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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DegNorm_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DegNorm ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DegNorm session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGWbivG/file800464c305e82/DegNorm
→ BiocVersion: 3.24
→ Package: DegNorm
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DegNorm.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpGWbivG/file800464c305e82/DegNorm
→ installDir: /tmp/RtmpGWbivG/file80046277c54fb
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DegNorm ────────────────────────────────────────────────
* 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 4.0.0 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...
* 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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (35%).
* 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:
    • DegNorm.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/RtmpGWbivG/file800464c305e82/DegNorm/vignettes/DegNorm.Rmd
* Checking package installation calls in R code...
* Checking for library/require of DegNorm...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/coverage_cal_functions.R (line 34, column 13)
    • ...
    • cat() in R/SummaryPlot.R (line 37, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/coverage_cal_functions.R (line 25, column 20)
    • ...
    • R/SummaryPlot.R (line 168, column 7)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/NMF_functions_short.R (line 40, column 50)
    • ...
    • R/SummaryPlot.R (line 67, column 57)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/coverage_cal_functions.R (line 91, column 5)
  • suppressMessages() in R/coverage_cal_functions.R (line 139, column 8)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_coverage() (R/SummaryPlot.R): 64 lines
    • ...
    • degnorm() (R/NMF_functions_short.R): 51 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; 9 lines (1%) are > 80 characters long.
  First few lines:
    • man/plot_coverage.Rd#L10 plot_coverage(gene_name, coverage_output ...
    • ...
    • vignettes/DegNorm.Rmd#L66 2. We fixed a bug in `DegNorm` funciton. ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 13 lines (1%) are not.
  First few lines:
    • R/coverage_cal_functions.R#L142 .export=c(".p ...
    • ...
    • man/read_coverage_batch.Rd#L20 \item Users can modify \code{scanBamPa ...
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 | ⚠ 0 WARNINGS | ℹ 13 NOTES
ℹ See the DegNorm.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.