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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('HMMcopy_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing HMMcopy ──────────────────────────────────────────────────────────
✔ Package installed successfully
── HMMcopy session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpB9cG18/fileb18ef47186977/HMMcopy
→ BiocVersion: 3.24
→ Package: HMMcopy
→ PackageVersion: 1.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/HMMcopy.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpB9cG18/fileb18ef47186977/HMMcopy
→ installDir: /tmp/RtmpB9cG18/fileb18ef540c6dbf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HMMcopy ────────────────────────────────────────────────
* 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 2.10.0 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: WholeGenome
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • HMMcopy.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • HMMcopy.Rnw
* Checking package installation calls in R code...
* Checking for library/require of HMMcopy...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • correction.R (line 8, column 13)
    • ...
    • segmentation.R (line 276, column 19)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/correction.R (line 66, column 3)
    • cat() in R/correction.R (line 79, column 5)
    • cat() in R/correction.R (line 81, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/correction.R (line 25, column 8)
    • ...
    • R/segmentation.R (line 329, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/correction.R (line 2, column 26)
    • ...
    • R/segmentation.R (line 195, column 28)
* 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:
    • manualSegment() (R/segmentation.R): 154 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/HMMcopy-output.Rd
    • man/HMMcopy-visualize.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; 52 lines (3%) are > 80 characters long.
  First few lines:
    • R/correction.R#L94 out <- data.frame(sample = sample, chr ...
    • ...
    • vignettes/HMMcopy.Rnw#L435 % Integrating copy number polymorphisms ...
ℹ NOTE: Consider 4 spaces instead of tabs; 55 lines (3%) contain tabs.
  First few lines:
    • R/segmentation.R#L249 # Perform one last round of E-step to ...
    • ...
    • man/wigsToRangedData.Rd#L57 value. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 473 lines (27%) are
not.
  First few lines:
    • R/correction.R#L2 if (verbose) { message(paste("Slurping ...
    • ...
    • vignettes/HMMcopy.Rnw#L409 ylab = "Tumour Copy Number", xlab = "C ...
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 | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the HMMcopy.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.