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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('VariantAnnotation_1.58.0.tar.gz','quit-with-status'=TRUE)"
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── Installing VariantAnnotation ────────────────────────────────────────────────
✔ Package installed successfully
── VariantAnnotation session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpocdB9L/file9a16c398dee07/VariantAnnotation
→ BiocVersion: 3.23
→ Package: VariantAnnotation
→ PackageVersion: 1.58.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/VariantAnnotation.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpocdB9L/file9a16c398dee07/VariantAnnotation
→ installDir: /tmp/RtmpocdB9L/file9a16c6a14eef2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on VariantAnnotation ──────────────────────────────────────
* 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 4.0.0 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: Coverage,
Alignment, GenomeAssembly, 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 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 (79%).
* 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:
    • VariantAnnotation.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ensemblVEP.Rmd
    • vignettes/filterVcf.Rmd
* Checking package installation calls in R code...
* Checking for library/require of VariantAnnotation...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/methods-genotypeToSnpMatrix.R (line 23, column 28)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllClasses.R (line 144, column 12)
    • ...
    • R/methods-writeVcf.R (line 86, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • methods-genotypeToSnpMatrix.R (line 120, column 22)
    • ...
    • methods-snpSummary.R (line 39, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/methods-VRanges-class.R (line 677, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 184, column 10)
    • ...
    • R/use_vep_api.R (line 66, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/methods-PolyPhenDb-class.R (line 109, column 17)
    • ...
    • R/methods-VariantType-class.R (line 68, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/methods-predictCoding.R (line 59, column 18)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/methods-VRanges-class.R (line 515, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/AllUtilities.R (line 30, column 20)
  • ...
  • suppressWarnings() in R/methods-scanVcf.R (line 89, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • vranges2Vcf() (R/methods-VRanges-class.R): 131 lines
    • ...
    • .makeResult() (R/methods-locateVariants.R): 74 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/defunct.Rd
    • ...
    • man/VariantType-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • defunct.Rd
  • getTranscriptSeqs-methods.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
  Found in files:
    • filterVcf-methods.Rd
    • locateVariants-methods.Rd
    • VcfFile-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • filterVcf-methods.Rd
    • locateVariants-methods.Rd
    • VcfFile-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; 22 lines (0%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L158 setValidity("VCFHeader", .valid.VCFHeade ...
    • ...
    • vignettes/VariantAnnotation.Rmd#L411 functions offered in `r
    Biocpkg("snpStat ...
ℹ NOTE: Consider 4 spaces instead of tabs; 28 lines (0%) contain tabs.
  First few lines:
    • R/methods-expand.R#L16 ghdr <- geno(header(x)) ...
    • ...
    • R/methods-expand.R#L105 gvar[!isA & !isR] <- endoapply(gvar[!is ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 819 lines (12%) are
not.
  First few lines:
    • R/AllClasses.R#L26 "must have the ...
    • ...
    • vignettes/VariantAnnotation.Rmd#L530 readVcf(TabixFile(fl, yieldSi ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 22 NOTES
ℹ See the VariantAnnotation.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.