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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ORFhunteR_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ORFhunteR ────────────────────────────────────────────────────────
✔ Package installed successfully
── ORFhunteR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpaFws9G/filefb1f27a74815d/ORFhunteR
→ BiocVersion: 3.24
→ Package: ORFhunteR
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ORFhunteR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpaFws9G/filefb1f27a74815d/ORFhunteR
→ installDir: /tmp/RtmpaFws9G/filefb1f25cf36852
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ORFhunteR ──────────────────────────────────────────────
* 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...
* 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: Alignment,
SequenceMatching, 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...
ℹ NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (15%).
* 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:
    • ORFhunteR.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ORFhunteR.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ORFhunteR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/translateORFs.r (line 38, column 31)
    • R/vectorizeORFs.R (line 18, column 48)
    • R/vectorizeORFs.R (line 26, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classifyORFsCandidates.R (line 60, column 30)
    • ...
    • vectorizeORFs.R (line 39, column 64)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/annotateORFs.r (line 100, column 13)
    • R/vectorizeORFs.R (line 12, column 15)
    • R/vectorizeORFs.R (line 14, column 11)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • annotateORFs() (R/annotateORFs.r): 88 lines
    • ...
    • getSeqORFs() (R/getSeqORFs.r): 57 lines
* Checking man page documentation...
Warning: replacing previous import ‘stringr::str_wrap’ by ‘xfun::str_wrap’ when loading ‘ORFhunteR’
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • classifyORFsCandidates.Rd
  • predictORF.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
  Found in files:
    • classifyORFsCandidates.Rd
    • predictORF.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • classifyORFsCandidates.Rd
    • predictORF.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 51 lines (5%) are > 80 characters long.
  First few lines:
    • R/classifyORFsCandidates.R#L13 #' @param showAccuracy logic TRUE or FAL
    ...
    • ...
    • vignettes/ORFhunteR.Rmd#L228 Yatskou M. M., Skakun V. V., Grinev V. V ...
ℹ NOTE: Consider 4 spaces instead of tabs; 5 lines (0%) contain tabs.
  First few lines:
    • vignettes/ORFhunteR.Rmd#L103 i) the randomForest type plots: the sort ...
    • ...
    • vignettes/ORFhunteR.Rmd#L108 Recall $$Recall = \frac{TP}{TP + FN}$$ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 208 lines (20%) are
not.
  First few lines:
    • R/annotateORFs.r#L56 tr, ...
    • ...
    • vignettes/ORFhunteR.Rmd#L208 workDir = NULL ...
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 | ⚠ 0 WARNINGS | ℹ 18 NOTES
ℹ See the ORFhunteR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.