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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('compEpiTools_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing compEpiTools ─────────────────────────────────────────────────────
✔ Package installed successfully
── compEpiTools session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPooGWU/file787016f3a19e4/compEpiTools
→ BiocVersion: 3.24
→ Package: compEpiTools
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/compEpiTools.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpPooGWU/file787016f3a19e4/compEpiTools
→ installDir: /tmp/RtmpPooGWU/file787013dd590ab
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on compEpiTools ───────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Microarray,
ChipOnChip, FunctionalGenomics, Transcriptomics, GeneSetEnrichment, Pathways,
RNASeq, SystemsBiology, GO
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 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 (71%).
* 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...
✖ ERROR: 'NAMESPACE' contains exportPattern with '[[:alpha:]]'; use explicit
exports instead.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • compEpiTools.rnw
* Checking package installation calls in R code...
* Checking for library/require of compEpiTools...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/featuresLength.R (line 22, column 16)
    • ...
    • R/ucsc2GRanges.R (line 10, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • countOverlapsInBins.R (line 19, column 25)
    • ...
    • topGOres.R (line 74, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/heatmapData.R (line 70, column 9)
    • print() in R/stallingIndex.R (line 48, column 9)
    • print() in R/stallingIndex.R (line 49, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/findLncRNA.R (line 115, column 37)
    • ...
    • R/unionMaxScore.R (line 25, column 37)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
  • suppressWarnings() in R/distanceFromTSS.R (line 41, column 5)
  • ...
  • suppressWarnings() in R/stallingIndex.R (line 144, column 8)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • stallingIndex() (R/stallingIndex.R): 259 lines
    • ...
    • heatmapData() (R/heatmapData.R): 123 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/countOverlapsInBins-methods.Rd
    • ...
    • man/unionMaxScore-methods.Rd

* Checking package NEWS...
* 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; 275 lines (7%) are > 80 characters long.
  First few lines:
    • R/countOverlapsInBins.R#L1 setGeneric('countOverlapsInBins', functi ...
    • ...
    • vignettes/compEpiTools.rnw#L262 <<GRheat2,fig.width=6,fig.height=9,out.w
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 86 lines (2%) contain tabs.
  First few lines:
    • R/heatmapPlot.R#L93 clRes <- hclust(dist(clmat), method = ...
    • ...
    • vignettes/compEpiTools.rnw#L140 upstream=2000, downstream=1000, userAnn
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1071 lines (28%) are
not.
  First few lines:
    • R/countOverlapsInBins.R#L2 standardGeneric('countOverlap ...
    • ...
    • man/unionMaxScore-methods.Rd#L24 \item score2: numeric; the scores ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the compEpiTools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.