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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TRESS_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing TRESS ────────────────────────────────────────────────────────────
✔ Package installed successfully
── TRESS session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvqBg5s/file14f8881a0ee533/TRESS
→ BiocVersion: 3.24
→ Package: TRESS
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TRESS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvqBg5s/file14f8881a0ee533/TRESS
→ installDir: /tmp/RtmpvqBg5s/file14f8888f56682
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TRESS ──────────────────────────────────────────────────
* 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 4.1.0 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...
No vignettes found.
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Normalization
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', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of TRESS...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CovR.parallel.R (line 13, column 15)
    • ...
    • MLE.parallel.R (line 20, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/CallCandidates.R (line 51, column 3)
    • ...
    • cat() in R/TRESS_peak.R (line 139, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/adjustHessian.R (line 3, column 12)
    • ...
    • R/WaldTest.R (line 15, column 13)
* 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 23
functions greater than 50 lines.
  The longest 5 functions are:
    • CallCandidates() (R/CallCandidates.R): 145 lines
    • ...
    • EstiPhi.JointUpdate() (R/EstiPhi.JointUpdate.R): 109 lines
* Checking man page documentation...
ℹ NOTE: Auto-generated '%% ~' comments found in Rd man pages.
  • man/DivideBins.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • DivideBins.Rd
  • TRESS_DMRfit.Rd
  • TRESS_peak.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
  Found in files:
    • DivideBins.Rd
    • TRESS_DMRfit.Rd
    • TRESS_peak.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • DivideBins.Rd
    • TRESS_DMRfit.Rd
    • TRESS_peak.Rd
* 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; 5 lines (0%) are > 80 characters long.
  First few lines:
    • R/getGeneID.R#L4 ### Path_To_OrgdbSqlite: path to obtai ...
    • ...
    • R/TRESS_peak.R#L123 Path_To_Orgdb ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1838 lines (60%) are
not.
  First few lines:
    • R/adjustHessian.R#L5 tmp.svd = svd(Hessian) ...
    • ...
    • TRESS/NAMESPACE#L31 ) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the TRESS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.