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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('clusterProfiler_4.20.0.tar.gz','quit-with-status'=TRUE)"
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── Installing clusterProfiler ──────────────────────────────────────────────────
✔ Package installed successfully
── clusterProfiler session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgonoBQ/file759295a5c11af/clusterProfiler
→ BiocVersion: 3.23
→ Package: clusterProfiler
→ PackageVersion: 4.20.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/clusterProfiler.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpgonoBQ/file759295a5c11af/clusterProfiler
→ installDir: /tmp/RtmpgonoBQ/file7592953eaa711
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on clusterProfiler ────────────────────────────────────────
* 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 4.2.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
FunctionalGenomics
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...
ℹ Bioconductor dependencies found in Imports & Depends (19%).
* 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...
! WARNING: Quarto vignette found but 'SystemRequirements' field not in
DESCRIPTION.
* Checking package installation calls in R code...
* Checking for library/require of clusterProfiler...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/enrichKEGG.R (line 292, column 22)
    • require() in R/gson.R (line 88, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/compareCluster.R (line 181, column 22)
    • ...
    • R/utilities.R (line 9, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • compareCluster.R (line 191, column 15)
    • ...
    • uniprot.R (line 25, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/enrichKEGG.R (line 288, column 5)
    • ...
    • print() in R/plot_interpret.R (line 70, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/compareCluster.R (line 123, column 23)
    • ...
    • R/taxa.R (line 8, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/bitr.R (line 52, column 21)
    • R/bitr.R (line 92, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • F in R/kegg-utilities.R (line 105, column 66)
    • ...
    • T in R/utilities.R (line 7, column 37)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/GFFparser.R (line 83, column 24)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/bitr.R (line 43, column 12)
  • ...
  • suppressMessages() in R/gson.R (line 96, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 24
functions greater than 50 lines.
  The longest 5 functions are:
    • interpret_agent() (R/interpret.R): 209 lines
    • ...
    • enrichGO() (R/enrichGO.R): 146 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/DataSet.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gson_WP.Rd
    • man/plot.interpretation.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • append_kegg_category.Rd
    • ...
    • uniprot_get.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • compareCluster.Rd
    • ...
    • interpret.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • compareCluster.Rd
    • ...
    • interpret.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • clusterProfiler/NEWS
    • clusterProfiler/NEWS.md
* 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; 306 lines (5%) are > 80 characters long.
  First few lines:
    • R/accessor.R#L3 as.data.frame.compareClusterResult <- ge ...
    • ...
    • vignettes/clusterProfiler.qmd#L83 [clusterProfiler
    homepage](https://guang ...
ℹ NOTE: Consider 4 spaces instead of tabs; 20 lines (0%) contain tabs.
  First few lines:
    • R/AllGenerics.R#L14 ## setGeneric("plot", function(x, ...) ...
    • ...
    • vignettes/clusterProfiler.qmd#L52 * and many others ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 967 lines (15%) are
not.
  First few lines:
    • R/00-AllClasses.R#L22 "groupGOResult", ...
    • ...
    • R/wikiPathways.R#L92 gmtfile[grep(organism, ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 18 NOTES
ℹ See the clusterProfiler.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.