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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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Package 2019/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialFeatureExperiment 1.8.2  (landing page)
Lambda Moses
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/SpatialFeatureExperiment
git_branch: RELEASE_3_20
git_last_commit: 9e527aa
git_last_commit_date: 2024-11-14 11:38:24 -0500 (Thu, 14 Nov 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped


CHECK results for SpatialFeatureExperiment on lconway

To the developers/maintainers of the SpatialFeatureExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialFeatureExperiment.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SpatialFeatureExperiment
Version: 1.8.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.8.2.tar.gz
StartedAt: 2024-11-20 02:56:22 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:14:59 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 1117.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SpatialFeatureExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.8.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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 ‘SpatialFeatureExperiment’ 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.seu_to_sfe: warning in do.call(setdiff, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe: warning in do.call(intersect, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe : <anonymous>: warning in do.call(setdiff, arg = assays_n):
  partial argument match of 'arg' to 'args'
.aggregate_sample_tx: no visible binding for global variable ‘.N’
.aggregate_sample_tx: no visible global function definition for ‘.’
.aggregate_sample_tx: no visible binding for global variable ‘gene’
.aggregate_sample_tx: no visible binding for global variable ‘L1’
.aggregate_sample_tx: no visible binding for global variable ‘grid_id’
.filter_polygons: no visible binding for global variable ‘ID_row’
.no_raw_bytes: no visible binding for global variable ‘xoa_version’
.no_raw_bytes: no visible binding for global variable ‘major_version’
.no_raw_bytes: no visible binding for global variable ‘minor_version’
.no_raw_bytes: no visible binding for global variable
  ‘instrument_version’
.read10xVisium: no visible global function definition for
  ‘spatialCoordsNames<-’
addTxTech: no visible binding for global variable ‘gene_col’
addTxTech: no visible binding for global variable ‘cell_col’
addTxTech: no visible binding for global variable ‘fn’
aggregateTx: no visible binding for global variable ‘.N’
aggregateTx: no visible global function definition for ‘.’
aggregateTx: no visible binding for global variable ‘gene’
aggregateTx: no visible binding for global variable ‘grid_id’
aggregateTxTech: no visible binding for global variable ‘gene_col’
aggregateTxTech: no visible binding for global variable ‘cell_col’
aggregateTxTech: no visible binding for global variable ‘fn’
aggregateTxTech: no visible binding for global variable ‘xoa_version’
aggregateTxTech: no visible binding for global variable ‘major_version’
aggregateTxTech: no visible binding for global variable ‘minor_version’
aggregateTxTech: no visible binding for global variable
  ‘instrument_version’
findVisiumHDGraph: no visible binding for global variable ‘..cols’
formatTxTech: no visible binding for global variable ‘gene_col’
formatTxTech: no visible binding for global variable ‘cell_col’
formatTxTech: no visible binding for global variable ‘fn’
readVizgen: no visible binding for global variable ‘img_df’
readXenium: no visible binding for global variable ‘xoa_version’
readXenium: no visible binding for global variable ‘major_version’
readXenium: no visible binding for global variable ‘minor_version’
readXenium: no visible binding for global variable ‘instrument_version’
readXenium: no visible binding for global variable ‘img_df’
Undefined global functions or variables:
  . ..cols .N ID_row L1 cell_col fn gene gene_col grid_id img_df
  instrument_version major_version minor_version spatialCoordsNames<-
  xoa_version
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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
Img-set-SpatialExperiment-method 13.179  1.506  13.625
formatTxSpots                    13.625  0.846  14.954
rowGeometries                     7.516  0.482   8.170
readXenium                        7.490  0.441   7.993
removeEmptySpace                  6.145  0.279   6.627
spatialGraphs                     4.423  0.293   5.066
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.


Installation output

SpatialFeatureExperiment.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SpatialFeatureExperiment’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘toSpatialFeatureExperiment’ with signature ‘"Seurat"’: no definition for class “Seurat”
Creating a generic function for ‘NROW’ from package ‘base’ in package ‘SpatialFeatureExperiment’
Creating a generic function for ‘NCOL’ from package ‘base’ in package ‘SpatialFeatureExperiment’
Creating a generic function for ‘saveRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’
Creating a generic function for ‘readRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialFeatureExperiment)

Tests output

SpatialFeatureExperiment.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(SpatialFeatureExperiment)

Attaching package: 'SpatialFeatureExperiment'

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

    scale

> 
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
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

Attaching package: 'BiocGenerics'

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

    saveRDS

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand, unname

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: GenomeInfoDb
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


Attaching package: 'arrow'

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

    type

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

    matches

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

    timestamp

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2443c28c90/xenium2 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2443c28c90/vizgen_cellbound_Cellpose 
>>> 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
>>> 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
>>> 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`
>>> 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-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/xenium_lr 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    unit

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')`
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/tmp/Rtmp6LhM8M/file3a245d85a51/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a245d85a51/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a245d85a51/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a244a4633cf/vizgen_cellbound 
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a244a4633cf/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a244a4633cf/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> Checking polygon validity
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk

