Denes Turei
| Snapshot Date: 2025-12-21 13:40 -0500 (Sun, 21 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: f5182b3 |
| git_last_commit_date: 2025-12-10 07:50:10 -0500 (Wed, 10 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-22 11:34 -0500 (Mon, 22 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4878 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 1491/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.5 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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: 3.19.5 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.5.tar.gz |
| StartedAt: 2025-12-22 01:46:57 -0500 (Mon, 22 Dec 2025) |
| EndedAt: 2025-12-22 02:26:40 -0500 (Mon, 22 Dec 2025) |
| EllapsedTime: 2382.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.5’
* 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
[2025-12-22 01:47:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-22 01:47:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:47:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 01:47:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-22 01:47:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-22 01:47:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:08:48 UTC; unix
[2025-12-22 01:47:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-22 01:47:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-22 01:47:37] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-22 01:47:37] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-22 01:47:37] [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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); 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 1.1.0.8.1(2025-12-08); 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 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-22 01:47:37] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-22 01:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:47:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-22 01:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-22 01:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-22 01:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:47:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-22 01:47:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:47:37] [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
[2025-12-22 01:48:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-22 01:48:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:48:01] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 01:48:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-22 01:48:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-22 01:48:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:08:48 UTC; unix
[2025-12-22 01:48:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-22 01:48:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-22 01:48:03] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-22 01:48:03] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-22 01:48:04] [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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); 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 1.1.0.8.1(2025-12-08); 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 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-22 01:48:04] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-22 01:48:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:48:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-22 01:48:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-22 01:48:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-22 01:48:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-22 01:48:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 01:48:04] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
patch_httr2_keep_handle: no visible binding for global variable
‘handle’
patch_httr2_keep_handle: no visible global function definition for
‘ORIGINAL’
Undefined global functions or variables:
ORIGINAL enzyme_genesymbol handle
* 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 79.364 0.021 81.755
curated_ligrec_stats 42.968 2.701 146.903
filter_extra_attrs 31.283 5.377 38.744
omnipath-interactions 34.596 1.688 75.142
extra_attrs_to_cols 27.360 1.965 32.338
nichenet_gr_network_omnipath 25.333 1.049 31.508
extra_attr_values 24.572 1.805 43.989
all_uniprots 24.281 1.394 41.992
uniprot_organisms 19.680 1.215 24.127
go_annot_download 19.106 1.141 23.559
