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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('fgsea_1.39.0.tar.gz','quit-with-status'=TRUE)"
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── Installing fgsea ────────────────────────────────────────────────────────────
✔ Package installed successfully
── fgsea session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmOInOL/file2f7c38307e81c3/fgsea
→ BiocVersion: 3.24
→ Package: fgsea
→ PackageVersion: 1.39.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/fgsea.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpmOInOL/file2f7c38307e81c3/fgsea
→ installDir: /tmp/RtmpmOInOL/file2f7c385a1a599f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on fgsea ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1 to 4.6.0
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (9%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • fgsea-tutorial.Rmd
    • geseca-tutorial.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/geseca-tutorial.Rmd (chunk no. 32, line 472, column 32)
* Checking package installation calls in R code...
* Checking for library/require of fgsea...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/fgsea.R (line 386, column 22)
    • ...
    • R/plot.R (line 87, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • fgseaMultilevel.R (line 204, column 21)
    • geseca-multilevel.R (line 132, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/fgsea.R (line 265, column 9)
    • ...
    • R/pathways.R (line 31, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/fgsea.R (line 50, column 17)
    • ...
    • R/geseca-multilevel.R (line 171, column 17)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/fgsea.R (line 632, column 13)
  • set.seed() in R/geseca-simple.R (line 105, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/geseca-tutorial.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/geseca-multilevel.R (line 257, column 9)
  • ...
  • suppressMessages() in R/geseca-plot.R (line 539, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • fgseaMultilevel() (R/fgseaMultilevel.R): 212 lines
    • ...
    • fgseaLabel() (R/fgsea.R): 135 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/exampleExpressionMatrix.Rd
    • man/examplePathways.Rd
    • man/exampleRanks.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/collapsePathwaysGeseca.Rd
    • man/mapIdsList.Rd
    • man/writeGmtPathways.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • fgseaLabel.Rd
    • ...
    • plotGesecaTable.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • fgseaLabel.Rd
    • plotEnrichment.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • plotEnrichment.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test_gsea_analysis.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 340 lines (9%) are > 80 characters long.
  First few lines:
    • R/fgsea.R#L6 #' For compatibility with the previous i ...
    • ...
    • vignettes/geseca-tutorial.Rmd#L525 theme(plot.title = element_t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 422 lines (12%) are
not.
  First few lines:
    • R/fgsea.R#L29 minSize = min ...
    • ...
    • vignettes/geseca-tutorial.Rmd#L473 reduction.key="PCR_", npc ...
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...
* 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 v1.49.6 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the fgsea.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.