
| chalmers_gem_id_mapping_table | 0.010 | 0.000 | 0.009 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_network | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_raw | 0.006 | 0.002 | 0.008 | |
| chalmers_gem_reactions | 0.008 | 0.000 | 0.008 | |
| common_name | 0.133 | 0.000 | 0.133 | |
| complex_genes | 0.865 | 0.048 | 3.173 | |
| complex_resources | 0.184 | 0.015 | 0.946 | |
| complexes | 0.326 | 0.018 | 1.121 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.009 | 0.000 | 0.009 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 12.559 | 1.059 | 29.289 | |
| curated_ligrec_stats | 66.692 | 4.592 | 176.676 | |
| database_summary | 2.985 | 0.204 | 6.490 | |
| descendants | 0.024 | 0.002 | 0.050 | |
| ensembl_dataset | 0.091 | 0.003 | 0.110 | |
| ensembl_id_mapping_table | 4.031 | 0.267 | 19.942 | |
| ensembl_id_type | 0.004 | 0.000 | 0.004 | |
| ensembl_name | 0.510 | 0.026 | 0.663 | |
| ensembl_organisms | 2.511 | 0.415 | 284.447 | |
| ensembl_organisms_raw | 1.887 | 0.404 | 223.687 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.214 | 0.188 | 4.949 | |
| enzsub_resources | 0.209 | 0.014 | 0.972 | |
| enzyme_substrate | 1.132 | 0.036 | 1.866 | |
| evex_download | 0.006 | 0.001 | 0.009 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 11.288 | 1.291 | 15.421 | |
| extra_attrs | 6.503 | 1.133 | 7.667 | |
| extra_attrs_to_cols | 13.248 | 1.365 | 14.626 | |
| filter_by_resource | 7.728 | 0.334 | 10.639 | |
| filter_extra_attrs | 23.231 | 4.546 | 28.584 | |
| filter_intercell | 6.452 | 0.394 | 11.659 | |
| filter_intercell_network | 0.016 | 0.002 | 0.017 | |
| find_all_paths | 5.130 | 0.177 | 5.302 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_ontology_db | 0.009 | 0.001 | 0.009 | |
| giant_component | 9.116 | 0.496 | 12.878 | |
| go_annot_download | 11.865 | 0.690 | 13.495 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.008 | 0.001 | 0.009 | |
| guide2pharma_download | 0.008 | 0.000 | 0.007 | |
| harmonizome_download | 0.007 | 0.000 | 0.007 | |
| has_extra_attrs | 7.126 | 1.104 | 8.239 | |
| hmdb_id_mapping_table | 0.008 | 0.001 | 0.008 | |
| hmdb_id_type | 0.002 | 0.000 | 0.002 | |
| hmdb_metabolite_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.009 | 0.000 | 0.008 | |
| homologene_download | 0.008 | 0.000 | 0.008 | |
| homologene_raw | 0.055 | 0.002 | 0.058 | |
| homologene_uniprot_orthology | 0.01 | 0.00 | 0.01 | |
| hpo_download | 2.711 | 0.125 | 3.147 | |
| htridb_download | 0.007 | 0.001 | 0.009 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.042 | 0.001 | 0.042 | |
| inbiomap_download | 0.001 | 0.000 | 0.000 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.669 | 0.032 | 0.953 | |
| interaction_graph | 0.507 | 0.018 | 1.478 | |
| interaction_resources | 0.128 | 0.009 | 0.918 | |
| interaction_types | 0.073 | 0.002 | 0.075 | |
| intercell | 0.861 | 0.070 | 1.791 | |
| intercell_categories | 0.689 | 0.023 | 0.961 | |
| intercell_consensus_filter | 1.371 | 0.073 | 3.299 | |
| intercell_generic_categories | 0.074 | 0.001 | 0.076 | |
| intercell_network | 0.008 | 0.000 | 0.008 | |
| intercell_resources | 0.175 | 0.007 | 0.933 | |
| intercell_summary | 0.092 | 0.002 | 0.094 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.085 | 0.001 | 0.086 | |
| is_trembl | 0.058 | 0.000 | 0.058 | |
