| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-23 12:07 -0500 (Thu, 23 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4493 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4394 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2019/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.8.4 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
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. |
| Package: SpatialFeatureExperiment |
| Version: 1.8.4 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.8.4.tar.gz |
| StartedAt: 2025-01-21 06:11:09 -0500 (Tue, 21 Jan 2025) |
| EndedAt: 2025-01-21 06:37:30 -0500 (Tue, 21 Jan 2025) |
| EllapsedTime: 1580.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpatialFeatureExperiment.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.8.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SpatialFeatureExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpatialFeatureExperiment' version '1.8.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 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 whether startup messages can be suppressed ... 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 21.63 4.11 80.11
formatTxSpots 20.48 1.77 24.49
readXenium 11.54 0.91 12.81
rowGeometries 11.75 0.62 13.22
removeEmptySpace 8.48 0.72 9.54
dimGeometries 7.71 0.56 8.54
spatialGraphs 7.56 0.54 8.34
findVisiumGraph 7.08 0.65 7.95
findSpatialNeighbors-SpatialFeatureExperiment-method 6.62 0.58 7.41
cbind-SpatialFeatureExperiment-method 6.44 0.56 7.72
SFE-transform 4.84 0.33 5.28
readVizgen 4.69 0.46 5.42
* 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:
`expected`: TRUE
── Failure ('test-read.R:209:5'): readVizgen flip geometry, use cellpose ───────
sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-read.R:402:5'): Version with Cellpose directory ──────────────
sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 29 | WARN 0 | SKIP 10 | PASS 1207 ]
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, 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log'
for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)
SpatialFeatureExperiment.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 3.12.2, GDAL 3.9.3, PROJ 9.4.1; 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc6d3240d\xenium2
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc6d3240d\vizgen_cellbound_Cellpose
>>> 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`
>>> 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 F:\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7c4e5986\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7c4e5986\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7c4e5986\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc4f46da2\vizgen_cellbound
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc4f46da2\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc4f46da2\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc1baa7209\vizgen_cellbound
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc562f149c\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc1b9f70c0\xenium2
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
terra 1.8.10
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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc4a9d66fd\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc5a9c56d4\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, watershed
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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc4d677969\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc50742323\xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc22dd5211\vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc635b55ca\xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc5ac111da\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edcec72f7b\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc5e86145d\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc5e86145d\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc5e86145d\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc459a3baa\vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc459a3baa\vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc459a3baa\vizgen_cellbound/hdf5s_micron_space.parquet
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc6781130f\vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc72e7e2e\vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc1bf936c7\vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edce287e72\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ddd10c6\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ddd10c6\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ddd10c6\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7c83586a\vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc261856bc\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc261856bc\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc261856bc\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ca1aec\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ca1aec\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ca1aec\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc769b6830\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc769b6830\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc769b6830\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc610411ee\vizgen_cellbound_Cellpose
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc610411ee\vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc610411ee\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7ba63349\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc16eb64d3/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc16eb64d3/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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc706e1d7a\vizgen_cellbound
>>> 1 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc706e1d7a\vizgen_cellbound/cell_boundaries.parquet
>>> using -> F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc706e1d7a\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc1490467e\vizgen_cellbound
>>> 2 `.parquet` files exist:
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc1490467e\vizgen_cellbound/cell_boundaries.parquet
F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc1490467e\vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7c83586a\vizgen_cellbound_Cellpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc678324c6\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edcd75c75\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2ed31041\cosmx
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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|
|=================================== | 50%
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|======================================================================| 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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc7cec300e\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc246b5f66\cosmx
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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>>> 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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2c44898\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc11ef55b1\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc68ef38c1\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc4b292b1c\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edcce843df\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc2f5f3afc\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc71a35c75\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc77ec76d0\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc12234622\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc37e123a5\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc25c870db\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 F:\biocbuild\bbs-3.20-bioc\tmpdir\RtmpayxK5u\file17edc35544de8\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 29 | WARN 0 | SKIP 10 | PASS 1207 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test-read.R:685:5'
• Skipping (6): 'test-graph_wrappers.R:169:5', '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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-coerce.R:65:5'): Convert SPE to SFE, stored images ───────────
`v1` (`actual`) not equal to `v2` (`expected`).
