[ Started: 2024-12-07 12:36:31 CET ]
[ OmnipathR v3.12.4 for BioC-3.19 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_19 (edb3c69 2024-10-02 12:46:04) ]

Loading required package: BiocCheck
─ BiocCheckVersion: 1.40.0
─ BiocVersion: 3.19
─ Package: OmnipathR
─ PackageVersion: 3.12.4
─ sourceDir: /tmp/RtmpZTHyTD/file2f09534153e9e9/OmnipathR
─ installDir: /tmp/RtmpZTHyTD/file2f0953e3c94eb
─ BiocCheckDir: /mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-12-07_1230/OmnipathR/OmnipathR.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.0 to 4.4.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      GenePrediction
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    * WARNING: No Bioconductor dependencies detected. Note that some
      infrastructure packages may not have Bioconductor dependencies.
      For more information, reach out to the Bioconductor community
      and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of OmnipathR...
* Checking coding practice...
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * WARNING: .Deprecated / .Defunct usage (found 26 times)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 63 functions greater than 50 lines.
* Checking man page documentation...
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 12:37:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 12:37:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpZTHyTD/file2f0953e3c94eb/lib/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpZTHyTD/file2f0953e3c94eb/lib/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpZTHyTD/file2f0953e3c94eb/lib/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpZTHyTD/file2f0953e3c94eb/lib/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-07 12:37:17] [TRACE]   [OmnipathR] Cache locked: FALSE
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 15% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 55 lines (0%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 55 lines
      (0%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      Bioc-Devel mailing list (requires admin credentials). Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
0 ERRORS | 2 WARNINGS | 12 NOTES

See the OmnipathR.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.
[ Finished: 2024-12-07 12:37:20 CET ]