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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('DelayedArray_0.38.1.tar.gz','quit-with-status'=TRUE)"
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── Installing DelayedArray ─────────────────────────────────────────────────────
✔ Package installed successfully
── DelayedArray session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmppGHmik/file767137825bd07/DelayedArray
→ BiocVersion: 3.23
→ Package: DelayedArray
→ PackageVersion: 0.38.1
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/DelayedArray.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmppGHmik/file767137825bd07/DelayedArray
→ installDir: /tmp/RtmppGHmik/file7671316ce4781
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DelayedArray ───────────────────────────────────────────
* 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...
ℹ Package version 0.38.1; pre-release
* 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: KEGG
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 (60%).
* 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: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • A-Working_with_large_arrays.Rnw
    • C-DelayedArray_HDF5Array_update.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • A-Working_with_large_arrays.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/A-Working_with_large_arrays.Rnw
    • vignettes/C-DelayedArray_HDF5Array_update.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DelayedArray...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/showtree.R (line 54, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AutoGrid.R (line 201, column 23)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/RealizationSink-class.R (line 117, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/DelayedAbind-class.Rd
ℹ Found @ in man/DelayedAperm-class.Rd
ℹ Found @ in man/DelayedNaryIsoOp-class.Rd
ℹ Found @ in man/DelayedSetDimnames-class.Rd
ℹ Found @ in man/DelayedSubassign-class.Rd
ℹ Found @ in man/DelayedSubset-class.Rd
ℹ Found @ in man/DelayedUnaryIsoOpStack-class.Rd
ℹ Found @ in man/DelayedUnaryIsoOpWithArgs-class.Rd
ℹ Found @ in man/simplify.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/DelayedArray-utils.R (line 607, column 30)
  • suppressWarnings() in R/DelayedArray-utils.R (line 672, column 30)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • BLOCK_rowsum() (R/DelayedMatrix-rowsum.R): 98 lines
    • ...
    • .compute_rowVars_for_horizontal_strips() (R/matrixStats-methods.R): 72
    lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/DelayedAbind-class.Rd
    • ...
    • man/matrixStats-methods.Rd
Warning: .onUnload failed in unloadNamespace() for 'DelayedArray', details:
  call: library.dynam.unload("DelayedArray", libpath)
  error: shared object ‘DelayedArray.so’ was not loaded
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • chunkGrid.Rd
  • compat.Rd
  • DelayedOp-class.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • DelayedArray-class.Rd
    • DelayedArray-utils.Rd
    • RleArray-class.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • DelayedArray-class.Rd
    • DelayedArray-utils.Rd
    • RleArray-class.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; 17 lines (0%) are > 80 characters long.
  First few lines:
    • R/DelayedMatrix-mult.R#L550 # this, and all other calls, had bet ...
    • ...
    • vignettes/C-DelayedArray_HDF5Array_update.Rnw#L11 %
    https://tex.stackexchange.com/questi ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2068 lines (12%) are
not.
  First few lines:
    • R/AutoBlock-global-settings.R#L34 "auto.block.size shoul ...
    • ...
    • vignettes/C-DelayedArray_HDF5Array_update.Rnw#L210 \end{block} ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the DelayedArray.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.