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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('IRanges_2.46.0.tar.gz','quit-with-status'=TRUE)"
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── Installing IRanges ──────────────────────────────────────────────────────────
✔ Package installed successfully
── IRanges session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnjktD8/file7db4d3c61fba/IRanges
→ BiocVersion: 3.23
→ Package: IRanges
→ PackageVersion: 2.46.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/IRanges.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpnjktD8/file7db4d3c61fba/IRanges
→ installDir: /tmp/RtmpnjktD8/file7db4d33edc5f4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on IRanges ────────────────────────────────────────────────
* 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...
* 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:
    • IRangesOverview.Rnw
* Checking package installation calls in R code...
* Checking for library/require of IRanges...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AtomicList-utils.R (line 69, column 13)
    • ...
    • R/Views-class.R (line 347, column 11)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • IPosRanges-comparison.R (line 35, column 25)
    • RleViews-class.R (line 110, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AtomicList-class.R (line 374, column 13)
    • ...
    • cat() in R/RleViews-class.R (line 112, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/nearest-methods.R (line 197, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/read.Mask.R (line 111, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AtomicList-class.R (line 91, column 49)
    • ...
    • Views-class.R (line 110, column 31)
! WARNING: .Deprecated / .Defunct usage (found 6 times)
  • .Deprecated() in R/CompressedDataFrameList-class.R (line 42, column 13)
  • ...
  • .Defunct() in R/Grouping-class.R (line 977, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/CompressedList-class.R (line 267, column 28)
  • ...
  • suppressWarnings() in R/RleViews-summarization.R (line 36, column 14)
* 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:
    • coverage_CompressedIRangesList() (R/coverage-methods.R): 83 lines
    • ...
    • .setListMethod() (R/CompressedAtomicList-class.R): 60 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AtomicList-summarization.Rd
    • ...
    • man/seqapply.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • range-squeezers.Rd
  • Vector-class-leftovers.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • Views-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • Views-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; 77 lines (0%) are > 80 characters long.
  First few lines:
    • R/CompressedAtomicList-summarization.R#L82 ans[singletons] <- unlist(rv,
    use.name ...
    • ...
    • man/Views-class.Rd#L139 \code{trim(narrow(x, start=start, ...
ℹ NOTE: Consider 4 spaces instead of tabs; 4 lines (0%) contain tabs.
  First few lines:
    • R/CompressedRangesList-class.R#L187 PACKAGE="IRanges") ...
    • ...
    • man/makeIRangesFromDataFrame.Rd#L100 object from a data.frame or
    \link[S4V ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4497 lines (20%) are
not.
  First few lines:
    • R/AtomicList-class.R#L13 prototype = prototype(elementTy ...
    • ...
    • vignettes/IRangesOverview.Rnw#L420 \end{center} ...
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 | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the IRanges.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.