##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('baySeq_2.47.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing baySeq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── baySeq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq
→ BiocVersion: 3.24
→ Package: baySeq
→ PackageVersion: 2.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/baySeq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq
→ installDir: /tmp/RtmpZPB1WH/file59b74e069a8b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on baySeq ─────────────────────────────────────────────────
* 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 2.3.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/CDPost.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/CDPriors.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/mobAnnotation.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/mobData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/pairData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/simData.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/summarisePosteriors.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpZPB1WH/file59b742ebd93c2/baySeq/man/zimData.Rd'
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (25%).
* 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:
    • baySeq_generic.Rnw
    • baySeq.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • baySeq_generic.Rnw
    • baySeq.Rnw
* Checking package installation calls in R code...
* Checking for library/require of baySeq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/allModels.R (line 13, column 14)
    • ...
    • R/utilityFunctions.R (line 51, column 31)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • allModels.R (line 4, column 14)
    • ...
    • utilityFunctions.R (line 53, column 40)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/countData-accessors.R (line 43, column 11)
    • print() in R/countData-accessors.R (line 69, column 5)
    • cat() in R/getLikelihoods.R (line 593, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bimodalSeparator.R (line 67, column 13)
    • ...
    • R/summarisePosteriors.R (line 11, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/allModels.Rd
ℹ Found @ in man/makeOrderings.Rd
ℹ Found @ in man/marginaliseEqual.Rd
ℹ Found @ in man/marginalisePairwise.Rd
ℹ Found @ in vignettes/baySeq_generic.Rnw
ℹ Found @ in vignettes/baySeq.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/countData-accessors.R (line 54, column 27)
  • suppressWarnings() in R/countData-accessors.R (line 55, column 21)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • `getLikelihoods`() (R/getLikelihoods.R): 474 lines
    • ...
    • `getPriors`() (R/getPriors_Generic.R): 246 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/densityFunction.Rd
  • man/makeOrderings.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • densityFunctions.Rd
  • methObservables.Rd
  • plotNullPrior.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
  Found in files:
    • getLikelihoods.Rd
    • ...
    • marginalisePairwise.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getLikelihoods.Rd
    • ...
    • marginalisePairwise.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; 872 lines (17%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L2 setClass("densityFunction", representati ...
    • ...
    • vignettes/baySeq.Rnw#L412 \bibitem{molnar} Attila Molnar and Charl ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1413 lines (28%) are
not.
  First few lines:
    • R/allModels.R#L4 replevs <- 1:length(levels(CD@replicat ...
    • ...
    • vignettes/baySeq.Rnw#L326 col = rgb(red = exp(cDPair@pos ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | ℹ 19 NOTES
ℹ See the baySeq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.