##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('BiocStyle_2.40.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing BiocStyle ────────────────────────────────────────────────────────
✔ Package installed successfully
── BiocStyle session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYfvJ58/file7402c7f6df1d4/BiocStyle
→ BiocVersion: 3.23
→ Package: BiocStyle
→ PackageVersion: 2.40.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocStyle.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpYfvJ58/file7402c7f6df1d4/BiocStyle
→ installDir: /tmp/RtmpYfvJ58/file7402c5eb6d0d5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BiocStyle ──────────────────────────────────────────────
* 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...
✖ ERROR: Add biocViews other than Software
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 that Package field matches directory/tarball name...
* 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...
* 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:
    • LatexStyle2.Rnw
✖ ERROR: More than one VignetteEngine specified.
  Found in files:
    • vignettes/AuthoringRmdVignettes.Rmd
! WARNING: Evaluate more vignette chunks.
ℹ 30 out of 53 code chunks = 56% unevaluated
ℹ 
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • LatexStyle2.Rnw
* Checking package installation calls in R code...
* Checking for library/require of BiocStyle...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/html_document.R (line 56, column 3)
    • ...
    • require() in R/pdf_document.R (line 48, column 3)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/auth_affil.R (line 21, column 15)
    • ...
    • R/markdown.R (line 75, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • auth_affil.R (line 87, column 32)
    • ...
    • utils.R (line 25, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/latex.R (line 49, column 3)
    • ...
    • cat() in R/markdown.R (line 70, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/auth_affil.R (line 1, column 18)
    • ...
    • R/utils.R (line 66, column 8)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/zzz.R (line 5, column 15)
  • <<- in R/zzz.R (line 6, column 22)
  • <<- in R/zzz.R (line 7, column 22)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 11
functions greater than 50 lines.
  The longest 5 functions are:
    • pdf_document() (R/pdf_document.R): 189 lines
    • ...
    • create_html_template() (R/html_document.R): 82 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/BiocStyle-defunct.Rd
    • man/use_vignette.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • html_document.Rd
    • ...
    • pdf_document.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 40% of man
pages use at least one of these tags.
  Found in files:
    • html_document.Rd
    • ...
    • pdf_document.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • html_document.Rd
    • ...
    • pdf_document.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; 142 lines (5%) are > 80 characters long.
  First few lines:
    • R/auth_affil.R#L36 affil_marks <- sapply(affil, fun ...
    • ...
    • vignettes/LatexStyle2.Rnw#L611 continue using \Rpackage{xtable} in your
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 870 lines (30%) are
not.
  First few lines:
    • R/auth_affil.R#L2 auth <- m$author ...
    • ...
    • vignettes/LatexStyle2.Rnw#L545 \sin^2 \theta + \cos^2 \theta \equiv 1 ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 5 WARNINGS | ℹ 13 NOTES
ℹ See the BiocStyle.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.