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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RTNduals_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RTNduals ─────────────────────────────────────────────────────────
✔ Package installed successfully
── RTNduals session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0dzDES/file126a83435ce726/RTNduals
→ BiocVersion: 3.24
→ Package: RTNduals
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RTNduals.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0dzDES/file126a83435ce726/RTNduals
→ installDir: /tmp/Rtmp0dzDES/file126a837fd9a4e8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RTNduals ───────────────────────────────────────────────
* 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 4.4.0 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: Transcription,
Network, GeneticVariability, GeneSetEnrichment
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
* Checking package installation calls in R code...
* Checking for library/require of RTNduals...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllSupplementsMBR.R (line 9, column 12)
    • ...
    • R/MBR-methods.R (line 303, column 15)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllPlotsMBR.R (line 428, column 13)
    • ...
    • MBR-methods.R (line 375, column 28)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllPlotsMBR.R (line 714, column 5)
    • ...
    • cat() in R/MBR-methods.R (line 531, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllPlotsMBR.R (line 108, column 26)
    • ...
    • R/AllSupplementsMBR.R (line 83, column 43)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/MBR-methods.R (line 257, column 20)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 8 times:
    • T in R/AllPlotsMBR.R (line 117, column 35)
    • ...
    • F in R/AllPlotsMBR.R (line 413, column 70)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • AllChecks.R (line 32, column 20)
* 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:
    • mbr.checks() (R/AllChecks.R): 233 lines
    • ...
    • _anonymous_.80() (R/MBR-methods.R): 54 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • mbrPlotDuals.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • mbrPlotDuals.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; 105 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllChecks.R#L71 stop("NOTE: 'pCutoff' should be a ...
    • ...
    • vignettes/RTNduals.Rmd#L139 Also, when prior evidences are available ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 926 lines (43%) are
not.
  First few lines:
    • R/AllChecks.R#L5 if(name == "gexp") { ...
    • ...
    • R/MBR-methods.R#L633 } ...
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 | ⚠ 3 WARNINGS | ℹ 15 NOTES
ℹ See the RTNduals.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.