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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('GSVA_2.6.1.tar.gz','quit-with-status'=TRUE)"
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── Installing GSVA ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── GSVA session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpslqkNU/file7caa551e32ae4/GSVA
→ BiocVersion: 3.23
→ Package: GSVA
→ PackageVersion: 2.6.1
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/GSVA.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpslqkNU/file7caa551e32ae4/GSVA
→ installDir: /tmp/RtmpslqkNU/file7caa558bf077a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GSVA ───────────────────────────────────────────────────
* 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:
GeneExpression, TissueMicroarray, Clustering, Survival
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (71%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GSVA_proteomics.Rmd
    • GSVA_scRNAseq.Rmd
    • GSVA.Rmd
* Checking package installation calls in R code...
* Checking for library/require of GSVA...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • genesets.R (line 592, column 35)
    • ...
    • genesets.R (line 619, column 58)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/GsvaMethodParam.R (line 93, column 15)
    • cat() in R/GsvaMethodParam.R (line 102, column 15)
    • cat() in R/GsvaMethodParam.R (line 117, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 3 times)
  • <<- in R/genesets.R (line 167, column 18)
  • <<- in R/genesets.R (line 168, column 17)
  • <<- in R/genesets.R (line 170, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 26
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.433() (R/gsva.R): 108 lines
    • ...
    • .processMatrixCols() (R/block_processing.R): 78 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • igsva.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • igsva.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; 140 lines (2%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L24 function(gSets, uniqGenes=uni ...
    • ...
    • vignettes/GSVA.Rmd#L983 [Bioconductor Contributor Code of Conduc ...
ℹ NOTE: Consider 4 spaces instead of tabs; 13 lines (0%) contain tabs.
  First few lines:
    • R/genesets.R#L973 return(gSets[gSetsLen >= minSize ...
    • ...
    • vignettes/GSVA_proteomics.Rmd#L294 ylab="Correlation before/after
    imputati ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1552 lines (18%) are
not.
  First few lines:
    • R/AllClasses.R#L42 c("matrix", "dgCMatrix", " ...
    • ...
    • vignettes/GSVA.Rmd#L925 method="complete") ...
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 GSVA.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.