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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('chipseq_1.63.0.tar.gz','quit-with-status'=TRUE)"
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── Installing chipseq ──────────────────────────────────────────────────────────
✔ Package installed successfully
── chipseq session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJlDnd7/file65bed10d78cb0/chipseq
→ BiocVersion: 3.24
→ Package: chipseq
→ PackageVersion: 1.63.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/chipseq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpJlDnd7/file65bed10d78cb0/chipseq
→ installDir: /tmp/RtmpJlDnd7/file65bed189f5727
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on chipseq ────────────────────────────────────────────────
* 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 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpJlDnd7/file65bed10d78cb0/chipseq/man/chipseqFilter.Rd'
* 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 (69%).
* 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:
    • Workflow.Rmd
* Checking package installation calls in R code...
* Checking for library/require of chipseq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/diffPeaks.R (line 114, column 13)
    • ...
    • R/subsets.R (line 42, column 48)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • islands.R (line 16, column 24)
    • islands.R (line 16, column 52)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/subsets.R (line 33, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • subsetSummary() (R/subsets.R): 124 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/coverageplot.Rd
    • man/islandDepthPlot.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • peakSummary-methods.Rd
    • subsetSummary.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 18 lines (1%) are > 80 characters long.
  First few lines:
    • R/diffPeaks.R#L86 ## an ...
    • ...
    • vignettes/Workflow.Rmd#L456 views <- browserView(session, head(peak. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 428 lines (22%) are
not.
  First few lines:
    • R/context.R#L5 if (!is(txdb, "TxDb")) ...
    • ...
    • vignettes/Workflow.Rmd#L416 subset(peakSum ...
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 email is ok.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 13 NOTES
ℹ See the chipseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.