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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Rhisat2_1.29.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Rhisat2 ──────────────────────────────────────────────────────────
✔ Package installed successfully
── Rhisat2 session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbUtweA/file11d0c2490cb59f/Rhisat2
→ BiocVersion: 3.24
→ Package: Rhisat2
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Rhisat2.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpbUtweA/file11d0c2490cb59f/Rhisat2
→ installDir: /tmp/RtmpbUtweA/file11d0c2d39c67d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Rhisat2 ────────────────────────────────────────────────
* 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 4.4.0 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...
* 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...
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:
    • Rhisat2.Rmd
* Checking package installation calls in R code...
* Checking for library/require of Rhisat2...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/Rhisat2.R (line 216, column 5)
    • print() in R/Rhisat2.R (line 231, column 5)
    • print() in R/Rhisat2.R (line 246, column 5)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/helpers.R (line 26, column 15)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • hisat2() (R/Rhisat2.R): 72 lines
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • Rhisat2/NEWS
    • src/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; 2 lines (0%) are > 80 characters long.
  First few lines:
    • vignettes/Rhisat2.Rmd#L61 [https://ccb.jhu.edu/software/hisat2/man ...
    • vignettes/Rhisat2.Rmd#L108 [https://ccb.jhu.edu/software/hisat2/man ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 41 lines (7%) are not.
  First few lines:
    • R/extract_splice_sites.R#L43 "file does not exist.") ...
    • ...
    • vignettes/Rhisat2.Rmd#L124 force=TRUE, strict=TRUE, execute= ...
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 10 NOTES
ℹ See the Rhisat2.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.