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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('comapr_1.17.0.tar.gz','quit-with-status'=TRUE)"
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── Installing comapr ───────────────────────────────────────────────────────────
✔ Package installed successfully
── comapr session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCQypAM/file7801d19127d09/comapr
→ BiocVersion: 3.24
→ Package: comapr
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/comapr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCQypAM/file7801d19127d09/comapr
→ installDir: /tmp/RtmpCQypAM/file7801d4ade7f2e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on comapr ─────────────────────────────────────────────────
* 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 4.1.0 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...
* 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 (29%).
* 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:
    • getStarted.Rmd
    • single-sperm-co-analysis.Rmd
* Checking package installation calls in R code...
* Checking for library/require of comapr...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressMessages() in R/diagnostic-qc-checks.R (line 125, column 14)
  • ...
  • suppressMessages() in R/read-hap-state.R (line 166, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • readColMM() (R/read-col-mm.R): 146 lines
    • ...
    • readHapState() (R/read-hap-state.R): 62 lines
* Checking man page documentation...
* Checking package NEWS...
! WARNING: news(package='comapr') failed with news file: inst/NEWS.md:news()
failed to parse news file: inst/NEWS.md Refer to
https://contributions.bioconductor.org/news.html to be included in Bioconductor
release announcements.
* 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; 65 lines (2%) are > 80 characters long.
  First few lines:
    • R/count-gt.R#L6 #' helps identify poor samples or poor m ...
    • ...
    • vignettes/single-sperm-co-analysis.Rmd#L319 A p-value can be calculated
    using the ` ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/read-col-mm.R#L56 stop("readMM(): row values 'i' ar ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1029 lines (27%) are
not.
  First few lines:
    • R/bootstrap.R#L5 ...
    • ...
    • vignettes/single-sperm-co-analysis.Rmd#L326 n2 = perms$nSample[2]) ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 10 NOTES
ℹ See the comapr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.