##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Voyager.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Voyager_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Voyager.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-12 00:59:21 UTC
* using option ‘--no-vignettes’
* checking for file ‘Voyager/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Voyager’ version ‘1.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Voyager’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
'::' or ':::' import not declared from: ‘spatialreg’
* checking S3 generic/method consistency ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
.get_tx_df: no visible global function definition for ‘getTechTxFields’
.get_tx_df: no visible global function definition for
  ‘gdalParquetAvailable’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘gdalParquetAvailable’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘rowGeometryNames’
.get_tx_df : <anonymous>: no visible global function definition for
  ‘readSelectTx’
.plot_var_sf: no visible binding for global variable ‘gene’
plotBivariate: no visible global function definition for ‘bi_class’
plotBivariate: no visible binding for global variable ‘bi_class’
plotBivariate: no visible global function definition for
  ‘bi_scale_fill’
plotBivariate: no visible global function definition for
  ‘bi_scale_color’
plotTxBin2D: no visible binding for global variable ‘X’
plotTxBin2D: no visible binding for global variable ‘Y’
Undefined global functions or variables:
  X Y bi_class bi_scale_color bi_scale_fill gdalParquetAvailable gene
  getTechTxFields readSelectTx rowGeometryNames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculateBivariate.Rd: lee, lee.mc, lee.test, localmoran_bv,
    BiocParallelParam, colGraphNames, colGeometryNames, localResults
  calculateMultivariate.Rd: localC, colGraphNames, BiocParallelParam,
    reducedDim
  calculateUnivariate.Rd: BiocParallelParam, colGeometry,
    annotGeometry, colGraphNames, colGeometryNames, annotGeometryNames,
    annotGraphNames, reducedDimNames, geometryFeatureData,
    colFeatureData
  clusterCorrelograms.Rd: BlusterParam-class
  clusterMoranPlot.Rd: BlusterParam-class
  clusterVariograms.Rd: BlusterParam-class
  moranPlot.Rd: colGeometryNames, geom_bin2d, geom_hex, geom_density2d
  plotBivariate.Rd: colGeometryNames, wrap_plots
  plotCellBin2D.Rd: geom_bin2d, geom_hex, wrap_plots
  plotColDataHistogram.Rd: facet_grid
  plotColGraph.Rd: colGeometryNames, wrap_plots
  plotCorrelogram.Rd: colFeatureData, colGeometryNames, moran.test,
    geary.test
  plotGeometry.Rd: colGeometryNames, wrap_plots, formatTxSpots, imgData
  plotImage.Rd: wrap_plots
  plotLocalResult.Rd: colGeometryNames, wrap_plots, formatTxSpots,
    imgData, geom_bin2d, geom_hex
  plotMoranMC.Rd: colGeometryNames, geom_density, geom_histogram,
    geom_freqpoly
  plotSpatialFeature.Rd: colGeometryNames, wrap_plots, formatTxSpots,
    imgData, geom_bin2d, geom_hex
  plotTxBin2D.Rd: geom_bin2d, geom_hex, wrap_plots, formatTxSpots
  plotVariogram.Rd: colFeatureData, colGeometryNames
  plotVariogramMap.Rd: colGeometryNames
  spatialReducedDim.Rd: colGeometryNames, wrap_plots, formatTxSpots,
    imgData, geom_bin2d, geom_hex
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking Rd \usage sections ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotImage             6.296  0.759   5.838
calculateMultivariate 5.353  0.165   5.635
clusterVariograms     4.708  0.092   5.117
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot.R:1161:9'): Bivariate plot ────────────────────────────────
  Error in `bi_class(df, feature1, feature2, dim = dim, style = style)`: could not find function "bi_class"
  Backtrace:
      ▆
   1. ├─Voyager (local) expect_ggplot(...) at test-plot.R:1160:5
   2. │ └─testthat::expect_s3_class(g, "ggplot") at test-plot.R:16:5
   3. │   └─testthat::quasi_label(enquo(object))
   4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
   5. └─Voyager::plotBivariate(...) at test-plot.R:1161:9
  
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 651 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Voyager.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Voyager
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘Voyager’ ...
** this is package ‘Voyager’ version ‘1.13.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package can be loaded from final location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package keeps a record of temporary installation path
* DONE (Voyager)

R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Voyager)
Loading required package: SpatialFeatureExperiment
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation

Attaching package: 'SpatialFeatureExperiment'