giant_component 19.283 0.805 25.965
filter_by_resource 16.242 0.864 23.907
pivot_annotations 14.826 1.197 30.894
nichenet_signaling_network_omnipath 15.233 0.621 21.743
has_extra_attrs 14.122 1.692 16.484
with_extra_attrs 12.954 1.408 18.610
filter_intercell 12.423 0.826 25.640
extra_attrs 10.819 1.308 12.810
omnipath_for_cosmos 10.694 0.608 32.785
find_all_paths 9.708 0.280 10.749
translate_ids_multi 9.088 0.301 25.546
print_interactions 8.150 0.308 15.940
curated_ligand_receptor_interactions 6.994 0.656 22.174
static_table 6.019 0.380 14.666
omnipath_query 5.760 0.232 6.102
hpo_download 5.122 0.183 8.199
signed_ptms 5.052 0.130 6.152
kegg_conv 2.828 0.119 13.342
print_path_vs 2.523 0.198 6.849
ensembl_id_mapping_table 2.482 0.176 18.649
enzsub_graph 2.326 0.088 5.563
kinasephos 2.089 0.143 25.489
metalinksdb_sqlite 1.974 0.182 16.353
kegg_picture 1.815 0.034 6.000
kegg_link 1.662 0.174 7.779
kegg_rm_prefix 1.641 0.051 6.246
annotated_network 1.511 0.094 5.828
biomart_query 1.210 0.085 5.442
translate_ids 1.157 0.054 10.887
uniprot_full_id_mapping_table 1.070 0.045 13.100
omnipath_cache_load 1.051 0.050 5.335
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.5’ ** 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 [2025-12-21 15:09:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-21 15:09:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-21 15:09:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-21 15:09:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21 [2025-12-21 15:09:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:08:48 UTC; unix [2025-12-21 15:09:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5 [2025-12-21 15:09:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-21 15:09:03] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-21 15:09:03] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-21 15:09:03] [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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); 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 1.1.0.8.1(2025-12-08); 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 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2025-12-21 15:09:03] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-12-21 15:09:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-21 15:09:03] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-21 15:09:03] [TRACE] [OmnipathR] Contains 9 files. [2025-12-21 15:09:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-21 15:09:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-21 15:09:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-21 15:09:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-21 15:09:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-21 15:09:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-21 15:09:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-21 15:09:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-21 15:09:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:03] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-12-21 15:09:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-21 15:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-21 15:09:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-21 15:09:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21 [2025-12-21 15:09:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:08:48 UTC; unix [2025-12-21 15:09:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5 [2025-12-21 15:09:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-21 15:09:06] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-21; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-21 15:09:06] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-21 15:09:06] [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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); 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 1.1.0.8.1(2025-12-08); 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 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2025-12-21 15:09:06] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-12-21 15:09:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-21 15:09:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-21 15:09:06] [TRACE] [OmnipathR] Contains 1 files. [2025-12-21 15:09:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-21 15:09:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-21 15:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-21 