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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RAIDS_1.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RAIDS ────────────────────────────────────────────────────────────
✔ Package installed successfully
── RAIDS session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmppQdBom/file1070c836937bd5/RAIDS
→ BiocVersion: 3.24
→ Package: RAIDS
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RAIDS.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmppQdBom/file1070c836937bd5/RAIDS
→ installDir: /tmp/RtmppQdBom/file1070c857b6c48
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RAIDS ──────────────────────────────────────────────────
* 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 4.2.0 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...
You have biocViews from multiple branches.
ℹ NOTE: Consider adding these automatically suggested biocViews:
GenomeWideAssociation, QualityControl, 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 (59%).
* 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 RAIDS...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/tools.R (line 123, column 5)
    • ...
    • cat() in R/tools.R (line 129, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/processStudy_internal.R (line 588, column 22)
    • ...
    • R/tools_internal.R (line 873, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/synthetic_internal.R (line 126, column 14)
    • R/synthetic.R (line 371, column 14)
    • R/synthetic.R (line 533, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/synthetic.R (line 876, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 43
functions greater than 50 lines.
  The longest 5 functions are:
    • syntheticGeno() (R/synthetic.R): 257 lines
    • ...
    • readSNVBAM() (R/tools_internal.R): 137 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • addBlockFromDetFile.Rd
    • ...
    • runRNAAncestry.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • computeAncestryFromSynthetic.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; 166 lines (1%) are > 80 characters long.
  First few lines:
    • R/allelicFraction_internal.R#L418 lM1 <- s ...
    • ...
    • vignettes/Wrappers.Rmd#L654 [https://labshare.cshl.edu/shares/krasni ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • vignettes/RAIDS.Rmd#L136 data/ ...
    • vignettes/RAIDS.Rmd#L137 refGDS ...
    • vignettes/RAIDS.Rmd#L138 profileGDS ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 186 lines (1%) are
not.
  First few lines:
    • R/allelicFraction_internal.R#L422 ...
    • ...
    • vignettes/Wrappers.Rmd#L595 ...
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 14 NOTES
ℹ See the RAIDS.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.