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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('gwascat_2.44.0.tar.gz','quit-with-status'=TRUE)"
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── Installing gwascat ──────────────────────────────────────────────────────────
✔ Package installed successfully
── gwascat session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnyTDuL/file15cad81f7fb7b6/gwascat
→ BiocVersion: 3.23
→ Package: gwascat
→ PackageVersion: 2.44.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/gwascat.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpnyTDuL/file15cad81f7fb7b6/gwascat
→ installDir: /tmp/RtmpnyTDuL/file15cad8da990fb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gwascat ────────────────────────────────────────────────
* 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 4.1.0 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 (75%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/gwascat.Rmd
    • vignettes/gwascatOnt.Rmd
* Checking package installation calls in R code...
* Checking for library/require of gwascat...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bindcadd_snv.R (line 42, column 10)
    • ...
    • R/obotools.R (line 21, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bindcadd_snv.R (line 61, column 13)
    • ...
    • obotools.R (line 109, column 17)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/funcs.R (line 67, column 8)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/addSeqlengths.R (line 2, column 15)
    • ...
    • R/zzz.R (line 89, column 12)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/funcs.R (line 37, column 29)
    • ...
    • R/ldtagr.R (line 83, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • bindcadd_snv.R (line 63, column 35)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressWarnings() in R/cache_current_gwascat.R (line 21, column 28)
  • ...
  • suppressWarnings() in R/zzz.R (line 87, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • process_gwas_dataframe() (R/process_gwas_dataframe.R): 62 lines
    • ...
    • gwdf2GRanges() (R/zzz.R): 53 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/as_GRanges.Rd
    • ...
    • man/subsetByTraits.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • as_GRanges.Rd
    • ...
    • traitsManh.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • bindcadd_snv.Rd
    • ...
    • traitsManh.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • bindcadd_snv.Rd
    • riskyAlleleCount.Rd
    • traitsManh.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; 91 lines (4%) are > 80 characters long.
  First few lines:
    • R/bindcadd_snv.R#L30 bindcadd_snv = function(gr, fn="http://k ...
    • ...
    • vignettes/gwascatOnt.Rmd#L85 sapply(graph::nodeData(graph::subGraph(p ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 513 lines (24%) are
not.
  First few lines:
    • R/addSeqlengths.R#L3 stopifnot(inherits(src, "Seqinfo")) ...
    • ...
    • vignettes/gwascat.Rmd#L502 chklocs("20", gwtrunc) ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the gwascat.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.