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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('vsn_3.80.0.tar.gz','quit-with-status'=TRUE)"
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── Installing vsn ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── vsn session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgtrYU8/file9a4728241d9/vsn
→ BiocVersion: 3.23
→ Package: vsn
→ PackageVersion: 3.80.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/vsn.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpgtrYU8/file9a4728241d9/vsn
→ installDir: /tmp/RtmpgtrYU8/file9a472289480ed
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on vsn ────────────────────────────────────────────────────
* 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 4.0.0 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: Normalization
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 that Package field matches directory/tarball name...
* 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 (50%).
* 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 vsn...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/meanSdPlot-methods.R (line 28, column 19)
    • R/plotLikelihood.R (line 18, column 12)
    • R/RGList_to_NChannelSet.R (line 14, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plotLikelihood.R (line 3, column 24)
    • ...
    • vsnLogLik.R (line 50, column 35)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plotLikelihood.R (line 38, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 4, column 24)
    • ...
    • R/vsnLogLik.R (line 62, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/sagmbSimulateData.R (line 63, column 10)
* 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 4
functions greater than 50 lines.
  The longest 5 functions are:
    • vsnMatrix() (R/vsn2.R): 99 lines
    • ...
    • validityVsnInput() (R/AllClasses.R): 58 lines
* Checking man page documentation...
* 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; 155 lines (5%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L8 return(sprintf("'%s' must be a numer ...
    • ...
    • vignettes/D-convergence.Rmd#L15 Please see the .Rnw and .pdf file in the
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • vignettes/A-vsn.Rmd#L159 allpositive = TRUE) ...
    • vignettes/A-vsn.Rmd#L162 allpositive = allpositive) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 711 lines (25%) are
not.
  First few lines:
    • R/AllClasses.R#L5 ## S4 already makes sure s is numeric ...
    • ...
    • vignettes/C-likelihoodcomputations.Rmd#L261 \frac{1}{2}\sum_{k=1}^n
    \log(1+Y_{ki}^ ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 13 NOTES
ℹ See the vsn.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.