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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('BSgenomeForge_1.13.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BSgenomeForge ────────────────────────────────────────────────────
✔ Package installed successfully
── BSgenomeForge session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpyq0ykL/file1aa3d0220e833/BSgenomeForge
→ BiocVersion: 3.24
→ Package: BSgenomeForge
→ PackageVersion: 1.13.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/BSgenomeForge.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpyq0ykL/file1aa3d0220e833/BSgenomeForge
→ installDir: /tmp/Rtmpyq0ykL/file1aa3d0790c76
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BSgenomeForge ──────────────────────────────────────────
* 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 4.3.0 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: Coverage,
MultipleSequenceAlignment
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (79%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • AdvancedBSgenomeForge.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 20 out of 30 code chunks = 66% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • AdvancedBSgenomeForge.Rnw
    • QuickBSgenomeForge.Rmd
* Checking package installation calls in R code...
* Checking for library/require of BSgenomeForge...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/AdvancedBSgenomeForge.R (line 1081, column 9)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AdvancedBSgenomeForge.R (line 924, column 18)
    • R/AdvancedBSgenomeForge.R (line 1116, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/utils.R (line 23, column 11)
* 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:
    • _anonymous_.858() (R/AdvancedBSgenomeForge.R): 119 lines
    • ...
    • forgeBSgenomeDataPkgFromTwobitFile()
    (R/forgeBSgenomeDataPkgFromTwobitFile.R): 63 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/AdvancedBSgenomeForge.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; 29 lines (1%) are > 80 characters long.
  First few lines:
    • R/AdvancedBSgenomeForge.R#L410 ondisk_seq_for ...
    • ...
    • vignettes/QuickBSgenomeForge.Rmd#L30 Bioconductor currently provides more
    tha ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 687 lines (17%) are
not.
  First few lines:
    • R/AdvancedBSgenomeForge.R#L81 genome=NA_char ...
    • ...
    • vignettes/QuickBSgenomeForge.Rmd#L89 circ_seqs=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 | ⚠ 4 WARNINGS | ℹ 11 NOTES
ℹ See the BSgenomeForge.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.