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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('chromVAR_1.35.1.tar.gz','quit-with-status'=TRUE)"
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── Installing chromVAR ─────────────────────────────────────────────────────────
✔ Package installed successfully
── chromVAR session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmptbfLwL/file69dc91cf06551/chromVAR
→ BiocVersion: 3.24
→ Package: chromVAR
→ PackageVersion: 1.35.1
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/chromVAR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmptbfLwL/file69dc91cf06551/chromVAR
→ installDir: /tmp/RtmptbfLwL/file69dc936356484
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on chromVAR ───────────────────────────────────────────────
* 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 3.5.0 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 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 (44%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Introduction.Rmd
* Checking package installation calls in R code...
* Checking for library/require of chromVAR...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • get_annotations.R (line 172, column 60)
    • ...
    • get_inputs.R (line 304, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressMessages() in R/get_annotations.R (line 169, column 33)
  • ...
  • suppressWarnings() in R/utils.R (line 278, column 12)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • deviations_tsne_shiny() (R/dimensionality_reduction.R): 101 lines
    • ...
    • get_overlap_kmers() (R/kmers.R): 85 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/example_counts.Rd
    • ...
    • man/mini_ix.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • assembleKmers.Rd
  • ...
  • readNarrowpeaks.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; 40 lines (1%) are > 80 characters long.
  First few lines:
    • R/RcppExports.R#L33 .Call(`_chromVAR_bg_sample_helper`, ...
    • ...
    • vignettes/Introduction.Rmd#L234 To plot the results, `plotDeviationsTsne
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2077 lines (39%) are
not.
  First few lines:
    • R/AllClasses.R#L22 if ("deviations" %ni% assa ...
    • ...
    • vignettes/Introduction.Rmd#L240 shiny = ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 13 NOTES
ℹ See the chromVAR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.