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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('segmentSeq_2.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing segmentSeq ───────────────────────────────────────────────────────
✔ Package installed successfully
── segmentSeq session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4olXgC/file12ed2124a4211d/segmentSeq
→ BiocVersion: 3.24
→ Package: segmentSeq
→ PackageVersion: 2.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/segmentSeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4olXgC/file12ed2124a4211d/segmentSeq
→ installDir: /tmp/Rtmp4olXgC/file12ed213e2f280a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on segmentSeq ─────────────────────────────────────────────
* 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/Rtmp4olXgC/file12ed2124a4211d/segmentSeq/man/hSL.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp4olXgC/file12ed2124a4211d/segmentSeq/man/segClass-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/Rtmp4olXgC/file12ed2124a4211d/segmentSeq/man/SL.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Coverage,
Bayesian
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...
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • methylationAnalysis.Rmd
    • segmentSeq.Rmd
* Checking package installation calls in R code...
* Checking for library/require of segmentSeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/classifySeg.R (line 176, column 16)
    • ...
    • R/utilityFunctions.R (line 411, column 29)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classifySeg.R (line 67, column 40)
    • ...
    • utilityFunctions.R (line 457, column 91)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/utilityFunctions.R (line 114, column 5)
    • ...
    • print() in R/utilityFunctions.R (line 118, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/classifySeg.R (line 97, column 35)
    • ...
    • R/utilityFunctions.R (line 367, column 23)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/classifySeg.R (line 458, column 13)
    • ...
    • R/utilityFunctions.R (line 107, column 56)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/findChunks.Rd
ℹ Found @ in man/getOverlaps.Rd
ℹ Found @ in vignettes/segmentSeq.Rmd
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/heuristicSeg.R (line 273, column 23)
  • suppressWarnings() in R/processTags.R (line 105, column 7)
  • suppressWarnings() in R/processTags.R (line 232, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 39
functions greater than 50 lines.
  The longest 5 functions are:
    • .partheuristicSeg() (R/heuristicSeg.R): 281 lines
    • ...
    • plotGenome() (R/plotGenome.R): 160 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • averageMethylationRegions.Rd
    • ...
    • summariseLoci.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • thresholdFinder.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • thresholdFinder.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; 1042 lines (14%) are > 80 characters long.
  First few lines:
    • R/alignmentClass-accessors.R#L34 validmess <- c(validmess, "The len ...
    • ...
    • vignettes/segmentSeq.Rmd#L173 <a name="Hardcastle2011" />Thomas J. Har
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • man/alignmentClass-class.Rd#L50 } ...
    • man/alignmentData-class.Rd#L71 } ...
    • man/alignmentMeth-class.Rd#L70 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2618 lines (34%) are
not.
  First few lines:
    • R/alignmentClass-accessors.R#L3 if(!missing(i)) ...
    • ...
    • vignettes/segmentSeq.Rmd#L116 showNumber = FALSE, cap = 50) ...
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.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 20 NOTES
ℹ See the segmentSeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.