actual vs expected
[, 1] [, 2] [, 3] [, 4] [, 5] [, 6] [, 7] [, 8] [, 9] [, 10] [, 11] [, 12] [, 13] [, 14] [, 15] [, 16] [, 17] [, 18] [, 19] [, 20] [, 21] [, 22] [, 23] [, 24] [, 25] [, 26] [, 27] [, 28] [, 29] [, 30] [, 31] [, 32] [, 33] [, 34] [, 35] [, 36] [, 37] [, 38] [, 39] [, 40] [, 41] [, 42] [, 43] [, 44] [, 45] [, 46] [, 47] [, 48] [, 49] [, 50] [, 51] [, 52] [, 53] [, 54] [, 55] [, 56] [, 57] [, 58] [, 59] [, 60] [, 61] [, 62] [, 63] [, 64] [, 65] [, 66] [, 67] [, 68] [, 69] [, 70] [, 71] [, 72] [, 73] [, 74] [, 75] [, 76] [, 77] [, 78] [, 79] [, 80] [, 81] [, 82] [, 83] [, 84] [, 85] [, 86] [, 87] [, 88] [, 89] [, 90] [, 91] [, 92] [, 93] [, 94] [, 95] [, 96] [, 97] [, 98] [, 99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148] [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177] [,178] [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187] [,188] [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208] [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217] [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227] [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237] [,238] [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248] [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257] [,258] [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267] [,268] [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277] [,278] [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288] [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298] [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307] [,308] [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317] [,318] [,319] [,320] [,321] [,322]
- actual[1, ] 54 52 49 65 63 70 57 48 54 54 46 44 43 48 76 71 49 63 70 66 60 55 49 49 46 48 48 51 73 63 51 71 123 82 62 55 50 48 46 50 60 62 50 56 56 61 123 120 56 55 66 71 57 68 66 46 35 49 93 99 71 92 60 56 56 65 51 55 46 34 33 52 102 176 96 101 85 89 44 37 35 34 33 32 32 48 88 109 129 74 111 113 41 32 33 33 33 41 33 34 63 62 76 57 51 46 33 32 32 32 38 49 33 33 33 33 33 35 34 33 33 33 37 37 46 50 33 33 33 33 33 33 33 32 33 44 56 72 102 94 48 34 33 33 33 33 35 41 46 54 61 56 54 59 92 46 35 34 35 61 61 65 63 56 51 48 49 45 50 52 55 40 50 171 98 49 46 45 87 60 49 50 45 71 111 61 59 94 81 45 46 45 44 43 52 87 45 54 63 65 56 52 51 46 45 46 45 41 41 44 44 48 59 59 50 52 48 45 44 48 48 44 43 43 44 49 73 67 57 50 44 48 46 46 56 52 49 48 76 82 95 116 101 81 51 50 48 50 78 59 45 43 68 62 62 59 79 63 57 51 44 45 55 51 43 43 45 46 48 48 51 52 50 51 45 44 48 49 44 48 46 45 45 43 44 48 59 56 48 46 46 49 54 56 48 44 44 44 44 45 74 78 82 57 50 51 49 54 49 49 46 45 46 44 51 59 95 65 50 52 56 63
+ expected[1, ] 49 49 46 45 46 44 51 59 95 65 50 52 56 63 48 44 44 44 44 45 74 78 82 57 50 51 49 54 46 45 45 43 44 48 59 56 48 46 46 49 54 56 45 46 48 48 51 52 50 51 45 44 48 49 44 48 68 62 62 59 79 63 57 51 44 45 55 51 43 43 76 82 95 116 101 81 51 50 48 50 78 59 45 43 44 49 73 67 57 50 44 48 46 46 56 52 49 48 44 48 59 59 50 52 48 45 44 48 48 44 43 43 45 54 63 65 56 52 51 46 45 46 45 41 41 44 45 71 111 61 59 94 81 45 46 45 44 43 52 87 50 52 55 40 50 171 98 49 46 45 87 60 49 50 92 46 35 34 35 61 61 65 63 56 51 48 49 45 48 34 33 33 33 33 35 41 46 54 61 56 54 59 33 33 33 33 33 33 33 32 33 44 56 72 102 94 33 33 33 33 33 35 34 33 33 33 37 37 46 50 33 34 63 62 76 57 51 46 33 32 32 32 38 49 32 48 88 109 129 74 111 113 41 32 33 33 33 41 33 52 102 176 96 101 85 89 44 37 35 34 33 32 35 49 93 99 71 92 60 56 56 65 51 55 46 34 50 56 56 61 123 120 56 55 66 71 57 68 66 46 73 63 51 71 123 82 62 55 50 48 46 50 60 62 76 71 49 63 70 66 60 55 49 49 46 48 48 51 54 52 49 65 63 70 57 48 54 54 46 44 43 48
