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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CrispRVariants_1.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CrispRVariants ───────────────────────────────────────────────────
✔ Package installed successfully
── CrispRVariants session metadata ─────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0lgvRb/file7b0fc5a322185/CrispRVariants
→ BiocVersion: 3.24
→ Package: CrispRVariants
→ PackageVersion: 1.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CrispRVariants.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0lgvRb/file7b0fc5a322185/CrispRVariants
→ installDir: /tmp/Rtmp0lgvRb/file7b0fc5a44cb5f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CrispRVariants ─────────────────────────────────────────
* 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 4.3.0 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: SangerSeq
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 (56%).
* 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:
    • user_guide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of CrispRVariants...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/CrisprRun.R (line 121, column 20)
    • ...
    • R/utils.R (line 63, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • abifToFastq.R (line 45, column 50)
    • ...
    • seqsToAln.R (line 108, column 32)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/alleleLabels.R (line 352, column 5)
    • ...
    • cat() in R/mergeChimeras.R (line 141, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/abifToFastq.R (line 77, column 12)
    • ...
    • R/utils.R (line 55, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/CrisprSet.R (line 167, column 23)
    • ...
    • R/seqsToAln.R (line 40, column 14)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • plotVariants.R (line 54, column 22)
    • ...
    • seqsToAln.R (line 176, column 53)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 11 times)
  • <<- in R/CrisprRun.R (line 67, column 14)
  • ...
  • <<- in R/CrisprSet.R (line 123, column 28)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/CrisprSet.R (line 822, column 20)
  • suppressWarnings() in R/CrisprSet.R (line 931, column 20)
  • suppressWarnings() in R/plotVariants.R (line 185, column 18)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • plotChimeras() (R/plotChimeras.R): 268 lines
    • ...
    • plotVariants() (R/CrisprSet.R): 133 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • abifToFastq.Rd
  • findSNVs.Rd
  • readsByPCRPrimer.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • abifToFastq.Rd
* Checking package NEWS...
* 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; 336 lines (4%) are > 80 characters long.
  First few lines:
    • R/accessors.R#L74 #'@param filter.cols A vector of control ...
    • ...
    • vignettes/user_guide.Rmd#L1187 # With chimera.to.target = 100, an addit
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1991 lines (26%) are
not.
  First few lines:
    • R/abifToFastq.R#L35 message(sprintf("failed on %s", s ...
    • ...
    • vignettes/user_guide.Rmd#L1181 chimera.to.target ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the CrispRVariants.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.