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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('geomeTriD_1.7.0.tar.gz','quit-with-status'=TRUE)"
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── Installing geomeTriD ────────────────────────────────────────────────────────
✔ Package installed successfully
── geomeTriD session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpKxB7pA/filea59617f6e6299/geomeTriD
→ BiocVersion: 3.24
→ Package: geomeTriD
→ PackageVersion: 1.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/geomeTriD.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpKxB7pA/filea59617f6e6299/geomeTriD
→ installDir: /tmp/RtmpKxB7pA/filea59615982d8d0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on geomeTriD ──────────────────────────────────────────────
* 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 4.4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: SingleCell,
Spatial, Alignment
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 (29%).
* 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:
    • geomeTriD.Rmd
* Checking package installation calls in R code...
* Checking for library/require of geomeTriD...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/createTADGeometries.R (line 156, column 3)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • cellClusters.R (line 500, column 13)
    • spatialDistanceMatrix.R (line 111, column 13)
    • spatialDistanceMatrix.R (line 112, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/create3dGenomicSignals.R (line 161, column 14)
    • ...
    • R/create3dGenomicSignals.R (line 1002, column 5)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/create3dGenomicSignals.R (line 274, column 13)
* 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 35
functions greater than 50 lines.
  The longest 5 functions are:
    • view3dStructure() (R/view3dStructure.R): 592 lines
    • ...
    • FUN() (R/rglViewer.R): 233 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/threeJsGeometry-class.Rd
Warning: 'rgl.init' failed, will use the null device.
See '?rgl.useNULL' for ways to avoid this warning.
* 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; 109 lines (2%) are > 80 characters long.
  First few lines:
    • R/cellClusters.R#L4 #' @param xyzs A list of data.frame with ...
    • ...
    • vignettes/geomeTriD.Rmd#L573 rotation = c(pi, 0, pi), ## we need to ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 3191 lines (44%) are
not.
  First few lines:
    • R/alignCoor.R#L21 if (is(query, "GRanges")) { ...
    • ...
    • vignettes/geomeTriD.Rmd#L575 package = 'geomeTri ...
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 | ⚠ 1 WARNINGS | ℹ 11 NOTES
ℹ See the geomeTriD.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.