- actual[2, ] 49 44 31 79 86 68 70 34 34 30 31 23 23 23 63 43 35 105 193 84 37 37 33 29 26 29 35 41 41 42 35 63 137 175 59 42 35 30 33 47 70 88 29 43 61 54 87 98 47 47 58 111 115 132 100 37 24 31 118 146 94 68 55 70 51 101 56 55 34 23 23 31 114 233 179 113 107 97 29 28 23 23 22 22 23 27 80 149 190 120 119 64 24 23 23 22 22 24 23 24 51 83 52 64 54 26 23 23 23 22 23 40 23 23 24 26 24 24 23 23 23 23 23 23 26 95 23 23 23 23 23 23 23 23 23 24 52 85 36 80 24 23 23 23 23 23 23 24 26 51 92 94 44 94 29 24 23 23 24 34 30 48 38 82 47 28 30 29 30 48 42 24 29 108 69 34 28 29 58 28 28 24 27 48 54 29 42 71 55 26 31 24 26 24 24 28 26 33 36 51 49 44 34 34 33 24 24 24 24 24 26 28 44 52 40 37 33 31 28 28 27 28 26 24 28 38 86 58 43 30 30 37 28 31 29 35 30 27 75 125 107 68 91 54 36 35 26 27 29 38 29 26 77 136 113 44 100 68 38 34 24 24 30 48 27 24 27 30 36 28 41 42 33 31 26 24 28 36 29 28 26 26 26 24 28 28 35 33 28 24 24 30 41 35 29 26 24 24 26 24 27 37 43 33 29 30 36 57 27 29 27 26 31 26 26 33 43 44 28 37 47 42
+ expected[2, ] 27 29 27 26 31 26 26 33 43 44 28 37 47 42 29 26 24 24 26 24 27 37 43 33 29 30 36 57 26 26 26 24 28 28 35 33 28 24 24 30 41 35 27 30 36 28 41 42 33 31 26 24 28 36 29 28 77 136 113 44 100 68 38 34 24 24 30 48 27 24 75 125 107 68 91 54 36 35 26 27 29 38 29 26 28 38 86 58 43 30 30 37 28 31 29 35 30 27 26 28 44 52 40 37 33 31 28 28 27 28 26 24 26 33 36 51 49 44 34 34 33 24 24 24 24 24 27 48 54 29 42 71 55 26 31 24 26 24 24 28 30 48 42 24 29 108 69 34 28 29 58 28 28 24 29 24 23 23 24 34 30 48 38 82 47 28 30 29 24 23 23 23 23 23 23 24 26 51 92 94 44 94 23 23 23 23 23 23 23 23 23 24 52 85 36 80 23 23 24 26 24 24 23 23 23 23 23 23 26 95 23 24 51 83 52 64 54 26 23 23 23 22 23 40 23 27 80 149 190 120 119 64 24 23 23 22 22 24 23 31 114 233 179 113 107 97 29 28 23 23 22 22 24 31 118 146 94 68 55 70 51 101 56 55 34 23 29 43 61 54 87 98 47 47 58 111 115 132 100 37 41 42 35 63 137 175 59 42 35 30 33 47 70 88 63 43 35 105 193 84 37 37 33 29 26 29 35 41 49 44 31 79 86 68 70 34 34 30 31 23 23 23
- actual[3, ] 23 21 23 42 48 58 38 30 37 35 34 20 21 23 42 27 53 54 53 30 21 21 30 30 20 20 24 28 59 24 29 58 80 57 35 24 23 29 25 35 43 44 47 49 23 33 58 78 28 25 53 49 39 61 76 39 29 69 40 58 58 47 33 61 74 80 90 47 38 20 21 59 58 97 76 63 53 78 30 30 30 21 19 19 19 44 88 82 71 47 52 63 24 18 18 18 20 35 19 23 52 50 74 66 63 33 19 18 18 19 28 66 19 19 19 19 21 21 20 19 18 21 28 29 63 78 20 19 19 19 19 19 19 19 21 63 83 63 71 62 38 19 19 19 19 19 30 48 56 85 72 40 27 40 73 40 21 19 20 38 111 83 63 48 30 29 28 20 40 88 77 35 42 88 61 24 21 32 23 38 38 21 32 43 69 91 53 42 50 24 24 33 24 20 21 32 21 24 35 74 62 24 37 25 20 33 35 24 21 19 19 20 21 34 28 23 32 30 19 24 27 21 23 20 20 32 50 47 39 24 21 23 21 28 24 20 23 20 50 56 80 63 59 48 28 33 20 28 27 33 23 27 28 57 40 35 50 58 24 25 20 20 33 40 20 23 21 24 23 20 23 29 25 33 20 20 27 24 19 20 27 37 28 20 20 25 25 33 21 20 20 20 21 21 21 24 20 20 20 20 29 32 27 25 24 28 25 30 20 34 28 20 29 25 20 20 28 32 38 52 38 39
