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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methrix_1.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing methrix ──────────────────────────────────────────────────────────
✔ Package installed successfully
── methrix session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsAXS1a/filed58cd1e90577f/methrix
→ BiocVersion: 3.24
→ Package: methrix
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methrix.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsAXS1a/filed58cd1e90577f/methrix
→ installDir: /tmp/RtmpsAXS1a/filed58cd57b18682
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methrix ────────────────────────────────────────────────
* 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 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...
* 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 (53%).
* 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:
    • methrix.Rmd
* Checking package installation calls in R code...
* Checking for library/require of methrix...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/methrix_operations.R (line 299, column 28)
    • R/methrix_operations.R (line 317, column 59)
    • R/methrix_operations.R (line 336, column 24)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • accessory_funcs.R (line 181, column 24)
    • ...
    • write_bedgraphs.R (line 57, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/extract_CpGs.R (line 22, column 13)
    • ...
    • print() in R/snp_removal.R (line 151, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/accessory_funcs.R (line 2, column 7)
    • ...
    • R/write_bigwigs.R (line 41, column 39)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/accessory_funcs_2.R (line 42, column 17)
    • ...
    • R/write_bedgraphs.R (line 109, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 16 times:
    • T in R/methrix_operations.R (line 343, column 70)
    • ...
    • T in R/snp_removal.R (line 113, column 113)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 14 times)
  • suppressWarnings() in R/accessory_funcs.R (line 164, column 15)
  • ...
  • suppressWarnings() in R/methrix_report.R (line 196, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
  The longest 5 functions are:
    • methrix_report() (R/methrix_report.R): 201 lines
    • ...
    • get_region_summary() (R/methrix_operations.R): 137 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/write_bigwigs.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • combine_methrix.Rd
  • ...
  • read_bedgraphs.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:
    • extract_CPGs.Rd
    • ...
    • read_bedgraphs.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • extract_CPGs.Rd
    • ...
    • read_bedgraphs.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; 475 lines (13%) are > 80 characters long.
  First few lines:
    • R/accessory_funcs_2.R#L3 merge_vect_code <- function(files, col_i ...
    • ...
    • vignettes/methrix.Rmd#L275 If you prefer to work with [bsseq](https ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 462 lines (13%) are
not.
  First few lines:
    • R/accessory_funcs_2.R#L51 function(x) x[, .(cov) ...
    • ...
    • vignettes/methrix.Rmd#L125 coldata = sample_anno ...
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 | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the methrix.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.