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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('deepSNV_1.59.0.tar.gz','quit-with-status'=TRUE)"
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── Installing deepSNV ──────────────────────────────────────────────────────────
✔ Package installed successfully
── deepSNV session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp4h1VlK/file7f86863002401/deepSNV
→ BiocVersion: 3.24
→ Package: deepSNV
→ PackageVersion: 1.59.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/deepSNV.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp4h1VlK/file7f86863002401/deepSNV
→ installDir: /tmp/Rtmp4h1VlK/file7f868eeba042
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on deepSNV ────────────────────────────────────────────────
* 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 2.13.0 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: Coverage,
GenomicVariation, VariantAnnotation, VariantDetection, Alignment,
QualityControl, SequenceMatching
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 (60%).
* 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: Vignette(s) missing Vignette metadata. See
https://r-pkgs.org/vignettes.html
  Update the following files:
    • shearwaterML.Rmd
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • deepSNV.Rnw
    • shearwater.Rnw
! WARNING: Vignette(s) missing '\%VignetteIndexEntry{Vignette Title}'.
  Update the following files:
    • shearwaterML.Rmd
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • deepSNV.Rnw
    • shearwater.Rnw
    • shearwaterML.Rmd
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/deepSNV.Rnw (chunk no. 9, line 140, column 36)
    • vignettes/deepSNV.Rnw (chunk no. 9, line 140, column 71)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/shearwaterML.Rmd
* Checking package installation calls in R code...
* Checking for library/require of deepSNV...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/deepSNV-functions.R (line 135, column 19)
    • ...
    • R/shearwater-functions.R (line 231, column 38)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • deepSNV-functions.R (line 10, column 50)
    • ...
    • shearwaterML.R (line 210, column 37)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/betabinom.R (line 12, column 12)
    • ...
    • R/shearwaterML.R (line 213, column 19)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 17 times:
    • T in R/deepSNV-experimental.R (line 39, column 59)
    • ...
    • F in R/shearwaterML.R (line 78, column 52)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • deepSNV-methods.R (line 111, column 43)
    • ...
    • shearwater-functions.R (line 20, column 27)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/deepSNV.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* 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:
    • bbb() (R/shearwater-functions.R): 126 lines
    • ...
    • betabinLRT() (R/shearwaterML.R): 73 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/counts.Rd
    • ...
    • man/trueSNVs.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot.deepSNV.Rd
    • man/show-deepSNV-method.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • betabinLRT.Rd
    • ...
    • qvals2Vcf.Rd
* Checking package NEWS...
* 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; 392 lines (13%) are > 80 characters long.
  First few lines:
    • R/deepSNV-class.R#L9 #' This class stores the contents of the ...
    • ...
    • vignettes/shearwaterML.Rmd#L29 files <- c(system.file("extdata", "test.
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1162 lines (39%) contain tabs.
  First few lines:
    • R/betabinom.R#L13 disp <- (1-rho)/rho ...
    • ...
    • vignettes/shearwater.Rnw#L395 vcfList[[gene]] <- bf2Vcf(BF = BF, coun ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 147 lines (5%) are
not.
  First few lines:
    • R/deepSNV-functions.R#L374 as.integer(keepflag), ...
    • ...
    • vignettes/shearwater.Rnw#L285 \end{cases} ...
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 | ⚠ 8 WARNINGS | ℹ 17 NOTES
ℹ See the deepSNV.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.