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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Rbowtie2_2.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing Rbowtie2 ─────────────────────────────────────────────────────────
✔ Package installed successfully
── Rbowtie2 session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpR0GiwZ/file10837777368d51/Rbowtie2
→ BiocVersion: 3.24
→ Package: Rbowtie2
→ PackageVersion: 2.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Rbowtie2.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpR0GiwZ/file10837777368d51/Rbowtie2
→ installDir: /tmp/RtmpR0GiwZ/file1083771a6ac7f1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Rbowtie2 ───────────────────────────────────────────────
* 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...
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...
ℹ NOTE: 'Date:' field format is not 'YYYY-MM-DD': 2021-10-5
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* 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...
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 Rbowtie2...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/bowtie2.R (line 299, column 9)
    • print() in R/bowtie2.R (line 309, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bowtie2.R (line 254, column 11)
    • ...
    • R/bowtie2.R (line 401, column 20)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/adapterremoval.R (line 294, 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 are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • bowtie2_samtools() (R/bowtie2.R): 177 lines
    • remove_adapters() (R/adapterremoval.R): 69 lines
    • bowtie2_build() (R/bowtie2.R): 69 lines
* Checking man page documentation...
* Checking package NEWS...
* 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; 42 lines (4%) are > 80 characters long.
  First few lines:
    • R/adapterremoval.R#L191 "--output1| ...
    • ...
    • R/checkUtils.R#L95 ", file exist: ", filePa ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 49 lines (4%) are not.
  First few lines:
    • R/adapterremoval.R#L64 shQuote(file1),"--inter ...
    • ...
    • vignettes/Rbowtie2-Introduction.Rmd#L164 "bt2", "reads", " ...
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 13 NOTES
ℹ See the Rbowtie2.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.