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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('GEOquery_2.81.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GEOquery ─────────────────────────────────────────────────────────
✔ Package installed successfully
── GEOquery session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTg3sry/file1b0bcb7c885c88/GEOquery
→ BiocVersion: 3.24
→ Package: GEOquery
→ PackageVersion: 2.81.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/GEOquery.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTg3sry/file1b0bcb7c885c88/GEOquery
→ installDir: /tmp/RtmpTg3sry/file1b0bcb710bd6e0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GEOquery ───────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: GeneExpression
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 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 (24%).
* 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...
! WARNING: Quarto vignette found but 'SystemRequirements' field not in
DESCRIPTION.
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GEOquery.qmd
    • single-cell.qmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/single-cell.qmd
* Checking package installation calls in R code...
* Checking for library/require of GEOquery...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/getGSEDataTables.R (line 34, column 15)
    • R/getGSEDataTables.R (line 35, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classes.R (line 58, column 21)
    • ...
    • parseGEO.R (line 442, column 15)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/classes.R (line 59, column 13)
    • ...
    • print() in R/classes.R (line 79, column 20)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/GDS2MA.R (line 47, column 15)
    • ...
    • R/parseGEO.R (line 612, column 17)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/GDS2MA.R (line 10, column 12)
  • ...
  • suppressWarnings() in R/parseGEO.R (line 219, column 17)
* 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:
    • parseGSEMatrix() (R/parseGEO.R): 149 lines
    • getGEOfile() (R/getGEOfile.R): 87 lines
    • getGEOSuppFiles() (R/getGEOSuppFiles.R): 53 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/browseGEOAccession.Rd
    • ...
    • man/getGEOSuppFileURL.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • browseGEOAccession.Rd
    • ...
    • searchGEO.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 15% of man
pages use at least one of these tags.
  Found in files:
    • browseGEOAccession.Rd
    • ...
    • searchGEO.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • browseGEOAccession.Rd
    • ...
    • searchGEO.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; 152 lines (6%) are > 80 characters long.
  First few lines:
    • R/classes.R#L5 setClass("GEODataTable", representation( ...
    • ...
    • vignettes/single-cell.qmd#L100 sce2 = DropletUtils::read10xCounts(sampl
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 213 lines (8%) are
not.
  First few lines:
    • R/browseGEOAccession.R#L19 paste0("https://www.ncbi.nlm.nih.gov/g ...
    • ...
    • vignettes/GEOquery.qmd#L200 ...
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 | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the GEOquery.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.