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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('Glimma_2.23.1.tar.gz','quit-with-status'=TRUE)"
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── Installing Glimma ───────────────────────────────────────────────────────────
✔ Package installed successfully
── Glimma session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDQHRHy/filea717cc6780c1/Glimma
→ BiocVersion: 3.24
→ Package: Glimma
→ PackageVersion: 2.23.1
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/Glimma.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpDQHRHy/filea717cc6780c1/Glimma
→ installDir: /tmp/RtmpDQHRHy/filea717c6cfa7cbc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Glimma ─────────────────────────────────────────────────
* 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...
* 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (56%).
* 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:
    • DESeq2.Rmd
    • limma_edger.Rmd
    • single_cell_edger.Rmd
* Checking package installation calls in R code...
* Checking for library/require of Glimma...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/glimmaMA.R (line 168, column 15)
    • ...
    • R/v1-jsonConvert.R (line 55, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • glimmaMA.R (line 184, column 20)
    • ...
    • v1-utilities.R (line 42, column 43)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/v1-glimma.R (line 78, column 5)
    • cat() in R/v1-glimma.R (line 99, column 5)
    • cat in R/v1-jsHelper.R (line 6, column 14)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/glimmaMDS.R (line 190, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/glimmaMDS.R (line 113, column 12)
    • ...
    • R/v1-textUtils.R (line 11, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/glimmaXY.R (line 62, column 34)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/glimmaMDS.R (line 159, column 9)
  • suppressWarnings() in R/v1-glMDSPlot.R (line 129, column 11)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
  The longest 5 functions are:
    • glimmaVolcano.MArrayLM() (R/glimmaVolcano.R): 157 lines
    • ...
    • glMDPlot.DESeqResults() (R/v1-glMDPlot.R): 136 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • glMDPlot.Rd
    • glMDSPlot.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • glXYPlot.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; 296 lines (6%) are > 80 characters long.
  First few lines:
    • R/glimmaMA.R#L4 #' Generic function for drawing a two-pa ...
    • ...
    • vignettes/single_cell_edger.Rmd#L155 sc_dge <- sc_dge[,
    colData(sce)$level1cl ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/v1-glMDUtils.R#L133 paste0("[Click here for interactive ve ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 634 lines (12%) are
not.
  First few lines:
    • R/glimmaMA.R#L27 UseMethod("glimmaMA") ...
    • ...
    • vignettes/single_cell_edger.Rmd#L87 colData(sce)$level2class) ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the Glimma.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.