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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicFeatures_1.64.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GenomicFeatures ──────────────────────────────────────────────────
✔ Package installed successfully
── GenomicFeatures session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2ZoJLC/file7bbe862b77824/GenomicFeatures
→ BiocVersion: 3.23
→ Package: GenomicFeatures
→ PackageVersion: 1.64.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GenomicFeatures.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp2ZoJLC/file7bbe862b77824/GenomicFeatures
→ installDir: /tmp/Rtmp2ZoJLC/file7bbe868c3cce9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenomicFeatures ────────────────────────────────────────
* 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 3.5.0 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: Microarray,
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 (69%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of GenomicFeatures...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/select-methods.R (line 6, column 12)
    • R/TxDb-schema.R (line 199, column 15)
    • R/TxDb-SELECT-helpers.R (line 100, column 11)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/utils.R (line 36, column 9)
    • cat() in R/utils.R (line 38, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/coordinate-mapping-methods.R (line 155, column 24)
    • R/transcripts.R (line 155, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/coordinate-mapping-methods.R (line 69, column 14)
    • ...
    • R/select-methods.R (line 343, column 24)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/transcriptLengths.R (line 9, column 19)
    • ...
    • R/transcripts.R (line 308, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/coverageByTranscript.R (line 188, column 5)
  • suppressWarnings() in R/coverageByTranscript.R (line 214, column 5)
  • suppressWarnings() in R/extractUpstreamSeqs.R (line 17, column 26)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
  The longest 5 functions are:
    • .mapToTranscripts() (R/coordinate-mapping-methods.R): 99 lines
    • ...
    • .TxDb.genes() (R/transcripts.R): 64 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/FeatureDb-class.Rd
    • man/select-methods.Rd
    • man/TxDb-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • tRNAs.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:
    • nearest-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • nearest-methods.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; 52 lines (1%) are > 80 characters long.
  First few lines:
    • R/select-methods.R#L258 ## Then sort rows and columns and drop ...
    • ...
    • vignettes/GenomicFeatures.Rmd#L15 %\VignetteDepends{GenomicFeatures,TxDb
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/transcriptLengths.R#L46 ...) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1531 lines (17%) are
not.
  First few lines:
    • R/coordinate-mapping-methods.R#L51 by=ifel ...
    • ...
    • vignettes/GenomicFeatures.Rmd#L402 cdsBy( ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 18 NOTES
ℹ See the GenomicFeatures.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.