15:09:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-21 15:09:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-21 15:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-21 15:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-21 15:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-21 15:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-21 15:09:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-12-22 02:07:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-22 02:07:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 02:07:12] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 02:07:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-22 02:07:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-21
[2025-12-22 02:07:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-21 20:08:48 UTC; unix
[2025-12-22 02:07:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-22 02:07:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-22 02:07:12] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-22 02:07:12] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-22 02:07:13] [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 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-21); 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); 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 1.1.0.8.1(2025-12-08); 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 1.3.2(2025-12-19); 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 0.55(2025-12-16); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-22 02:07:13] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Contains 22 files.
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-22 02:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 02:07:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-22 02:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-22 02:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-22 02:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-22 02:07:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-22 02:07:13] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
44.337 2.575 90.325
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.015 | 0.002 | 0.016 | |
| all_uniprots | 24.281 | 1.394 | 41.992 | |
| ancestors | 0.009 | 0.000 | 0.009 | |
| annotated_network | 1.511 | 0.094 | 5.828 | |
| annotation_categories | 79.364 | 0.021 | 81.755 | |
| annotation_resources | 0.121 | 0.007 | 1.288 | |
| annotations | 0.724 | 0.037 | 2.040 | |
| biomart_query | 1.210 | 0.085 | 5.442 | |
| bioplex1 | 0.009 | 0.000 | 0.009 | |
| bioplex2 | 0.006 | 0.002 | 0.008 | |
| bioplex3 | 0.007 | 0.002 | 0.009 | |
| bioplex_all | 0.008 | 0.000 | 0.009 | |
| bioplex_hct116_1 | 0.007 | 0.001 | 0.008 | |
| bma_motif_es | 0.813 | 0.062 | 2.125 | |
| bma_motif_vs | 0.261 | 0.011 | 1.132 | |
| chalmers_gem | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.001 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_network | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_raw | 0.028 | 0.000 | 0.028 | |
| chalmers_gem_reactions | 0.008 | 0.000 | 0.008 | |
| common_name | 0.127 | 0.001 | 0.128 | |
| complex_genes | 0.762 | 0.029 | 3.580 | |
| complex_resources | 0.120 | 0.004 | 0.987 | |
| complexes | 0.324 | 0.010 | 1.273 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.008 | 0.000 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.994 | 0.656 | 22.174 | |
| curated_ligrec_stats | 42.968 | 2.701 | 146.903 | |
| database_summary | 1.617 | 0.087 | 4.227 | |
| descendants | 0.01 | 0.00 | 0.01 | |
| ensembl_dataset | 0.047 | 0.002 | 0.050 | |
| ensembl_id_mapping_table | 2.482 | 0.176 | 18.649 | |
| ensembl_id_type | 0.003 | 0.000 | 0.002 | |
| ensembl_name | 0.342 | 0.002 | 0.344 | |
| ensembl_organisms | 0.102 | 0.019 | 0.122 | |
| ensembl_organisms_raw | 0.101 | 0.017 | 0.119 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 2.326 | 0.088 | 5.563 | |
| enzsub_resources | 0.162 | 0.007 | 1.129 | |
| enzyme_substrate | 1.142 | 0.034 | 2.138 | |
| evex_download | 0.009 | 0.000 | 0.009 | |
| evidences | 0.001 | 0.000 | 0.000 | |
| extra_attr_values | 24.572 | 1.805 | 43.989 | |
| extra_attrs | 10.819 | 1.308 | 12.810 | |
| extra_attrs_to_cols | 27.360 | 1.965 | 32.338 | |
| filter_by_resource | 16.242 | 0.864 | 23.907 | |
| filter_extra_attrs | 31.283 | 5.377 | 38.744 | |
| filter_intercell | 12.423 | 0.826 | 25.640 | |
| filter_intercell_network | 0.041 | 0.000 | 0.041 | |