| is_uniprot | 0.008 | 0.000 | 0.009 | |
| kegg_api_templates | 0.000 | 0.000 | 0.001 | |
| kegg_conv | 1.406 | 0.081 | 10.750 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.678 | 0.034 | 2.013 | |
| kegg_find | 0.662 | 0.024 | 2.146 | |
| kegg_info | 0.009 | 0.000 | 0.009 | |
| kegg_link | 0.735 | 0.040 | 6.017 | |
| kegg_list | 0.718 | 0.032 | 1.730 | |
| kegg_open | 0.008 | 0.001 | 0.009 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.008 | 0.014 | 0.021 | |
| kegg_organisms | 0.017 | 0.006 | 0.023 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.009 | 0.000 | 0.009 | |
| kegg_pathway_list | 0.007 | 0.001 | 0.008 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.175 | 0.027 | 5.767 | |
| kegg_process | 0.016 | 0.001 | 0.016 | |
| kegg_query | 0.007 | 0.000 | 0.007 | |
| kegg_request | 0.058 | 0.004 | 0.062 | |
| kegg_rm_prefix | 0.745 | 0.050 | 5.902 | |
| kinasephos | 1.003 | 0.071 | 17.647 | |
| latin_name | 0.261 | 0.005 | 0.265 | |
| load_db | 0.066 | 0.012 | 0.078 | |
| metalinksdb_sqlite | 0.925 | 0.158 | 11.346 | |
| metalinksdb_table | 0.197 | 0.017 | 0.213 | |
| metalinksdb_tables | 0.016 | 0.000 | 0.016 | |
| ncbi_taxid | 0.249 | 0.002 | 0.250 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.007 | 0.001 | 0.009 | |
| nichenet_gr_network | 0.021 | 0.002 | 0.024 | |
| nichenet_gr_network_evex | 0.007 | 0.001 | 0.008 | |
| nichenet_gr_network_harmonizome | 0.007 | 0.001 | 0.008 | |
| nichenet_gr_network_htridb | 0.008 | 0.000 | 0.007 | |
| nichenet_gr_network_omnipath | 14.053 | 0.491 | 17.068 | |
| nichenet_gr_network_pathwaycommons | 0.009 | 0.000 | 0.009 | |
| nichenet_gr_network_regnetwork | 0.006 | 0.002 | 0.008 | |
| nichenet_gr_network_remap | 0.007 | 0.001 | 0.007 | |
| nichenet_gr_network_trrust | 0.044 | 0.001 | 0.045 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.023 | 0.001 | 0.024 | |
| nichenet_lr_network_guide2pharma | 0.005 | 0.002 | 0.008 | |
| nichenet_lr_network_omnipath | 0.021 | 0.001 | 0.023 | |
| nichenet_lr_network_ramilowski | 0.007 | 0.000 | 0.008 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.035 | 0.004 | 0.039 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.020 | 0.003 | 0.024 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.024 | 0.000 | 0.024 | |
| nichenet_signaling_network_cpdb | 0.006 | 0.002 | 0.008 | |
| nichenet_signaling_network_evex | 0.006 | 0.002 | 0.008 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 10.267 | 0.326 | 13.432 | |
| nichenet_signaling_network_pathwaycommons | 0.009 | 0.000 | 0.009 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.000 | 0.008 | |
| nichenet_test | 0.001 | 0.000 | 0.000 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.095 | 0.006 | 0.147 | |
| oma_code | 0.129 | 0.003 | 0.131 | |
| oma_organisms | 0.116 | 0.009 | 0.125 | |
| oma_pairwise | 0.009 | 0.001 | 0.009 | |
| oma_pairwise_genesymbols | 0.008 | 0.001 | 0.009 | |
| oma_pairwise_translated | 0.008 | 0.001 | 0.009 | |
| omnipath-interactions | 29.669 | 1.667 | 59.788 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.007 | 0.000 | 0.007 | |
| omnipath_cache_clean_db | 0.087 | 0.011 | 0.098 | |
| omnipath_cache_download_ready | 0.575 | 0.063 | 0.822 | |
| omnipath_cache_filter_versions | 0.084 | 0.007 | 0.106 | |
