[ Started: 2024-09-24 15:42:54 CEST ]
[ OmnipathR v3.13.25 for BioC-3.20 from https://github.com/saezlab/OmnipathR@master (d07da8c 2024-09-07 17:02:07) ]

Loading required package: BiocCheck
── Installing OmnipathR ────────────────────────────────────────────────────────
✔ Package installed successfully
── OmnipathR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpkBUm2h/fileb08717aca6828/OmnipathR
→ BiocVersion: 3.20
→ Package: OmnipathR
→ PackageVersion: 3.13.25
→ BiocCheckDir: /mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2024-09-24_1535/OmnipathR/OmnipathR.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpkBUm2h/fileb08717aca6828/OmnipathR
→ installDir: /tmp/RtmpkBUm2h/fileb0871ac23292
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OmnipathR ──────────────────────────────────────────────
* 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...
ℹ 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: GenePrediction
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* 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
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/annotations.R (line 135, column 9)
• ...
• print() in R/uniprot.R (line 31, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/adecorate.R (line 38, column 23)
• ...
• R/homologene.R (line 250, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• misc.R (line 1112, column 24)
• misc.R (line 1119, column 28)
! WARNING: .Deprecated / .Defunct usage (found 27 times)
• .Deprecated() in R/annotations.R (line 180, column 5)
• ...
• .Deprecated() in R/resources.R (line 97, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
• suppressWarnings() in R/cache.R (line 66, column 5)
• ...
• suppressWarnings() in R/tfcensus.R (line 48, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 74
functions greater than 50 lines.
The longest 5 functions are:
• homology_translate() (R/homology.R): 220 lines
• ...
• obo_parser() (R/obo.R): 149 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/stitch_remove_prefixes.Rd
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-24 15:43:40] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-24 15:43:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpkBUm2h/fileb0871ac23292/lib/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpkBUm2h/fileb0871ac23292/lib/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpkBUm2h/fileb0871ac23292/lib/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpkBUm2h/fileb0871ac23292/lib/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-24 15:43:40] [TRACE]   [OmnipathR] Cache locked: FALSE
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
• consensuspathdb_download.Rd
• ...
• unnest_evidences.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man
pages use at least one of these tags.
Found in files:
• consensuspathdb_download.Rd
• ...
• unnest_evidences.Rd
ℹ NOTE: Use donttest instead of dontrun.
Found in files:
• consensuspathdb_download.Rd
• ...
• unnest_evidences.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 59 lines (0%) are > 80 characters long.
First few lines:
• R/annotations.R#L38 #' \url{https://archive.omnipathdb.org/o ...
• ...
• vignettes/omnipath_intro.Rmd#L765 `r BiocStyle::Biocpkg("OmnipathR")` prov
  ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 75 lines (0%) are not.
First few lines:
• R/chalmers_gem.R#L123 slice(metabolites, ...
• ...
• vignettes/drug_targets.Rmd#L158 print(all(drug_targets$in_OP)) ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ 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...
ℹ 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...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 4 WARNINGS | • 12 NOTES
ℹ See the OmnipathR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.
[ Finished: 2024-09-24 15:43:43 CEST ]