| find_all_paths | 9.708 | 0.280 | 10.749 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_ontology_db | 0.009 | 0.000 | 0.009 | |
| giant_component | 19.283 | 0.805 | 25.965 | |
| go_annot_download | 19.106 | 1.141 | 23.559 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.010 | 0.001 | 0.010 | |
| guide2pharma_download | 0.009 | 0.001 | 0.009 | |
| harmonizome_download | 0.009 | 0.000 | 0.009 | |
| has_extra_attrs | 14.122 | 1.692 | 16.484 | |
| hmdb_id_mapping_table | 0.032 | 0.002 | 0.071 | |
| hmdb_id_type | 0.006 | 0.001 | 0.013 | |
| hmdb_metabolite_fields | 0.000 | 0.002 | 0.006 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_table | 0.025 | 0.001 | 0.054 | |
| homologene_download | 0.021 | 0.002 | 0.049 | |
| homologene_raw | 0.115 | 0.002 | 0.162 | |
| homologene_uniprot_orthology | 0.019 | 0.001 | 0.020 | |
| hpo_download | 5.122 | 0.183 | 8.199 | |
| htridb_download | 0.018 | 0.002 | 0.021 | |
| id_translation_resources | 0.001 | 0.000 | 0.000 | |
| id_types | 0.092 | 0.004 | 0.095 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0.001 | 0.000 | 0.000 | |
| interaction_datasets | 1.867 | 0.057 | 2.522 | |
| interaction_graph | 0.764 | 0.024 | 1.847 | |
| interaction_resources | 0.170 | 0.014 | 1.347 | |
| interaction_types | 0.160 | 0.003 | 0.162 | |
| intercell | 1.307 | 0.087 | 2.585 | |
| intercell_categories | 1.055 | 0.052 | 1.393 | |
| intercell_consensus_filter | 1.941 | 0.137 | 4.200 | |
| intercell_generic_categories | 0.087 | 0.005 | 0.092 | |
| intercell_network | 0.010 | 0.001 | 0.011 | |
| intercell_resources | 0.163 | 0.009 | 1.213 | |
| intercell_summary | 0.287 | 0.023 | 0.310 | |
| is_ontology_id | 0.000 | 0.001 | 0.001 | |
| is_swissprot | 0.097 | 0.005 | 0.102 | |
| is_trembl | 0.100 | 0.005 | 0.105 | |
| is_uniprot | 0.016 | 0.002 | 0.018 | |
| kegg_api_templates | 0.002 | 0.004 | 0.006 | |
| kegg_conv | 2.828 | 0.119 | 13.342 | |
| kegg_databases | 0.001 | 0.000 | 0.000 | |
| kegg_ddi | 1.592 | 0.053 | 4.010 | |
| kegg_find | 1.514 | 0.052 | 4.396 | |
| kegg_info | 0.021 | 0.003 | 0.025 | |
| kegg_link | 1.662 | 0.174 | 7.779 | |
| kegg_list | 1.187 | 0.050 | 2.370 | |
| kegg_open | 0.015 | 0.002 | 0.017 | |
| kegg_operations | 0.000 | 0.001 | 0.000 | |
| kegg_organism_codes | 0.023 | 0.110 | 0.133 | |
| kegg_organisms | 0.029 | 0.004 | 0.052 | |
| kegg_pathway_annotations | 0.001 | 0.000 | 0.000 | |
| kegg_pathway_download | 0.013 | 0.002 | 0.015 | |
| kegg_pathway_list | 0.013 | 0.001 | 0.014 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 1.815 | 0.034 | 6.000 | |
| kegg_process | 0.028 | 0.003 | 0.031 | |
| kegg_query | 0.012 | 0.001 | 0.013 | |
| kegg_request | 0.109 | 0.007 | 0.116 | |
| kegg_rm_prefix | 1.641 | 0.051 | 6.246 | |
| kinasephos | 2.089 | 0.143 | 25.489 | |
| latin_name | 0.540 | 0.012 | 0.821 | |
| load_db | 0.173 | 0.015 | 0.189 | |
| metalinksdb_sqlite | 1.974 | 0.182 | 16.353 | |
| metalinksdb_table | 0.440 | 0.045 | 0.488 | |
| metalinksdb_tables | 0.048 | 0.001 | 0.050 | |
| ncbi_taxid | 0.526 | 0.005 | 0.571 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.022 | 0.003 | 0.024 | |
| nichenet_gr_network | 0.069 | 0.007 | 0.138 | |
| nichenet_gr_network_evex | 0.023 | 0.002 | 0.052 | |
| nichenet_gr_network_harmonizome | 0.021 | 0.002 | 0.036 | |
| nichenet_gr_network_htridb | 0.014 | 0.005 | 0.020 | |
| nichenet_gr_network_omnipath | 25.333 | 1.049 | 31.508 | |
| nichenet_gr_network_pathwaycommons | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_regnetwork | 0.008 | 0.000 | 0.009 | |
| nichenet_gr_network_remap | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_trrust | 0.009 | 0.000 | 0.008 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.025 | 0.002 | 0.026 | |
| nichenet_lr_network_guide2pharma | 0.008 | 0.002 | 0.009 | |
| nichenet_lr_network_omnipath | 0.025 | 0.005 | 0.029 | |
| nichenet_lr_network_ramilowski | 0.009 | 0.001 | 0.009 | |
| nichenet_main | 0.000 | 0.001 | 0.000 | |
| nichenet_networks | 0.033 | 0.012 | 0.045 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.023 | 0.003 | 0.026 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.022 | 0.006 | 0.028 | |
| nichenet_signaling_network_cpdb | 0.007 | 0.001 | 0.009 | |
| nichenet_signaling_network_evex | 0.009 | 0.000 | 0.009 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.001 | 0.009 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 15.233 | 0.621 | 21.743 | |
| nichenet_signaling_network_pathwaycommons | 0.073 | 0.000 | 0.074 | |
