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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('Category_2.78.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Category ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Category session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRCkMBP/file154ce664015ce7/Category
→ BiocVersion: 3.23
→ Package: Category
→ PackageVersion: 2.78.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Category.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpRCkMBP/file154ce664015ce7/Category
→ installDir: /tmp/RtmpRCkMBP/file154ce613465656
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Category ───────────────────────────────────────────────
* 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,
Microarray
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 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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (57%).
* 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:
    • Category.Rnw
    • ChromBand.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Category.Rnw
    • vignettes/ChromBand.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Category...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/DatPkg-accessors.R (line 260, column 9)
    • require() in R/gseaperm.R (line 2, column 22)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/categoryToEntrezBuilder-methods.R (line 201, column 16)
    • ...
    • R/universeBuilder-methods.R (line 69, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • catcode.R (line 48, column 14)
    • ...
    • mouse.R (line 48, column 24)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/mouse.R (line 32, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/catcode.R (line 3, column 13)
    • ...
    • R/MAPcode.R (line 255, column 14)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/AllGenerics.R (line 98, column 19)
    • R/DatPkg-accessors.R (line 19, column 14)
    • R/HyperGParams-accessors.R (line 40, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • HyperGParams-accessors.R (line 6, column 23)
    • HyperGParams-accessors.R (line 7, column 47)
    • MAPcode.R (line 253, column 20)
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/cb_test.R (line 104, column 5)
  • set.seed() in R/cb_test.R (line 113, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/Category.Rnw
ℹ Found @ in vignettes/ChromBand.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/categoryToEntrezBuilder-methods.R (line 174, column
  5)
  • suppressWarnings() in R/gseaperm.R (line 2, column 5)
  • suppressWarnings() in R/summary-methods.R (line 123, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • .doLinearMTest() (R/linearMTest-methods.R): 137 lines
    • ...
    • chrMap_hg_test() (R/hyperGTest-methods.R): 54 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/Category-defunct.Rd
    • man/GSEAGOHyperGParams.Rd
    • man/HyperGResult-accessors.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • categoryToEntrezBuilder.Rd
    • ...
    • universeBuilder.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:
    • DatPkg-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • DatPkg-class.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; 38 lines (0%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L56 setGeneric("pvalueCutoff<-", function(r, ...
    • ...
    • vignettes/ChromBand.Rnw#L721 <<dotplot1p362,fig=TRUE,include=FALSE,ec ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (0%) contain tabs.
  First few lines:
    • R/DatPkg-accessors.R#L65 return(getAnnMap("ORF", p@name) ...
    • ...
    • man/LinearMResultBase-class.Rd#L21 \description{ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2190 lines (27%) are
not.
  First few lines:
    • R/AllClasses.R#L2 contains="VIRTUAL", ...
    • ...
    • vignettes/ChromBand.Rnw#L736 genes.  } ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the Category.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.