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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2472cf2d81/vizgen_cellbound 
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a241d97fa97/cosmx 
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk

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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24d2f49c8/xenium2 
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
terra 1.7.78

Attaching package: 'terra'

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

    buffer

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

    distance, nearest, shift, trim, values, values<-, width

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

    distance, gaps, nearest, shift, trim, values, values<-, width

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

    distance, gaps, nearest, shift, trim, width

The following objects are masked from 'package:S4Vectors':

    values, values<-, width

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

    width

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

    centroids, crop, origin, rotate

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

    compare, describe

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a241427e5c/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?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 /private/tmp/Rtmp6LhM8M/file3a24137f6a83/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
BioFormats library version 7.3.0

Attaching package: 'EBImage'

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

    flip, rotate

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
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a243be67a6/xenium_lr 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Must use gene symbols as row names when adding transcript spots.
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 484 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
Actual mean:  0.9850527see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Testing dist_type none style W 
Testing dist_type idw style W 
Testing dist_type exp style W 
Testing dist_type dpd style W 
Testing dist_type idw style raw 
Testing dist_type idw style W 
Testing dist_type idw style B 
Testing dist_type idw style C 
Testing dist_type idw style U 
Testing dist_type idw style minmax 
Testing dist_type idw style S 
Testing dist_type none style W 
Testing dist_type idw style W 
Testing dist_type exp style W 
Testing dist_type dpd style W 
Testing dist_type idw style raw 
Testing dist_type idw style W 
Testing dist_type idw style B 
Testing dist_type idw style C 
Testing dist_type idw style U 
Testing dist_type idw style minmax 
Testing dist_type idw style S 
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/tmp/Rtmp6LhM8M/file3a244e3ae48c/xenium_lr 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2436fb4b4c/vizgen_cellbound 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a244a12f686/xenium_lr 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2439922aab/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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2483252b/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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
>>> 10X Visium data will be loaded: outs

>>> Adding spatial neighborhood graph to sample01

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

>>> Adding spatial neighborhood graph to sample02

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

>>> Adding spatial neighborhood graph to sample01

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 10785331 bytes (10.3 MB)
==================================================
downloaded 10.3 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Mouse_Kidney/V1_Mouse_Kidney_spatial.tar.gz'
Content type 'application/x-tar' length 8531653 bytes (8.1 MB)
==================================================
downloaded 8.1 MB

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

>>> Adding spatial neighborhood graph to sample01

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

>>> Adding spatial neighborhood graph to sample01

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

>>> Converting pixels to microns
>>> Adding spatial neighborhood graph to sample01

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

>>> Converting pixels to microns
>>> Adding spatial neighborhood graph to sample01

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a244919af0e/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a244919af0e/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a244919af0e/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 /private/tmp/Rtmp6LhM8M/file3a2449aa3337/vizgen_cellbound 
>>> Reading '.hdf5' files..
>>> Checking polygon validity
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a2449aa3337/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a2449aa3337/vizgen_cellbound/hdf5s_micron_space.parquet
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a245d8de5a9/vizgen_cellbound 
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a245264d517/vizgen_cellbound 
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2420f752c9/vizgen_cellbound 
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a245e433769/vizgen_cellbound 
>>> Reading '.hdf5' files..
>>> Checking polygon validity
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a242177071f/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a242177071f/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a242177071f/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 /private/tmp/Rtmp6LhM8M/file3a24171bca8e/vizgen_cellbound 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2442cc021a/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a2442cc021a/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a2442cc021a/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Sanity checks on cell segmentation polygons:
>>> ..found 3 cells with (nested) polygon lists
>>> ..applying filtering
>>> Casting MULTIPOLYGON geometry to POLYGON
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24c3a92f0/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a24c3a92f0/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a24c3a92f0/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a247b3c0be3/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a247b3c0be3/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a247b3c0be3/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 /private/tmp/Rtmp6LhM8M/file3a2455181240/vizgen_cellbound_Cellpose 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a2455181240/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a2455181240/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> Cell segmentations are found in `.parquet` file
Sanity checks on cell segmentation polygons:
>>> ..found 1 cells with (nested) polygon lists
>>> ..applying filtering
>>> Casting MULTIPOLYGON geometry to POLYGON
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a244febd69a/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a244564174/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a244564174/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 /private/tmp/Rtmp6LhM8M/file3a24361aaaea/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a24361aaaea/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp6LhM8M/file3a24361aaaea/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 /private/tmp/Rtmp6LhM8M/file3a24466b9ade/vizgen_cellbound 
>>> 2 `.parquet` files exist:
/private/tmp/Rtmp6LhM8M/file3a24466b9ade/vizgen_cellbound/cell_boundaries.parquet
/private/tmp/Rtmp6LhM8M/file3a24466b9ade/vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24171bca8e/vizgen_cellbound_Cellpose 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a247e2248ff/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24655380e8/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2464d6de53/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2414c00d60/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24682e1fdd/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=========                                                             |  12%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |==========================                                            |  38%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |============================================                          |  62%
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  |====================================================                  |  75%
  |                                                                            
  |=============================================================         |  88%
  |                                                                            
  |======================================================================| 100%