| nichenet_signaling_network_vinayagam | 0.011 | 0.002 | 0.012 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.206 | 0.049 | 0.818 | |
| oma_code | 0.147 | 0.001 | 0.148 | |
| oma_organisms | 0.066 | 0.005 | 0.072 | |
| oma_pairwise | 0.009 | 0.002 | 0.011 | |
| oma_pairwise_genesymbols | 0.008 | 0.001 | 0.009 | |
| oma_pairwise_translated | 0.009 | 0.000 | 0.009 | |
| omnipath-interactions | 34.596 | 1.688 | 75.142 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.003 | |
| omnipath_cache_clean | 0.015 | 0.001 | 0.032 | |
| omnipath_cache_clean_db | 0.167 | 0.017 | 0.268 | |
| omnipath_cache_download_ready | 0.973 | 0.082 | 1.406 | |
| omnipath_cache_filter_versions | 0.166 | 0.019 | 0.325 | |
| omnipath_cache_get | 0.146 | 0.017 | 0.237 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.092 | 0.008 | 0.101 | |
| omnipath_cache_load | 1.051 | 0.050 | 5.335 | |
| omnipath_cache_move_in | 0.799 | 0.058 | 0.903 | |
| omnipath_cache_remove | 0.271 | 0.038 | 0.420 | |
| omnipath_cache_save | 0.492 | 0.044 | 0.683 | |
| omnipath_cache_search | 0.002 | 0.000 | 0.002 | |
| omnipath_cache_set_ext | 0.321 | 0.023 | 0.357 | |
| omnipath_cache_update_status | 0.314 | 0.014 | 0.327 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 10.694 | 0.608 | 32.785 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.001 | 0.002 | |
| omnipath_msg | 0.004 | 0.001 | 0.006 | |
| omnipath_query | 5.760 | 0.232 | 6.102 | |
| omnipath_reset_config | 0.001 | 0.000 | 0.000 | |
| omnipath_save_config | 0.000 | 0.000 | 0.001 | |
| omnipath_set_cachedir | 0.041 | 0.010 | 0.050 | |
| omnipath_set_console_loglevel | 0.005 | 0.002 | 0.008 | |
| omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.006 | |
| omnipath_set_loglevel | 0.002 | 0.001 | 0.004 | |
| omnipath_show_db | 0.106 | 0.020 | 0.126 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.002 | 0.000 | 0.002 | |
| organism_for | 0.314 | 0.010 | 0.324 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.002 | |
| pivot_annotations | 14.826 | 1.197 | 30.894 | |
| preppi_download | 0.001 | 0.000 | 0.002 | |
| preppi_filter | 0.002 | 0.000 | 0.001 | |
| print_bma_motif_es | 1.252 | 0.065 | 2.891 | |
| print_bma_motif_vs | 0.357 | 0.018 | 1.315 | |
| print_interactions | 8.150 | 0.308 | 15.940 | |
| print_path_es | 0.878 | 0.084 | 3.500 | |
| print_path_vs | 2.523 | 0.198 | 6.849 | |
| pubmed_open | 3.942 | 0.104 | 4.042 | |
| query_info | 0.515 | 0.010 | 0.809 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| ramp_id_type | 0.002 | 0.000 | 0.003 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| recon3d | 0.002 | 0.000 | 0.002 | |
| recon3d_raw | 0.001 | 0.000 | 0.001 | |
| recon3d_raw_vmh | 0.000 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.176 | 0.024 | 0.523 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.090 | 0.024 | 0.245 | |
| remap_dorothea_download | 0.000 | 0.001 | 0.001 | |
| remap_filtered | 0.000 | 0.001 | 0.001 | |
| remap_tf_target_download | 0.000 | 0.001 | 0.001 | |
| resource_info | 0.601 | 0.053 | 0.961 | |
| resources | 0.157 | 0.008 | 1.135 | |
| resources_colname | 1.217 | 0.051 | 4.752 | |
| resources_in | 3.604 | 0.069 | 3.675 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 5.052 | 0.130 | 6.152 | |
| simplify_intercell_network | 0.000 | 0.001 | 0.002 | |
| static_table | 6.019 | 0.380 | 14.666 | |
| static_tables | 0.047 | 0.004 | 0.055 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.001 | 0.001 | |
| stitch_network | 0.000 | 0.001 | 0.001 | |
| stitch_remove_prefixes | 0.005 | 0.002 | 0.006 | |
| swap_relations | 0.062 | 0.014 | 0.203 | |
| swissprots_only | 0.129 | 0.005 | 0.134 | |
| tfcensus_download | 0.589 | 0.028 | 1.185 | |
| translate_ids | 1.157 | 0.054 | 10.887 | |
| translate_ids_multi | 9.088 | 0.301 | 25.546 | |
| trembls_only | 0.140 | 0.001 | 0.141 | |
| trrust_download | 0.000 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.070 | 0.045 | 13.100 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.000 | 0.001 | 0.001 | |
| uniprot_id_type | 0.002 | 0.000 | 0.002 | |
| uniprot_idmapping_id_types | 0.600 | 0.017 | 1.752 | |
| uniprot_organisms | 19.680 | 1.215 | 24.127 | |
| unique_intercell_network | 0.000 | 0.001 | 0.001 | |
| unnest_evidences | 0.000 | 0.000 | 0.001 | |
| uploadlists_id_type | 0.001 | 0.000 | 0.002 | |
| vinayagam_download | 0.001 | 0.000 | 0.000 | |
| walk_ontology_tree | 0.000 | 0.000 | 0.001 | |
| with_extra_attrs | 12.954 | 1.408 | 18.610 | |
| with_references | 1.031 | 0.072 | 3.524 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |