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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('affxparser_1.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing affxparser ───────────────────────────────────────────────────────
✔ Package installed successfully
── affxparser session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpHBQdPd/file1a76183c11d983/affxparser
→ BiocVersion: 3.24
→ Package: affxparser
→ PackageVersion: 1.85.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/affxparser.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpHBQdPd/file1a76183c11d983/affxparser
→ installDir: /tmp/RtmpHBQdPd/file1a76181acad462
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on affxparser ─────────────────────────────────────────────
* 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 2.14.0 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...
No vignettes found.
ℹ NOTE: Consider adding these automatically suggested biocViews: ChipOnChip,
QualityControl
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...
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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of affxparser...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/findFiles.R (line 155, column 16)
    • ...
    • R/writeCdf.private.R (line 79, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cdfAddPlasqTypes.R (line 64, column 14)
    • ...
    • writeCdf.private.R (line 288, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/compareCdfs.R (line 111, column 5)
    • ...
    • cat() in R/writeTpmap.R (line 37, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/readCcg.R (line 284, column 19)
    • ...
    • R/readCcg.R (line 287, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/private.readCelHeaderV3.R (line 46, column 10)
    • ...
    • R/writeCdf.private.R (line 121, column 10)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/readCelUnits.R (line 432, column 14)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/convertCel.R (line 151, column 3)
  • suppressWarnings() in R/writeCdf.private.R (line 221, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 59
functions greater than 50 lines.
  The longest 5 functions are:
    • readCelUnits() (R/readCelUnits.R): 515 lines
    • ...
    • findFiles() (R/findFiles.R): 211 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/1._Dictionary.Rd
    • man/2._Cell_coordinates_and_cell_indices.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • applyCdfGroupFields.Rd
    • ...
    • writeTpmap.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • readCdfUnitNames.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • readCdfUnitNames.Rd
* Checking package NEWS...
* 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; 366 lines (2%) are > 80 characters long.
  First few lines:
    • R/applyCdfGroupFields.R#L4 # @title "Applies a function to a list o ...
    • ...
    • man/writeCelHeader.Rd#L27 \item{outputVersion}{A \code{\link[ba ...
ℹ NOTE: Consider 4 spaces instead of tabs; 36 lines (0%) contain tabs.
  First few lines:
    • R/readCcg.R#L278 # Item Description Type ...
    • ...
    • R/writeCcg.R#L90 # 8 GDH[] Array of parent file headers ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4726 lines (32%) are
not.
  First few lines:
    • R/applyCdfBlocks.R#L2 # - - - - - - - - - - - - - - - - - - ...
    • ...
    • man/writeTpmap.Rd#L29 These functions are called for their s ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the affxparser.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.