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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('topGO_2.65.0.tar.gz','quit-with-status'=TRUE)"
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── Installing topGO ────────────────────────────────────────────────────────────
✔ Package installed successfully
── topGO session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZGADjr/file14e09141663799/topGO
→ BiocVersion: 3.24
→ Package: topGO
→ PackageVersion: 2.65.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/topGO.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZGADjr/file14e09141663799/topGO
→ installDir: /tmp/RtmpZGADjr/file14e091622747b8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on topGO ──────────────────────────────────────────────────
* 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 2.10.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZGADjr/file14e09141663799/topGO/man/geneList.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZGADjr/file14e09141663799/topGO/man/GOdata.Rd'
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • topGO_manual.Rmd
* Checking package installation calls in R code...
* Checking for library/require of topGO...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/topGOannotations.R (line 33, column 3)
    • ...
    • require() in R/topGOviz.R (line 354, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/topGOalgo.R (line 670, column 14)
    • ...
    • R/topGOviz.R (line 504, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • topGOfunctions.R (line 135, column 71)
    • ...
    • topGOviz.R (line 373, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/topGOgraph.R (line 344, column 16)
    • ...
    • cat() in R/topGOmethods.R (line 644, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/topGOmethods.R (line 64, column 30)
    • ...
    • R/topGOviz.R (line 404, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/topGOannotations.R (line 33, column 51)
    • ...
    • R/topGOgraph.R (line 253, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/topGOalgo.R (line 59, column 20)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 30 times:
    • T in R/topGOalgo.R (line 694, column 37)
    • ...
    • F in R/topGOviz.R (line 467, column 52)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • topGOmethods.R (line 952, column 33)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/topGOviz.R (line 28, column 3)
    • system() in R/topGOviz.R (line 29, column 3)
    • system() in R/topGOviz.R (line 31, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/topGOfunctions.R (line 72, column 54)
* 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:
    • .sigGroups.weight() (R/topGOalgo.R): 194 lines
    • ...
    • GOplot.counts() (R/topGOviz.R): 96 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/geneList.Rd
    • man/GOdata.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/printGraph-methods.Rd

✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • classicCount-class.Rd
    • ...
    • weightCount-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 13% of man
pages use at least one of these tags.
  Found in files:
    • annFUN.Rd
    • diagnosticMethods.Rd
    • printGraph-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annFUN.Rd
    • diagnosticMethods.Rd
    • printGraph-methods.Rd
* Checking package NEWS...
* 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; 745 lines (9%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L11 ## ExpressionSet class. In this way we c ...
    • ...
    • vignettes/topGO_manual.Rmd#L1219 We can emphasise differences between two
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 42 lines (0%) contain tabs.
  First few lines:
    • R/topGOmethods.R#L443 if(length(whichGO) == 0) { ...
    • ...
    • man/weightCount-class.Rd#L55 \describe{ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2464 lines (29%) are
not.
  First few lines:
    • R/AllClasses.R#L16 representation = representation ...
    • ...
    • vignettes/topGO_manual.Rmd#L1225 fn.prefix = "tGO", useInfo = ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the topGO.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.