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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RNAshapeQC_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RNAshapeQC ───────────────────────────────────────────────────────
✔ Package installed successfully
── RNAshapeQC session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpZcHtxj/file1231e439b48cb6/RNAshapeQC
→ BiocVersion: 3.24
→ Package: RNAshapeQC
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RNAshapeQC.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpZcHtxj/file1231e439b48cb6/RNAshapeQC
→ installDir: /tmp/RtmpZcHtxj/file1231e450ae414
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RNAshapeQC ─────────────────────────────────────────────
* 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 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 (35%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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 RNAshapeQC...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/SCISSOR.R (line 293, column 22)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plot_shape.R (line 39, column 97)
    • ...
    • SCISSOR.R (line 488, column 49)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plot_shape.R (line 423, column 5)
    • print() in R/plot_shape.R (line 539, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/SCISSOR.R (line 127, column 29)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/data_QC.R (line 63, column 21)
    • R/SCISSOR.R (line 127, column 35)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/SCISSOR.R (line 700, column 74)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_DIIwt() (R/plot_shape.R): 229 lines
    • ...
    • construct_pileup() (R/data_gen.R): 105 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; 345 lines (9%) are > 80 characters long.
  First few lines:
    • R/data_gen.R#L5 .build_regionsStr <- function(Gene, regi ...
    • ...
    • vignettes/RNAshapeQC_intro.Rmd#L401 [^1]: Choi, H.Y., Jo, H., Zhao, X. et
    al ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 36 lines (1%) are not.
  First few lines:
    • R/data_gen.R#L205 Gene, ...
    • ...
    • vignettes/RNAshapeQC_intro.Rmd#L221 - `DII`: _Degraded_ or _Intact_ label
    ...
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 12 NOTES
ℹ See the RNAshapeQC.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.