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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('SpatialArtifacts_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing SpatialArtifacts ─────────────────────────────────────────────────
✔ Package installed successfully
── SpatialArtifacts session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/RtmpYWmIx0/file1432d765dc9c29/SpatialArtifacts
→ BiocVersion: 3.24
→ Package: SpatialArtifacts
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/SpatialArtifacts.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYWmIx0/file1432d765dc9c29/SpatialArtifacts
→ installDir: /tmp/RtmpYWmIx0/file1432d71b745bb9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on SpatialArtifacts ───────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.4.0 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...
* 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 (50%).
* 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:
    • hippocampus-edge-detection.Rmd
* Checking package installation calls in R code...
* Checking for library/require of SpatialArtifacts...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • edge_helper_functions_visium.R (line 86, column 22)
    • ...
    • edge_helper_functions_VisiumHD.R (line 49, column 16)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/detectEdgeArtifacts.R (line 39, column 9)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • detectEdgeArtifacts_VisiumHD() (R/detectEdgeDryspots_VisiumHD.R): 313
    lines
    • ...
    • problemAreas() (R/edge_helper_functions_visium.R): 112 lines
* Checking man page documentation...
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • detectEdgeArtifacts_VisiumHD.Rd
    • detectEdgeArtifacts.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • detectEdgeArtifacts_VisiumHD.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; 210 lines (8%) are > 80 characters long.
  First few lines:
    • R/classifyEdgeArtifacts.R#L4 #' and size (large vs. small). This func ...
    • ...
    • vignettes/hippocampus-edge-detection.Rmd#L645 Overall,
    **SpatialArtifacts** provides a ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 837 lines (31%) are
not.
  First few lines:
    • R/classifyEdgeArtifacts.R#L106 spe, ...
    • ...
    • vignettes/hippocampus-edge-detection.Rmd#L639 - Without scaling,
    artifacts will be ...
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 | ⚠ 0 WARNINGS | ℹ 11 NOTES
ℹ See the SpatialArtifacts.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.