+ expected[3, ] 20 34 28 20 29 25 20 20 28 32 38 52 38 39 21 24 20 20 20 20 29 32 27 25 24 28 25 30 27 37 28 20 20 25 25 33 21 20 20 20 21 21 21 24 23 20 23 29 25 33 20 20 27 24 19 20 28 57 40 35 50 58 24 25 20 20 33 40 20 23 50 56 80 63 59 48 28 33 20 28 27 33 23 27 20 32 50 47 39 24 21 23 21 28 24 20 23 20 19 20 21 34 28 23 32 30 19 24 27 21 23 20 21 24 35 74 62 24 37 25 20 33 35 24 21 19 32 43 69 91 53 42 50 24 24 33 24 20 21 32 40 88 77 35 42 88 61 24 21 32 23 38 38 21 73 40 21 19 20 38 111 83 63 48 30 29 28 20 38 19 19 19 19 19 30 48 56 85 72 40 27 40 20 19 19 19 19 19 19 19 21 63 83 63 71 62 19 19 19 19 21 21 20 19 18 21 28 29 63 78 19 23 52 50 74 66 63 33 19 18 18 19 28 66 19 44 88 82 71 47 52 63 24 18 18 18 20 35 21 59 58 97 76 63 53 78 30 30 30 21 19 19 29 69 40 58 58 47 33 61 74 80 90 47 38 20 47 49 23 33 58 78 28 25 53 49 39 61 76 39 59 24 29 58 80 57 35 24 23 29 25 35 43 44 42 27 53 54 53 30 21 21 30 30 20 20 24 28 23 21 23 42 48 58 38 30 37 35 34 20 21 23
── Failure ('test-formatTxSpots.R:13:5'): Read MERFISH transcript spots into rowGeometries ──
sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:550:5'): Image is shifted after removing empty space ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:568:5'): Image is cropped after cropping SFE object ──
abs(cor(nCounts, v$mean, use = "complete.obs")) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:582:5'): Transpose SFE object with image ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:599:5'): Transpose SFE object with image, after cropping image ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:627:5'): Mirror SFE object with image, vertical ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:644:5'): Mirror SFE object with image after cropping ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:672:5'): Mirror SFE object with image, horizontal ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:689:5'): Rotate SFE object with image ───
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:693:5'): Rotate SFE object with image ───
abs(cor(nCounts, v2$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:713:5'): Rotate SFE object with image after cropping ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:717:5'): Rotate SFE object with image after cropping ──
abs(cor(nCounts, v2$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:736:5'): Scale SFE object with image ────
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:740:5'): Scale SFE object with image ────
abs(cor(nCounts, v2$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:760:5'): Scale SFE object with image after cropping ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:764:5'): Scale SFE object with image after cropping ──
abs(cor(nCounts, v2$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:785:5'): General affine transformation of SFE object with image ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:789:5'): General affine transformation of SFE object with image ──
abs(cor(nCounts, v2$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:811:5'): Affine transformation of SFE object with image, after cropping ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:815:5'): Affine transformation of SFE object with image, after cropping ──
abs(cor(nCounts, v2$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-geometry_operation.R:856:5'): Translate SFE object with image ──
abs(cor(nCounts, v$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-image.R:256:5'): affineImg, SpatRasterImage method, EBI behind the scene ──
as.numeric(imgRaster(ebi)[6, 3, 2]) (`actual`) not equal to 191 (`expected`).
