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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('SparseArray_1.12.2.tar.gz','quit-with-status'=TRUE)"
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── Installing SparseArray ──────────────────────────────────────────────────────
✔ Package installed successfully
── SparseArray session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpqcXhTG/file9689358a09478/SparseArray
→ BiocVersion: 3.23
→ Package: SparseArray
→ PackageVersion: 1.12.2
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/SparseArray.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpqcXhTG/file9689358a09478/SparseArray
→ installDir: /tmp/RtmpqcXhTG/file968934f5077e4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SparseArray ────────────────────────────────────────────
* 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 4.3.0 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: ATACSeq,
RNASeq
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 (55%).
* 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:
    • SparseArray_objects.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SparseArray...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/thread-control.R (line 117, column 5)
    • library() in R/thread-control.R (line 122, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/SparseArray-matrixStats.R (line 162, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • SparseArray-matrixStats.R (line 184, column 42)
    • thread-control.R (line 124, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/readSparseCSV.R (line 19, column 5)
    • cat() in R/readSparseCSV.R (line 78, column 9)
    • cat() in R/readSparseCSV.R (line 89, column 9)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/readSparseCSV.R (line 236, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/SVT_SparseArray-class.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/readSparseCSV.R (line 114, column 23)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • .OLD_rowStats_SparseArray() (R/SparseArray-matrixStats.R): 69 lines
    • ...
    • .rowStats_NaArray() (R/NaArray-matrixStats.R): 52 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/NaArray-abind.Rd
    • ...
    • man/SparseArray-subsetting.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • NaArray-aperm.Rd
  • read_block_as_sparse.Rd
  • SparseArray-aperm.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; 22 lines (0%) are > 80 characters long.
  First few lines:
    • man/NaArray-matrixStats.Rd#L66 \S4method{colAnys}{NaArray}(x, rows=NULL
    ...
    • ...
    • man/SparseArray-matrixStats.Rd#L122 \S4method{colMedians}{SparseArray}(x,
    ro ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1265 lines (10%) are
not.
  First few lines:
    • R/COO_SparseArray-class.R#L25 # nonzero eleme ...
    • ...
    • vignettes/SparseArray_objects.Rmd#L441 SVT\_SparseArray objects. ...
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 | ⚠ 3 WARNINGS | ℹ 13 NOTES
ℹ See the SparseArray.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.