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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('affycoretools_1.85.0.tar.gz','quit-with-status'=TRUE)"
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── Installing affycoretools ────────────────────────────────────────────────────
✔ Package installed successfully
── affycoretools session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1UrMOK/file4be8f7379f4a6/affycoretools
→ BiocVersion: 3.24
→ Package: affycoretools
→ PackageVersion: 1.85.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/affycoretools.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1UrMOK/file4be8f7379f4a6/affycoretools
→ installDir: /tmp/Rtmp1UrMOK/file4be8feac7c3f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on affycoretools ──────────────────────────────────────────
* 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp1UrMOK/file4be8f7379f4a6/affycoretools/man/affycoretools-defunct.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...
✖ 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 (48%).
* 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:
    • RefactoredAffycoretools.Rmd
* Checking package installation calls in R code...
* Checking for library/require of affycoretools...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/affystart.R (line 153, column 5)
    • ...
    • require() in R/mirnaFuns.R (line 112, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/affystart.R (line 160, column 12)
    • ...
    • R/vennSelect.R (line 72, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • affystart.R (line 127, column 29)
    • ...
    • vennSelect.R (line 217, column 45)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/geneSetTables.R (line 167, column 60)
    • ...
    • R/reportingTools.R (line 957, column 65)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/affystart.R (line 154, column 10)
    • ...
    • R/reportingTools.R (line 988, column 19)
! WARNING: .Deprecated / .Defunct usage (found 12 times)
  • .Defunct() in R/Defunct.R (line 1, column 24)
  • ...
  • .Defunct() in R/Defunct.R (line 12, column 29)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/geneSetTables.R (line 563, column 40)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • vennSelect2() (R/reportingTools.R): 103 lines
    • ...
    • makeGenePlots() (R/reportingTools.R): 55 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/dataAndHeatmapPage.Rd


✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • affystart.Rd
    • ...
    • writeFit.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man
pages use at least one of these tags.
  Found in files:
    • annotateEset.Rd
    • ...
    • vennPage.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annotateEset.Rd
    • ...
    • vennPage.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; 579 lines (15%) are > 80 characters long.
  First few lines:
    • R/affycoretools.R#L1 #' Make repetitive analyses of microarra ...
    • ...
    • vignettes/RefactoredAffycoretools.Rmd#L267 "and blue, whereas the ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 532 lines (14%) are
not.
  First few lines:
    • R/affystart.R#L54 plot=TRUE, pca=TRU ...
    • ...
    • vignettes/RefactoredAffycoretools.Rmd#L268 "one would use a more ...
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 | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the affycoretools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.