`actual`: 63.0
`expected`: 191.0
── Failure ('test-read.R:92:5'): Image is properly aligned in pixel space ──────
abs(cor(cg$nCounts, v_lo$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-read.R:96:5'): Image is properly aligned in pixel space ──────
abs(cor(cg$nCounts, v_hi$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-read.R:120:5'): Image is properly aligned in micron space ────
abs(cor(cg$nCounts, v_lo$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-read.R:124:5'): Image is properly aligned in micron space ────
abs(cor(cg$nCounts, v_hi$mean)) > 0.4 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-read.R:209:5'): readVizgen flip geometry, use cellpose ───────
sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-read.R:402:5'): Version with Cellpose directory ──────────────
sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 29 | WARN 0 | SKIP 10 | PASS 1207 ]
Error: Test failures
Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
| name | user | system | elapsed | |
| Img-set-SpatialExperiment-method | 21.63 | 4.11 | 80.11 | |
| SFE-image | 2.61 | 0.25 | 3.19 | |
| SFE-transform | 4.84 | 0.33 | 5.28 | |
| SpatRasterImage | 0 | 0 | 0 | |
| SpatialFeatureExperiment-coercion | 2.29 | 0.10 | 2.58 | |
| SpatialFeatureExperiment-subset | 2.45 | 0.25 | 2.86 | |
| SpatialFeatureExperiment | 0.52 | 0.06 | 0.57 | |
| addVisiumSpotPoly | 2.23 | 0.15 | 2.39 | |
| aggBboxes | 0 | 0 | 0 | |
| aggregate-SpatialFeatureExperiment-method | 0 | 0 | 0 | |
| annotGeometries | 2.50 | 0.25 | 2.90 | |
| annotOp | 2.66 | 0.32 | 3.21 | |
| annotPred | 2.95 | 0.29 | 3.36 | |
| annotSummary | 2.55 | 0.30 | 2.99 | |
| bbox-SpatialFeatureExperiment-method | 2.92 | 0.30 | 3.35 | |
| bbox_center | 0 | 0 | 0 | |
| cbind-SpatialFeatureExperiment-method | 6.44 | 0.56 | 7.72 | |
| changeSampleIDs | 2.96 | 0.41 | 3.51 | |
| colFeatureData | 3.36 | 0.48 | 4.23 | |
| colGeometries | 2.81 | 0.27 | 3.18 | |
| crop | 4.49 | 0.33 | 4.91 | |
| df2sf | 0.00 | 0.02 | 0.10 | |
| dimGeometries | 7.71 | 0.56 | 8.54 | |
| findSpatialNeighbors-SpatialFeatureExperiment-method | 6.62 | 0.58 | 7.41 | |
| findVisiumGraph | 7.08 | 0.65 | 7.95 | |
| formatTxSpots | 20.48 | 1.77 | 24.49 | |
| formatTxTech | 3.86 | 0.47 | 4.58 | |
| gdalParquetAvailable | 0 | 0 | 0 | |
| getParams | 3.33 | 0.32 | 3.75 | |
| getPixelSize | 3.56 | 0.57 | 4.12 | |
| imageIDs | 0.71 | 0.00 | 0.81 | |
| listw2sparse | 3.06 | 0.28 | 3.44 | |
| localResults | 0.95 | 0.05 | 1.02 | |
| multi_listw2sparse | 0 | 0 | 0 | |
| read10xVisiumSFE | 1.67 | 0.01 | 1.76 | |
| readCosMX | 3.19 | 0.34 | 3.72 | |
| readSelectTx | 0.02 | 0.00 | 0.01 | |
| readVisiumHD | 0 | 0 | 0 | |
| readVizgen | 4.69 | 0.46 | 5.42 | |
| readXenium | 11.54 | 0.91 | 12.81 | |
| removeEmptySpace | 8.48 | 0.72 | 9.54 | |
| rowGeometries | 11.75 | 0.62 | 13.22 | |
| sampleIDs | 2.49 | 0.24 | 2.89 | |
| saveRDS-SpatialFeatureExperiment-method | 1.72 | 0.05 | 1.77 | |
| show-SpatialFeatureExperiment-method | 2.51 | 0.27 | 2.89 | |
| spatialGraphs | 7.56 | 0.54 | 8.34 | |
| splitByCol | 0 | 0 | 0 | |
| st_any_pred | 0.03 | 0.02 | 0.05 | |
| unit-SpatialFeatureExperiment-method | 2.79 | 0.28 | 3.15 | |
| updateObject | 3.96 | 0.24 | 4.30 | |