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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('bsseq_1.48.0.tar.gz','quit-with-status'=TRUE)"
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── Installing bsseq ────────────────────────────────────────────────────────────
✔ Package installed successfully
── bsseq session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsufrPc/file74dc248684c67/bsseq
→ BiocVersion: 3.23
→ Package: bsseq
→ PackageVersion: 1.48.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/bsseq.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpsufrPc/file74dc248684c67/bsseq
→ installDir: /tmp/RtmpsufrPc/file74dc274b8c17d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on bsseq ──────────────────────────────────────────────────
* 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 4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
WholeGenome, 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 that Package field matches directory/tarball name...
* 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 (55%).
* 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:
    • bsseq.Rmd
* Checking package installation calls in R code...
* Checking for library/require of bsseq...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/BSmooth.R (line 21, column 19)
    • ...
    • R/plotting.R (line 261, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • BSmooth.fstat.R (line 83, column 17)
    • ...
    • plotting.R (line 286, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/BSmooth.fstat.R (line 8, column 17)
    • ...
    • cat() in R/plotting.R (line 92, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotting.R (line 30, column 22)
    • ...
    • R/plotting.R (line 35, column 19)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/BSmooth.R (line 279, column 14)
    • ...
    • R/read.bismark.R (line 477, column 14)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Defunct() in R/read.modbam2bed.R (line 3, column 5)
  • .Defunct() in R/read.modkit.R (line 5, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/BSmooth.fstat.R (line 124, column 9)
  • suppressWarnings() in R/BSmooth.tstat.R (line 14, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 28
functions greater than 50 lines.
  The longest 5 functions are:
    • BSmooth() (R/BSmooth.R): 219 lines
    • ...
    • .constructbedMethylCounts() (R/read.bedMethyl.R): 131 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/bsseq-deprecated.Rd
    • ...
    • man/read.bedMethyl.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • BSmooth.Rd
  • BSseqStat-class.Rd
  • plotRegion.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:
    • BSmooth.Rd
    • ...
    • read.bismark.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • BSmooth.Rd
    • read.bismark.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; 209 lines (3%) are > 80 characters long.
  First few lines:
    • R/BSmooth.fstat.R#L6 ## warning("Computing t-statisti ...
    • ...
    • vignettes/bsseq.Rmd#L300 % eval: (add-hook 'LaTeX-mode-hook '(lam ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 856 lines (14%) are
not.
  First few lines:
    • R/BSmooth.fstat.R#L11 confint = FALSE) ...
    • ...
    • vignettes/bsseq.Rmd#L182 ranges = IRanges(star ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the bsseq.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.