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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('Biobase_2.72.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Biobase ──────────────────────────────────────────────────────────
✔ Package installed successfully
── Biobase session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpkclzi1/file72f316d7d5a4a/Biobase
→ BiocVersion: 3.23
→ Package: Biobase
→ PackageVersion: 2.72.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Biobase.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpkclzi1/file72f316d7d5a4a/Biobase
→ installDir: /tmp/Rtmpkclzi1/file72f317bfcaf0e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Biobase ────────────────────────────────────────────────
* 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 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (33%).
* 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:
    • ExpressionSetIntroduction.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • BiobaseDevelopment.Rmd
    • esApply.Rmd
    • ExpressionSetIntroduction.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/esApply.Rmd (chunk no. 5, line 58, column 42)
* Checking package installation calls in R code...
* Checking for library/require of Biobase...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/methods-AnnotatedDataFrame.R (line 474, column 32)
    • ...
    • R/VersionsClass.R (line 134, column 29)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • environment.R (line 66, column 13)
    • ...
    • strings.R (line 54, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/methods-AnnotatedDataFrame.R (line 364, column 5)
    • ...
    • cat() in R/vignettes.R (line 69, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/environment.R (line 8, column 10)
    • ...
    • R/vignettes.R (line 109, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods-AssayData.R (line 155, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/methods-ExpressionSet.R (line 192, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • methods-ExpressionSet.R (line 61, column 20)
    • methods-ExpressionSet.R (line 88, column 38)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/tools.R (line 57, column 10)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • .Deprecated() in R/anyMissing.R (line 2, column 3)
  • .Defunct() in R/environment.R (line 112, column 5)
  • .Deprecated() in R/rowOp-methods.R (line 7, column 7)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/class.Versioned.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • copySubstitute() (R/tools.R): 109 lines
    • ...
    • readExpressionSet() (R/methods-ExpressionSet.R): 56 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/annotatedDataFrameFrom-methods.Rd
    • ...
    • man/validMsg.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • abstract.Rd
    • ...
    • userQuery.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • anyMissing.Rd
    • ...
    • updateOldESet.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • anyMissing.Rd
    • ...
    • updateOldESet.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; 349 lines (4%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L4 setGeneric("annotatedDataFrameFrom", fun ...
    • ...
    • vignettes/esApply.Rmd#L73 This is achieved by having an environmen ...
ℹ NOTE: Consider 4 spaces instead of tabs; 64 lines (1%) contain tabs.
  First few lines:
    • man/class.AnnotatedDataFrame.Rd#L84 and measured variables (columns).}
    ...
    • ...
    • man/snpCall.Rd#L21 probabilities and columns samples.} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3269 lines (34%) are
not.
  First few lines:
    • R/AllGenerics.R#L11 standardGeneric("description" ...
    • ...
    • vignettes/ExpressionSetIntroduction.Rnw#L493 ...
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 Biobase.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.