##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('dmrseq_1.33.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing dmrseq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── dmrseq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVAobjG/file83ca4264d2e59/dmrseq
→ BiocVersion: 3.24
→ Package: dmrseq
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/dmrseq.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpVAobjG/file83ca4264d2e59/dmrseq
→ installDir: /tmp/RtmpVAobjG/file83ca42ac383d4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on dmrseq ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5 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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* 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 (48%).
* 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: Vignette(s) found with missing chunk labels
  Found in files:
    • dmrseq.Rmd
* Checking package installation calls in R code...
* Checking for library/require of dmrseq...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • dmrseq.R (line 327, column 19)
    • helper_functions.R (line 555, column 73)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/plotDMRs.R (line 273, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/getAnnot.R (line 103, column 18)
    • R/helper_functions.R (line 813, column 21)
    • R/plotEmpiricalDistribution.R (line 57, column 16)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/dmrseq.R (line 617, column 29)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/dmrseq.R (line 264, column 14)
    • ...
    • R/plotEmpiricalDistribution.R (line 72, column 18)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • internal_plotting_functions.R (line 620, column 76)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/helper_functions.R (line 747, column 31)
  • suppressWarnings() in R/helper_functions.R (line 750, column 33)
  • suppressWarnings() in R/simDMRs.R (line 103, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 20
functions greater than 50 lines.
  The longest 5 functions are:
    • dmrseq() (R/dmrseq.R): 565 lines
    • ...
    • simDMRs() (R/simDMRs.R): 176 lines
* Checking man page documentation...
* Checking package NEWS...
* 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; 26 lines (1%) are > 80 characters long.
  First few lines:
    • R/dmrseq.R#L282 sampleSize <- table(testCov)[names(t ...
    • ...
    • vignettes/dmrseq.Rmd#L596 [Explore how many regions were significa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/helper_functions.R#L570 }else{ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 887 lines (21%) are
not.
  First few lines:
    • R/dmrseq.R#L170 minNumRegion = 5, smo ...
    • ...
    • vignettes/dmrseq.Rmd#L586 file="h1_imr90_results.csv") ...
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 17 NOTES
ℹ See the dmrseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.