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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('InPAS_2.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing InPAS ────────────────────────────────────────────────────────────
✔ Package installed successfully
── InPAS session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUaYHD8/filec2bb068788ead/InPAS
→ BiocVersion: 3.24
→ Package: InPAS
→ PackageVersion: 2.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/InPAS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpUaYHD8/filec2bb068788ead/InPAS
→ installDir: /tmp/RtmpUaYHD8/filec2bb02ee4c0b2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on InPAS ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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 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...
! WARNING: Invalid BiocViews term(s):
  • 'Alternative Polyadenylation'
  • ...
  • 'Gene Regulation': Did you mean 'GeneRegulation'?
* Checking for recommended biocViews...
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 if 'Package:' field matches directory / tarball...
* 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 (48%).
* 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 InPAS...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/00.get_GCandMappability.R (line 71, column 11)
    • ...
    • R/25.setup_GSEA.R (line 128, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • 00.get_lastCDSUTR3.R (line 135, column 53)
    • ...
    • 26.get_usage4plot.R (line 168, column 20)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/03.get_ssRleCov.R (line 300, column 15)
    • ...
    • print() in R/27.plot_utr3Usage.R (line 43, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/03.get_ssRleCov.R (line 143, column 10)
    • R/18.get_UTR3CDS.R (line 70, column 10)
    • R/19.get_regionCov.R (line 83, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 6 times:
    • F in R/00.get_lastCDSUTR3.R (line 89, column 58)
    • ...
    • F in R/25.setup_GSEA.R (line 125, column 46)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/filter_testOut.Rd
ℹ Found @ in man/setup_GSEA.Rd
ℹ Found @ in man/test_dPDUI.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressMessages() in R/14.get_PAscore2.R (line 63, column 5)
  • suppressMessages() in R/15.find_valleyBySpline.R (line 46, column 15)
  • suppressMessages() in R/15.find_valleyBySpline.R (line 56, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 36
functions greater than 50 lines.
  The longest 5 functions are:
    • extract_UTR3Anno() (R/02.extract_UTR3Anno.R): 510 lines
    • ...
    • get_ssRleCov() (R/03.get_ssRleCov.R): 233 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/addChr2Exclude.Rd
    • ...
    • man/setup_GSEA.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addChr2Exclude.Rd
    • ...
    • setup_parCPsSearch.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; 102 lines (1%) are > 80 characters long.
  First few lines:
    • R/00.get_lastCDSUTR3.R#L11 #' scaffolds to be excluded for InPAS ...
    • ...
    • vignettes/InPAS.Rmd#L270 InPAS package also provide functions, `g ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2970 lines (37%) are
not.
  First few lines:
    • R/00.get_GCandMappability.R#L22 if (!is(genome, "BSgenome")) { ...
    • ...
    • vignettes/InPAS.Rmd#L293 rnkFilename = "InPAS.rnk") ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the InPAS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.