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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('sangerseqR_1.49.0.tar.gz','quit-with-status'=TRUE)"
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── Installing sangerseqR ───────────────────────────────────────────────────────
✔ Package installed successfully
── sangerseqR session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1FKBCC/file1284b9337a1a11/sangerseqR
→ BiocVersion: 3.24
→ Package: sangerseqR
→ PackageVersion: 1.49.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/sangerseqR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp1FKBCC/file1284b9337a1a11/sangerseqR
→ installDir: /tmp/Rtmp1FKBCC/file1284b94a6673f8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on sangerseqR ─────────────────────────────────────────────
* 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: Alignment,
SangerSeq, SequenceMatching, DataImport
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: 'Date:' field format is not 'YYYY-MM-DD': 2024-4-23
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (40%).
* 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:
    • sangerseqRWalkthrough.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/sangerseqRWalkthrough.Rmd
* Checking package installation calls in R code...
* Checking for library/require of sangerseqR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/ReadFileFunctions.R (line 86, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • ReadFileFunctions.R (line 33, column 33)
    • ...
    • UnExportedFunctions.R (line 79, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/sangerseqmethods.R (line 306, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/sangerseqmethods.R (line 246, column 22)
    • ...
    • R/sangerseqmethods.R (line 302, column 9)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • sangerseqmethods.R (line 439, column 20)
    • sangerseqmethods.R (line 449, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/ReadFileFunctions.R (line 291, column 15)
  • suppressWarnings() in R/UnExportedFunctions.R (line 39, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.188() (R/sangerseqmethods.R): 123 lines
    • ...
    • _anonymous_.315() (R/sangerseqmethods.R): 70 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/sangerseq-class.Rd
    • man/sangerseqAccessors.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • PolyPeakParser.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • PolyPeakParser.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • PolyPeakParser.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...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 14 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L2 #'@importFrom Biostrings DNA_ALPHABET IU ...
    • ...
    • vignettes/sangerseqRWalkthrough.Rmd#L151 | `peakAmpMatrix` | A numerical
    matrix ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 435 lines (25%) are
not.
  First few lines:
    • R/AllClasses.R#L57 representation( ...
    • ...
    • vignettes/sangerseqRWalkthrough.Rmd#L228 showcalls='both') ...
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 | ⚠ 2 WARNINGS | ℹ 20 NOTES
ℹ See the sangerseqR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.