| omnipath_cache_get | 0.061 | 0.006 | 0.066 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.043 | 0.005 | 0.047 | |
| omnipath_cache_load | 0.750 | 0.035 | 4.057 | |
| omnipath_cache_move_in | 0.176 | 0.010 | 0.200 | |
| omnipath_cache_remove | 0.075 | 0.004 | 0.092 | |
| omnipath_cache_save | 0.191 | 0.013 | 0.379 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.061 | 0.006 | 0.081 | |
| omnipath_cache_update_status | 0.073 | 0.005 | 0.078 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 9.754 | 0.347 | 26.770 | |
| omnipath_load_config | 0.001 | 0.000 | 0.000 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.002 | 0.000 | 0.001 | |
| omnipath_msg | 0.004 | 0.001 | 0.004 | |
| omnipath_query | 3.428 | 0.075 | 3.500 | |
| 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 | 0.003 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.002 | |
| omnipath_show_db | 0.058 | 0.003 | 0.061 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.000 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.180 | 0.002 | 0.182 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.000 | |
| pivot_annotations | 9.293 | 0.458 | 19.216 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0.000 | 0.001 | 0.001 | |
| print_bma_motif_es | 0.657 | 0.052 | 1.741 | |
| print_bma_motif_vs | 0.220 | 0.014 | 0.984 | |
| print_interactions | 5.982 | 0.210 | 11.256 | |
| print_path_es | 0.938 | 0.052 | 2.842 | |
| print_path_vs | 2.608 | 0.132 | 6.144 | |
| pubmed_open | 4.013 | 0.056 | 4.067 | |
| query_info | 0.473 | 0.007 | 0.891 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.002 | 0.000 | 0.002 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.001 | 0.000 | |
| ramp_tables | 0 | 0 | 0 | |
| recon3d | 0.002 | 0.000 | 0.002 | |
| recon3d_raw | 0.000 | 0.000 | 0.001 | |
| recon3d_raw_vmh | 0.000 | 0.001 | 0.000 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.073 | 0.001 | 0.122 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.050 | 0.010 | 0.098 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.518 | 0.016 | 0.781 | |
| resources | 0.118 | 0.006 | 0.827 | |
| resources_colname | 1.134 | 0.025 | 3.691 | |
| resources_in | 3.427 | 0.066 | 3.498 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 4.755 | 0.070 | 5.579 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 5.475 | 0.175 | 6.518 | |
| static_tables | 0.041 | 0.008 | 0.057 | |
| 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 | 0.006 | 0.001 | 0.007 | |
| swap_relations | 0.081 | 0.009 | 0.129 | |
| swissprots_only | 0.168 | 0.002 | 0.171 | |
| tfcensus_download | 0.566 | 0.016 | 0.742 | |
| translate_ids | 1.085 | 0.045 | 10.720 | |
| translate_ids_multi | 8.004 | 0.301 | 26.278 | |
| trembls_only | 0.128 | 0.001 | 0.129 | |
| trrust_download | 0.000 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 0.941 | 0.043 | 12.122 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| uniprot_id_type | 0.002 | 0.000 | 0.001 | |
| uniprot_idmapping_id_types | 0.500 | 0.023 | 1.007 | |
| uniprot_organisms | 18.795 | 1.027 | 22.997 | |
| 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 | 0 | 0 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.001 | |
| with_extra_attrs | 11.962 | 1.147 | 15.789 | |
| with_references | 0.961 | 0.142 | 2.936 | |
| zenodo_download | 0.002 | 0.000 | 0.001 | |