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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ORFik_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ORFik ────────────────────────────────────────────────────────────
✔ Package installed successfully
── ORFik session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAxDtd5/filefb50a235adef5/ORFik
→ BiocVersion: 3.24
→ Package: ORFik
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ORFik.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAxDtd5/filefb50a235adef5/ORFik
→ installDir: /tmp/RtmpAxDtd5/filefb50a2282c892
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ORFik ──────────────────────────────────────────────────
* 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...
* 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 (50%).
* 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: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Annotation_Alignment.Rmd
    • ...
    • vignettes/Working_with_transcripts.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ORFik...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/experiment.R (line 23, column 25)
    • ...
    • R/utils_imports.R (line 211, column 43)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • codon_usage.R (line 129, column 13)
    • ...
    • STAR_multiQC.R (line 279, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/coverage_filters.R (line 58, column 3)
    • ...
    • cat() in R/utils.R (line 689, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/coverage_heatmaps.R (line 81, column 12)
    • ...
    • R/utils.R (line 193, column 10)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/coverage_heatmaps.R (line 166, column 11)
    • ...
    • R/utils_imports.R (line 531, column 17)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/covRLE_class.R (line 370, column 13)
    • ...
    • R/txdbHelpers.R (line 811, column 15)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/fastq_helpers.R (line 53, column 15)
    • ...
    • system() in R/utils.R (line 643, column 36)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/makeTxdbFromGenome.Rd
ℹ Found @ in vignettes/ORFikExperiment.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 10 times)
  • suppressWarnings() in R/codon_usage.R (line 15, column 19)
  • ...
  • suppressWarnings() in R/utils.R (line 643, column 19)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 66
functions greater than 50 lines.
  The longest 5 functions are:
    • pmapToTranscriptF() (R/ranges_helpers.R): 159 lines
    • ...
    • coverageScorings() (R/coverage_helpers.R): 105 lines
* Checking man page documentation...
Warning: no function found corresponding to methods exports from ‘ORFik’ for: ‘organism’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • config.Rd
  • ...
  • uniqueMappers.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • assignTSSByCage.Rd
    • ...
    • topMotif.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • assignTSSByCage.Rd
    • ...
    • topMotif.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; 1532 lines (6%) are > 80 characters long.
  First few lines:
    • R/cage_annotations.R#L311 original_meta <- original_meta[!(origi ...
    • ...
    • vignettes/Working_with_transcripts.Rmd#L207 The output relies on
    data.table package ...
ℹ NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
  First few lines:
    • vignettes/Annotation_Alignment.Rmd#L265 (a string: which steps to do?
    (default ...
    • ...
    • vignettes/Annotation_Alignment.Rmd#L269 To just do trim and alignment to
    genom ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 7886 lines (30%) are
not.
  First few lines:
    • R/cage_annotations.R#L11 preCleanup = TRUE ...
    • ...
    • vignettes/Working_with_transcripts.Rmd#L190 exclude.zero.c ...
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 19 NOTES
ℹ See the ORFik.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.