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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicAlignments_1.48.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GenomicAlignments ────────────────────────────────────────────────
✔ Package installed successfully
── GenomicAlignments session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpyYBGZj/file15ad946ec55e32/GenomicAlignments
→ BiocVersion: 3.23
→ Package: GenomicAlignments
→ PackageVersion: 1.48.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GenomicAlignments.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpyYBGZj/file15ad946ec55e32/GenomicAlignments
→ installDir: /tmp/RtmpyYBGZj/file15ad9443a6c41e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenomicAlignments ──────────────────────────────────────
* 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:
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (80%).
* 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:
    • GenomicAlignmentsIntroduction.Rnw
    • OverlapEncodings.Rnw
    • summarizeOverlaps.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • OverlapEncodings.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • OverlapEncodings.Rnw
    • WorkingWithAlignedNucleotides.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/summarizeOverlaps.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GenomicAlignments...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/encodeOverlaps-methods.R (line 386, column 20)
    • ...
    • R/summarizeOverlaps-methods.R (line 217, column 14)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • junctions-methods.R (line 283, column 33)
    • junctions-methods.R (line 284, column 48)
    • junctions-methods.R (line 285, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/findMateAlignment.R (line 139, column 5)
    • cat() in R/findMateAlignment.R (line 145, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/GAlignmentsList-class.R (line 202, column 25)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/summarizeOverlaps-methods.R (line 137, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • GappedReads-class.R (line 35, column 23)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/cigar-utils.R (line 38, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/OverlapEncodings.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/GAlignmentsList-class.R (line 158, column 23)
  • suppressWarnings() in R/junctions-methods.R (line 136, column 33)
  • suppressWarnings() in R/readGAlignments.R (line 78, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • extractQueryStartInTranscript() (R/encodeOverlaps-methods.R): 99 lines
    • ...
    • makeGAlignmentPairs() (R/findMateAlignment.R): 53 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/OverlapEncodings-class.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • sequenceLayer.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:
    • cigar-utils.Rd
    • sequenceLayer.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; 42 lines (0%) are > 80 characters long.
  First few lines:
    • R/findSpliceOverlaps-methods.R#L242 gr <- relist(GRanges(seqnms, unl ...
    • ...
    • vignettes/WorkingWithAlignedNucleotides.Rmd#L278 Like for our single-end
    reads, the follo ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2469 lines (17%) are
not.
  First few lines:
    • R/cigar-utils.R#L10 ...
    • ...
    • vignettes/summarizeOverlaps.Rnw#L318 countfiles=path(colData(ge ...
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 19 NOTES
ℹ See the GenomicAlignments.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.