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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scider_1.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scider ───────────────────────────────────────────────────────────
✔ Package installed successfully
── scider session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbMGtCl/file12b30a7019a793/scider
→ BiocVersion: 3.24
→ Package: scider
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scider.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpbMGtCl/file12b30a7019a793/scider
→ installDir: /tmp/RtmpbMGtCl/file12b30a2f763c32
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scider ─────────────────────────────────────────────────
* 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 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (23%).
* 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:
    • scider_userGuide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scider...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/contour2sf.R (line 112, column 21)
    • ...
    • R/plotImage.R (line 73, column 19)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • findNbrsGrid.R (line 77, column 36)
    • ...
    • realignVisium.R (line 58, column 21)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/corDensity.R (line 114, column 20)
    • ...
    • cat() in R/readST.R (line 118, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/computeDensity.R (line 70, column 18)
    • ...
    • R/selectRegion.R (line 61, column 28)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/allocateCells.R (line 43, column 25)
    • ...
    • R/spe2PB.R (line 109, column 21)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/plotGrid.R (line 86, column 24)
    • R/plotSpatial.R (line 85, column 24)
    • R/plotViolin.R (line 90, column 24)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • F in R/plotROI.R (line 90, column 21)
! WARNING: Remove set.seed usage (found 1 times)
  • set.seed() in R/getClusters.R (line 35, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/globalMoran.Rd
ℹ Found @ in man/localMoran.Rd
ℹ Found @ in man/plotLISA.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/findROI.R (line 133, column 11)
  • suppressMessages() in R/plotContour.R (line 77, column 5)
  • suppressMessages() in R/plotContour.R (line 93, column 7)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 35
functions greater than 50 lines.
  The longest 5 functions are:
    • contour2sf() (R/contour2sf.R): 417 lines
    • ...
    • spe2PB() (R/spe2PB.R): 136 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/coord_hash.Rd
    • ...
    • man/realignVisiumHD.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • plotImage.Rd
  • ...
  • realignVisiumHD.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; 159 lines (3%) are > 80 characters long.
  First few lines:
    • R/allocateCells.R#L45 janitor::make_clean_ ...
    • ...
    • vignettes/scider_userGuide.Rmd#L190 We can see the correlation between
    each ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/spe2PB.R#L43 keep.groups = NULL, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1739 lines (30%) are
not.
  First few lines:
    • R/allocateCells.R#L26 to.roi = TRUE, ...
    • ...
    • vignettes/scider_userGuide.Rmd#L20 font-size: 12pt; ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the scider.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.