>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2470402f8a/xenium_lr 
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 484 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
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a247ec648c3/xenium_lr 
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 484 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
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24690dd03/xenium_lr 
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Converting columns with raw bytes (ie 'arrow_binary') to character
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 163 cells with counts > 0
>>> filtering nucSeg geometries to match 163 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2420cc32b7/xenium_lr 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24575b7d1a/xenium_lr 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24893dfa2/xenium_lr 
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 484 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
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2427f30c30/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`
Actual mean  0.9095486see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a24588b5a80/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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a244a71bc7f/xenium2 
>>> Must use gene symbols as row names when adding transcript spots.
>>> 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.csv`
>>> 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`
Actual mean  0.9095486see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a241895fba0/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`
>>> 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
Actual mean  0.9095486>>> 10X Visium data will be loaded: outs

>>> Adding spatial neighborhood graph to sample01

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

>>> Adding spatial neighborhood graph to sample02

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp6LhM8M/file3a2473066a4f/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
>>> 10X Visium data will be loaded: outs

>>> Converting pixels to microns
>>> Adding spatial neighborhood graph to ob

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

>>> Converting pixels to microns
>>> Adding spatial neighborhood graph to kidney

[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'dgCMatrix'
updateObjectFromSlots(object = 'dgCMatrix' class = 'dgCMatrix')
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'integer'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'character'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
updateObject(object="ANY") default for object of class 'numeric'
[updateObject] Validating the updated object ... OK
updateObject(object = 'list')
[updateObject] Validating the updated object ... OK
heuristic updateObjectFromSlots, method 1
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] CompressedGRangesList object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of GRanges object is current.
[updateObject] Nothing to update.
[updateObject] Internal representation of IRanges object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Internal representation of PartitioningByEnd object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] DFrame object is current.
[updateObject] Nothing to update.
updateObject(object="ANY") default for object of class 'NULL'
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
[updateObject] Validating the updated object ... OK
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/tmp/Rtmp6LhM8M/file3a242df086bb/xenium_lr 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 1199 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test-read.R:685:5'
• Skipping (6): 'test-graph_wrappers.R:160:5', 'test-read.R:144:5',
  'test-read.R:158:5', 'test-read.R:168:5', 'test-read.R:175:5',
  'test-read.R:187:5'
• gdalParquetAvailable() is not TRUE (3): 'test-formatTxSpots.R:113:5',
  'test-formatTxSpots.R:140:5', 'test-formatTxSpots.R:157:5'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 1199 ]
> 
> proc.time()
   user  system elapsed 
464.915  33.628 504.008 

Example timings

SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings

nameusersystemelapsed
Img-set-SpatialExperiment-method13.179 1.50613.625
SFE-image1.4500.1131.797
SFE-transform2.4540.1492.766
SpatRasterImage000
SpatialFeatureExperiment-coercion1.3820.0621.451
SpatialFeatureExperiment-subset1.6090.1201.893
SpatialFeatureExperiment0.3140.0080.323
addVisiumSpotPoly1.3260.0321.360
aggBboxes0.0000.0000.001
aggregate-SpatialFeatureExperiment-method0.0000.0000.001
annotGeometries1.5210.1241.852
annotOp1.6280.1181.913
annotPred2.0930.1432.429
annotSummary1.6030.1101.878
bbox-SpatialFeatureExperiment-method1.8130.1242.104
bbox_center000
cbind-SpatialFeatureExperiment-method3.5990.2294.162
changeSampleIDs1.7190.1061.988
colFeatureData2.3520.1882.732
colGeometries1.6290.1281.963
crop2.4150.1362.722
df2sf0.0100.0030.014
dimGeometries4.1990.2314.802
findSpatialNeighbors-SpatialFeatureExperiment-method3.8340.2394.417
findVisiumGraph3.7580.2204.306
formatTxSpots13.625 0.84614.954
formatTxTech2.3770.2922.861
gdalParquetAvailable0.0010.0010.001
getParams2.0280.1532.348
getPixelSize2.2580.2732.248
imageIDs0.4010.0090.411
listw2sparse1.6520.1141.927
localResults0.6960.0110.708
multi_listw2sparse000
read10xVisiumSFE1.0680.0211.090
readCosMX1.9100.1262.210
readSelectTx0.0150.0010.016
readVisiumHD000
readVizgen2.8370.1593.183
readXenium7.4900.4417.993
removeEmptySpace6.1450.2796.627
rowGeometries7.5160.4828.170
sampleIDs1.4860.1231.808
saveRDS-SpatialFeatureExperiment-method1.0830.0201.107
show-SpatialFeatureExperiment-method1.6930.1382.000
spatialGraphs4.4230.2935.066
splitByCol0.0000.0010.000
st_any_pred0.0210.0010.022
unit-SpatialFeatureExperiment-method1.6290.1231.917
updateObject1.7000.1332.003