##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methylSig_1.25.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing methylSig ────────────────────────────────────────────────────────
✔ Package installed successfully
── methylSig session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpigkCou/filed6d9f630cfd14/methylSig
→ BiocVersion: 3.24
→ Package: methylSig
→ PackageVersion: 1.25.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methylSig.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpigkCou/filed6d9f630cfd14/methylSig
→ installDir: /tmp/RtmpigkCou/filed6d9f299c5401
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methylSig ──────────────────────────────────────────────
* 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 3.6 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage
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...
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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (73%).
* 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:
    • updating-methylSig-code.Rmd
    • using-methylSig.Rmd
* Checking package installation calls in R code...
* Checking for library/require of methylSig...
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/diff_binomial.R (line 40, column 15)
    • ...
    • R/tile_by_windows.R (line 46, column 24)
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • diff_methylsig() (R/diff_methylsig.R): 365 lines
    • ...
    • filter_loci_by_group_coverage() (R/filter_loci_by_group_coverage.R): 81
    lines
* Checking man page documentation...
* 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; 173 lines (9%) are > 80 characters long.
  First few lines:
    • R/diff_binomial.R#L3 #' This function calculates differential ...
    • ...
    • vignettes/using-methylSig.Rmd#L322 The numerical covariate test. Note,
    here ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 8 lines (0%) are not.
  First few lines:
    • R/diff_binomial.R#L125 + unmeth_reads_con ...
    • ...
    • R/diff_methylsig.R#L435 result_gr$pvalue = stats::pchis ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 12 NOTES
ℹ See the methylSig.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.