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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('GOSemSim_2.38.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GOSemSim ─────────────────────────────────────────────────────────
✔ Package installed successfully
── GOSemSim session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAUWwcY/file7c3f817e37d03/GOSemSim
→ BiocVersion: 3.23
→ Package: GOSemSim
→ PackageVersion: 2.38.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GOSemSim.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpAUWwcY/file7c3f817e37d03/GOSemSim
→ installDir: /tmp/RtmpAUWwcY/file7c3f84543c614
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GOSemSim ───────────────────────────────────────────────
* 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...
* 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...
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 (11%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/GOSemSim.Rmd
* Checking package installation calls in R code...
* Checking for library/require of GOSemSim...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/clusterSim.R (line 19, column 13)
    • ...
    • R/WangMethod.R (line 81, column 34)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • buildGOmap.R (line 46, column 53)
    • ...
    • mgeneSim.R (line 28, column 43)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/parseGAF.R (line 44, column 3)
    • cat() in R/parseGAF.R (line 65, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/computeIC.R (line 7, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/TCSScutoff.R (line 115, column 11)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/TCSScutoff.R (line 186, column 40)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressMessages() in R/godata.R (line 95, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • is.empty() (R/ICMethods.R): 60 lines
    • ...
    • process_tcss() (R/processTCSS.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/go_term_table.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • buildGOmap.Rd
    • ...
    • wangMethod_internal.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • tcss_cutoff.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • tcss_cutoff.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • GOSemSim/NEWS
    • GOSemSim/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; 59 lines (3%) are > 80 characters long.
  First few lines:
    • R/buildGOmap.R#L3 #' provided by a data.frame of GO TERM ( ...
    • ...
    • vignettes/GOSemSim.Rmd#L52 For questions, please post to [Bioconduc ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 197 lines (10%) are
not.
  First few lines:
    • R/buildGOmap.R#L63 function(i) { ...
    • ...
    • vignettes/GOSemSim.Rmd#L25 message = FALSE) ...
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 | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the GOSemSim.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.