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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('chopsticks_1.79.0.tar.gz','quit-with-status'=TRUE)"
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── Installing chopsticks ───────────────────────────────────────────────────────
✔ Package installed successfully
── chopsticks session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpFcGbVS/file65ea07520954/chopsticks
→ BiocVersion: 3.24
→ Package: chopsticks
→ PackageVersion: 1.79.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/chopsticks.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpFcGbVS/file65ea07520954/chopsticks
→ installDir: /tmp/RtmpFcGbVS/file65ea04860d91d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on chopsticks ─────────────────────────────────────────────
* 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...
* 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...
! WARNING: Invalid BiocViews term(s):
  • 'SNPsAndGeneticVariability'
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: WholeGenome
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: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • chopsticks-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/chopsticks-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of chopsticks...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • glm_test.R (line 133, column 20)
    • ...
    • ss.R (line 31, column 105)
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/ss.R (line 30, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/single.R (line 10, column 11)
    • R/single.R (line 11, column 11)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/indata.R (line 21, column 10)
    • ...
    • R/indata.R (line 78, column 10)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • ld.snp.R (line 36, column 22)
    • ...
    • ld.with.R.eml.R (line 10, column 22)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • snp.rhs.tests() (R/glm_test.R): 194 lines
    • ...
    • single.snp.tests() (R/single.R): 105 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/snpMatrix-internal.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • glm.test.control.Rd
    • ...
    • write.snp.matrix.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:
    • read.HapMap.data.Rd
    • read.wtccc.signals.Rd
    • snp.dprime-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • read.HapMap.data.Rd
    • read.wtccc.signals.Rd
    • snp.dprime-class.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; 63 lines (1%) are > 80 characters long.
  First few lines:
    • R/contingency.table.R#L6 case <- c((1-sum.case$MAF), sum.cas ...
    • ...
    • vignettes/chopsticks-vignette.Rnw#L83
    http://www.affymetrix.com/support/tech ...
ℹ NOTE: Consider 4 spaces instead of tabs; 17 lines (0%) contain tabs.
  First few lines:
    • man/read.HapMap.data.Rd#L64 the hapmap genotype file, together with ...
    • ...
    • man/X.snp.matrix-class.Rd#L49 "X.snp.matrix")}: ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1774 lines (37%) are
not.
  First few lines:
    • R/contingency.table.R#L3 OR <- sum.case$MAF / (1-sum.case$MAF) ...
    • ...
    • vignettes/chopsticks-vignette.Rnw#L462 data = subject.support, snp.data =
    ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 17 NOTES
ℹ See the chopsticks.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.