The following object is masked from 'package:base':

    scale

> 
> test_check("Voyager")
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
Loading required package: sf
Linking to GEOS 3.13.0, GDAL 3.8.5, PROJ 9.5.1; sf_use_s2() is TRUE
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'ggplot2'

The following object is masked from 'package:SpatialFeatureExperiment':

    unit

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following object is masked from 'package:SpatialFeatureExperiment':

    scale

The following objects are masked from 'package:base':

    apply, scale, sweep

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
BioFormats library version 7.3.0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpJX8ptz/filebac1547f01f4/xenium2/xenium2 
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
Sanity checks on cell segmentation polygons:
>>> ..found 132 cells with (nested) polygon lists
>>> ..applying filtering
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
gstat does not fit anisotropic variograms. Variogram model is fitted to the whole dataset.
Only one cluster is present. Not using color_by.
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpJX8ptz/filebac152dec132/xenium2 
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
Sanity checks on cell segmentation polygons:
>>> ..found 132 cells with (nested) polygon lists
>>> ..applying filtering
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Must use gene symbols as row names when adding transcript spots.
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Reading transcript coordinates
>>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0

Attaching package: 'EBImage'

The following object is masked from 'package:SparseArray':

    abind

The following object is masked from 'package:S4Arrays':

    abind

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:SummarizedExperiment':

    resize

The following object is masked from 'package:Biobase':

    channel

The following objects are masked from 'package:GenomicRanges':

    resize, tile

The following objects are masked from 'package:IRanges':

    resize, tile

The following objects are masked from 'package:SpatialFeatureExperiment':

    affine, rotate, translate, transpose

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Ignoring unknown labels:
* shape : "Influential"
Ignoring unknown labels:
* shape : "Influential"
Ignoring unknown labels:
* shape : "Influential"
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Coordinate system already present.
i Adding new coordinate system, which will replace the existing one.
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
beginning bbox testssee ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 7521734 bytes (7.2 MB)
==================================================
downloaded 7.2 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/2.0.0/Visium_Mouse_Olfactory_Bulb/Visium_Mouse_Olfactory_Bulb_spatial.tar.gz'
Content type 'application/x-tar' length 7806681 bytes (7.4 MB)
==================================================
downloaded 7.4 MB

>>> 10X Visium data will be loaded: outs

>>> Adding spatial neighborhood graph to sample01

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /Users/biocbuild/bbs-3.23-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/Users/biocbuild/bbs-3.23-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /Users/biocbuild/bbs-3.23-bioc/meat/Voyager.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /Users/biocbuild/bbs-3.23-bioc/meat/Voyager.Rcheck/tests/testthat/xenium_test/xenium2 
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
Sanity checks on cell segmentation polygons:
>>> ..found 132 cells with (nested) polygon lists
>>> ..applying filtering
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Saving _problems/test-plot-1162.R
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 1 | WARN 0 | SKIP 18 | PASS 651 ]

══ Skipped tests (18) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-bivariate.R:123:1', 'test-bivariate.R:144:1',
  'test-gstat.R:184:1', 'test-plot.R:353:1', 'test-plot.R:399:1',
  'test-plot.R:436:1', 'test-plot.R:454:1', 'test-plot.R:468:1',
  'test-plot.R:472:1', 'test-plot.R:522:1', 'test-plot.R:600:1',
  'test-plot.R:633:1', 'test-plot.R:655:1', 'test-plot.R:815:1',
  'test-plot.R:821:1', 'test-plot.R:861:1', 'test-plot.R:917:1'
• gdalParquetAvailable() is not TRUE (1): 'test-plot-transcripts.R:65:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plot.R:1161:9'): Bivariate plot ────────────────────────────────
Error in `bi_class(df, feature1, feature2, dim = dim, style = style)`: could not find function "bi_class"
Backtrace:
    ▆
 1. ├─Voyager (local) expect_ggplot(...) at test-plot.R:1160:5
 2. │ └─testthat::expect_s3_class(g, "ggplot") at test-plot.R:16:5
 3. │   └─testthat::quasi_label(enquo(object))
 4. │     └─rlang::eval_bare(expr, quo_get_env(quo))
 5. └─Voyager::plotBivariate(...) at test-plot.R:1161:9

[ FAIL 1 | WARN 0 | SKIP 18 | PASS 651 ]
Error:
! Test failures.
Execution halted