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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('goProfiles_1.75.0.tar.gz','quit-with-status'=TRUE)"
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── Installing goProfiles ───────────────────────────────────────────────────────
✔ Package installed successfully
── goProfiles session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRpAUvI/fileaaad57ea86f75/goProfiles
→ BiocVersion: 3.24
→ Package: goProfiles
→ PackageVersion: 1.75.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/goProfiles.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpRpAUvI/fileaaad57ea86f75/goProfiles
→ installDir: /tmp/RtmpRpAUvI/fileaaad51c6f2a0b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on goProfiles ─────────────────────────────────────────────
* 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...
* 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: Sequencing
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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • goProfiles.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/goProfiles.Rnw (chunk no. 6, line 41, column 42)
    • vignettes/goProfiles.Rnw (chunk no. 6, line 41, column 76)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/goProfiles.Rnw
* Checking package installation calls in R code...
* Checking for library/require of goProfiles...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/BioCpack2EntrezIDS.R (line 4, column 13)
    • ...
    • require() in R/haveGO.R (line 12, column 20)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/as.GOTerms.frame.R (line 8, column 7)
    • ...
    • R/varDifStatPP0.ExpandedGOProfile.R (line 41, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • chiDisjoint.R (line 27, column 25)
    • ...
    • toNumVec.R (line 6, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/basicProfile.R (line 18, column 17)
    • ...
    • cat() in R/profileEquiv_topDown2.R (line 192, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/fisherGOProfiles.R (line 94, column 5)
    • R/fisherGOProfiles.R (line 95, column 5)
    • R/fisherGOProfiles.R (line 96, column 6)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/pvalueExcludingLinCombChisq.R (line 22, column 7)
    • ...
    • R/pvalueRestrictLinCombChisq.R (line 11, column 7)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/mergeProfiles.R (line 7, column 9)
    • R/mergeProfiles.R (line 15, column 16)
    • R/mergeProfilesLists.R (line 6, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 70 times:
    • T in R/as.GOTerms.frame.R (line 9, column 69)
    • ...
    • T in R/varDifStatPP0.R (line 2, column 53)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • internal.compareGOProf() (R/internal.compareGOProf.R): 209 lines
    • ...
    • `expandedProfile`() (R/expandedProfile.R): 83 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/CD4ids.Rd
    • man/hugoIds.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/equivClust2pdf.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • compareProfilesLists.Rd
    • ...
    • iterEquivClust.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:
    • equivClust.Rd
    • iterEquivClust.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • equivClust.Rd
    • iterEquivClust.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 430 lines (12%) are > 80 characters long.
  First few lines:
    • R/as.GOTerms.frame.R#L8 sapply(names(unlisted[is.na(unlist ...
    • ...
    • vignettes/goProfiles.Rnw#L176 \newblock {\em Journal of Statistical Pl
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 28 lines (1%) contain tabs.
  First few lines:
    • R/basicProfile.R#L3 ord=TRUE, multilevels=NULL, empty.cats ...
    • ...
    • goProfiles/NAMESPACE#L34 GO.db) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 828 lines (22%) are
not.
  First few lines:
    • R/as.GOTerms.frame.R#L3 unlisted<-unlist(myGOTermsList) ...
    • ...
    • vignettes/goProfiles.Rnw#L188 pharmacological targets in prostate ca ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 6 WARNINGS | ℹ 19 NOTES
ℹ See the goProfiles.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.