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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('Biostrings_2.80.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Biostrings ───────────────────────────────────────────────────────
✔ Package installed successfully
── Biostrings session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXZHfkL/file747937afb8130/Biostrings
→ BiocVersion: 3.23
→ Package: Biostrings
→ PackageVersion: 2.80.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Biostrings.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpXZHfkL/file747937afb8130/Biostrings
→ installDir: /tmp/RtmpXZHfkL/file747937a3d69e8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Biostrings ─────────────────────────────────────────────
* 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 4.1.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: LongRead,
GenomeAssembly
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • Biostrings2Classes.Rnw
    • BiostringsQuickOverview.Rnw
    • PairwiseAlignments.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • Biostrings2Classes.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Biostrings2Classes.Rnw
    • ...
    • vignettes/PairwiseAlignments.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Biostrings...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/letter.R (line 31, column 29)
    • ...
    • R/XStringCodec-class.R (line 123, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AMINO_ACID_CODE.R (line 44, column 39)
    • ...
    • XStringSet-class.R (line 512, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/MultipleAlignment.R (line 764, column 5)
    • ...
    • cat() in R/XStringViews-class.R (line 256, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/MultipleAlignment.R (line 457, column 7)
    • R/XString-class.R (line 456, column 42)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/XStringViews-class.R (line 369, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/letterFrequency.R (line 697, column 14)
    • R/seqtype.R (line 154, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/matchProbePair.R (line 87, column 9)
    • F in R/matchProbePair.R (line 91, column 39)
    • F in R/matchProbePair.R (line 95, column 55)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • XStringSet-io.R (line 442, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/matchPDict-exact.Rd
ℹ Found @ in man/XStringSet-class.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressWarnings() in R/dinucleotideFrequencyTest.R (line 172, column 19)
  • ...
  • suppressWarnings() in R/padAndClip.R (line 53, column 20)
* 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:
    • g.test() (R/dinucleotideFrequencyTest.R): 137 lines
    • ...
    • _anonymous_.832() (R/letterFrequency.R): 67 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AAString-class.Rd
    • ...
    • man/yeastSEQCHR1.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • Biostrings-internals.Rd
  • lcsuffix.Rd
  • MIndex-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • matchPDict-inexact.Rd
    • translate.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • matchPDict-inexact.Rd
    • translate.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; 126 lines (1%) are > 80 characters long.
  First few lines:
    • R/coloring.R#L124 stop("'colors' should be NUL ...
    • ...
    • vignettes/MultipleAlignments.Rmd#L252 ```{r figure1, echo=FALSE,
    fig=TRUE, eps ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • man/XStringViews-class.Rd#L128 ...)}}{ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3994 lines (17%) are
not.
  First few lines:
    • R/AMINO_ACID_CODE.R#L27 ## 21st and 22nd proteinogenic amino a ...
    • ...
    • vignettes/PairwiseAlignments.Rnw#L43 Seattle, WA} ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 21 NOTES
ℹ See the Biostrings.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.