##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "res<-BiocCheck::BiocCheck('GenomicRanges_1.64.0.tar.gz');q(status=length(res$error))"
###
##############################################################################
##############################################################################


── Installing GenomicRanges ────────────────────────────────────────────────────
✔ Package installed successfully
── GenomicRanges session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp3EWkyv/file39c23b226ff888/GenomicRanges
→ BiocVersion: 3.23
→ Package: GenomicRanges
→ PackageVersion: 1.64.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GenomicRanges.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp3EWkyv/file39c23b226ff888/GenomicRanges
→ installDir: /tmp/Rtmp3EWkyv/file39c23b57335b68
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenomicRanges ──────────────────────────────────────────
* 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
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 (50%).
* 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:
    • ExtendingGenomicRanges.Rnw
    • ...
    • Ten_things_slides.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GenomicRangesHOWTOs.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ExtendingGenomicRanges.Rnw
    • vignettes/GRanges_and_GRangesList_slides.Rnw
    • vignettes/Ten_things_slides.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GenomicRanges...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/constraint.R (line 69, column 19)
    • ...
    • R/genomicvars.R (line 92, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/GenomicRangesList-class.R (line 240, column 9)
    • cat() in R/GenomicRangesList-class.R (line 245, column 9)
    • cat() in R/GenomicRangesList-class.R (line 260, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/GRangesList-class.R (line 334, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/GRangesList-class.R (line 103, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • GenomicRanges-class.R (line 353, column 26)
    • ...
    • inter-range-methods.R (line 421, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 6 times)
  • suppressWarnings() in R/constraint.R (line 93, column 1)
  • ...
  • suppressWarnings() in R/setops-methods.R (line 143, column 23)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • .GenomicRanges_findPrecedeFollow() (R/nearest-methods.R): 112 lines
    • ...
    • _anonymous_.51() (R/findOverlaps-methods.R): 70 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/constraint.Rd
    • ...
    • man/intra-range-methods.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • genomic-range-squeezers.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • absoluteRanges.Rd
    • GPos-class.Rd
    • setops-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • absoluteRanges.Rd
    • GPos-class.Rd
    • setops-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; 49 lines (0%) are > 80 characters long.
  First few lines:
    • R/inter-range-methods.R#L30 revmap <- relist(mcols(unlist(rgl, u ...
    • ...
    • vignettes/GRanges_and_GRangesList_slides.Rnw#L1059
    \url{http://bioconductor.org ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2446 lines (15%) are
not.
  First few lines:
    • R/absoluteRanges.R#L66 "or couldn't be comput ...
    • ...
    • vignettes/Ten_things_slides.Rnw#L399 \end{exampleblock} ...
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 | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the GenomicRanges.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.