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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RNAmodR_1.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RNAmodR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── RNAmodR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0BMZzJ/file1221ee46f6756e/RNAmodR
→ BiocVersion: 3.24
→ Package: RNAmodR
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RNAmodR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp0BMZzJ/file1221ee46f6756e/RNAmodR
→ installDir: /tmp/Rtmp0BMZzJ/file1221ee462b5eab
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RNAmodR ────────────────────────────────────────────────
* 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: DataImport
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (60%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
    • RNAmodR.creation.Rmd
    • RNAmodR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RNAmodR...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/Modifier-class.R (line 364, column 5)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Modifier-roc.R (line 117, column 84)
    • R/Modifier-roc.R (line 304, column 14)
    • R/settings.R (line 143, column 37)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/RNAmodR.creation.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/SequenceDataFrame-class.R (line 288, column 14)
  • suppressWarnings() in R/utils.R (line 236, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • .SequenceData() (R/SequenceData-class.R): 79 lines
    • ...
    • .aggregate_data_frame_mean_sd() (R/SequenceData-normalized-end-pos.R): 63
    lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/ModInosine-internals.Rd
    • man/RNAmodR.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • Modifier-class.Rd
  • ...
  • SequenceData-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 16% of man
pages use at least one of these tags.
  Found in files:
    • ModInosine-functions.Rd
    • ...
    • SequenceModRNAStringSetTrack-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • ModInosine-functions.Rd
    • ...
    • SequenceModRNAStringSetTrack-class.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: test-0SequenceData.R
test-0SequenceDataFrame.R test-1SequenceDataSet.R test-2Modifier.R
test-3normalization.R test-3subset.R test-3zcomparison.R test-4roc.R
test-8visualization.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 74 lines (1%) are > 80 characters long.
  First few lines:
    • R/Gviz-ModifiedSequenceTrack-class.R#L53 ...
    • ...
    • vignettes/RNAmodR.Rmd#L417 ggplot2::geom_bar(mapping = ggplot2::a ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4274 lines (38%) are
not.
  First few lines:
    • R/AllGenerics.R#L18 name = "plotROC", ...
    • ...
    • vignettes/RNAmodR.Rmd#L419 position = "dodge") ...
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 | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the RNAmodR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.