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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('snpStats_1.62.0.tar.gz','quit-with-status'=TRUE)"
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── Installing snpStats ─────────────────────────────────────────────────────────
✔ Package installed successfully
── snpStats session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9J1Oqb/file95e6c7b765b29/snpStats
→ BiocVersion: 3.23
→ Package: snpStats
→ PackageVersion: 1.62.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/snpStats.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp9J1Oqb/file95e6c7b765b29/snpStats
→ installDir: /tmp/Rtmp9J1Oqb/file95e6c3fb2ebcf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on snpStats ───────────────────────────────────────────────
* 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...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* 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...
ℹ Bioconductor dependencies found in Imports & Depends (11%).
* 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:
    • data-input-vignette.Rnw
    • ...
    • tdt-vignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • imputation-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/data-input-vignette.Rnw
    • ...
    • vignettes/tdt-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of snpStats...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/imputation.R (line 57, column 14)
    • ...
    • R/ss.R (line 885, column 25)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • glm-test.R (line 137, column 22)
    • ...
    • tdt-single.R (line 177, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/contingency.table.R (line 4, column 3)
    • ...
    • cat() in R/tdt-single.R (line 226, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/ld.R (line 16, column 29)
    • ...
    • R/single.R (line 12, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/ss.R (line 832, column 24)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • F in R/ss.R (line 289, column 28)
    • T in R/xstuff.R (line 20, column 33)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • glm-test.R (line 335, column 38)
    • ...
    • single.R (line 89, column 22)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/ld-vignette.Rnw
ℹ Found @ in vignettes/snpStats-vignette.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 18
functions greater than 50 lines.
  The longest 5 functions are:
    • read.long() (R/long.R): 395 lines
    • ...
    • read.pedfile() (R/pedfile.R): 154 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotUncertainty.Rd
    • man/random.snps.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • convert.snpMatrix.Rd
    • ...
    • write.snp.matrix.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; 36 lines (0%) are > 80 characters long.
  First few lines:
    • R/contingency.table.R#L6 case <- c((1-sum.case$MAF), sum.cas ...
    • ...
    • vignettes/snpStats-vignette.Rnw#L90
    http://www.affymetrix.com/support/tech ...
ℹ NOTE: Consider 4 spaces instead of tabs; 48 lines (0%) contain tabs.
  First few lines:
    • R/long.R#L126 } ...
    • ...
    • vignettes/data-input-vignette.Rnw#L94 IGR1144a_1 287261 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3325 lines (35%) are
not.
  First few lines:
    • R/compare.R#L2 if (!row.wise && !col.wise) ...
    • ...
    • vignettes/tdt-vignette.Rnw#L115 p.values.2df = p.value(tests, 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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the snpStats.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.