| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-25 12:08 -0400 (Mon, 25 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
| 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 2045/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.11.1 (landing page) Lambda Moses
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SpatialFeatureExperiment |
| Version: 1.11.1 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SpatialFeatureExperiment_1.11.1.tar.gz |
| StartedAt: 2025-08-22 12:39:23 -0000 (Fri, 22 Aug 2025) |
| EndedAt: 2025-08-22 13:08:07 -0000 (Fri, 22 Aug 2025) |
| EllapsedTime: 1724.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpatialFeatureExperiment.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SpatialFeatureExperiment_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.11.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 loading without being on the library search path ... 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'
.filter_polygons: no visible binding for global variable ‘gmax’
.filter_polygons: no visible binding for global variable ‘area’
.filter_polygons: no visible binding for global variable ‘name’
.filter_polygons: no visible binding for global variable ‘gi’
.filter_polygons: no visible binding for global variable ‘.N’
.filter_polygons: no visible binding for global variable ‘i’
.filter_polygons: no visible binding for global variable ‘.I’
.filter_polygons: no visible binding for global variable ‘ID_row’
.get_tb1: no visible global function definition for ‘clahe’
.get_tb1_concave: no visible global function definition for
‘st_concave_hull’
.mols2geo: no visible global function definition for ‘txtProgressBar’
.mols2geo: no visible binding for global variable ‘gene’
.mols2geo: no visible global function definition for ‘syms’
.mols2geo: no visible global function definition for ‘write_parquet’
.mols2geo: no visible global function definition for
‘setTxtProgressBar’
.mols2geo_split: no visible binding for global variable ‘grp’
aggregateTx: no visible binding for global variable ‘gene’
aggregateTx : <anonymous>: no visible binding for global variable
‘gene’
findVisiumHDGraph: no visible binding for global variable ‘..cols’
formatTxSpots: no visible binding for global variable ‘rng’
Undefined global functions or variables:
..cols .I .N ID_row area clahe gene gi gmax grp i name rng
setTxtProgressBar st_concave_hull syms txtProgressBar write_parquet
Consider adding
importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
SpatialFeatureExperiment-coercion.Rd: DataFrame
SpatialFeatureExperiment.Rd: DataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'findSpatialNeighbors' and siglist 'SpatialFeatureExperiment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'aggregateTx.Rd'
‘progressbar’
Documented arguments not in \usage in Rd file 'aggregateTx.Rd':
‘pregressbar’
Objects in \usage without \alias in Rd file 'findSpatialNeighbors.Rd':
‘\S4method{findSpatialNeighbors}{SpatialFeatureExperiment}’
Undocumented arguments in Rd file 'formatTxSpots.Rd'
‘progressbar’
Undocumented arguments in Rd file 'getTissueBoundaryConcave.Rd'
‘colGeometryName’
Undocumented arguments in Rd file 'getTissueBoundaryImg.Rd'
‘image_id’
Documented arguments not in \usage in Rd file 'read10xVisiumSFE.Rd':
‘load’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SpatialFeatureExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read10xVisiumSFE
> ### Title: Read 10X Visium data as SpatialFeatureExperiment
> ### Aliases: read10xVisiumSFE
>
> ### ** Examples
>
> dir <- system.file("extdata", package = "SpatialFeatureExperiment")
>
> sample_ids <- c("sample01", "sample02")
> samples <- file.path(dir, sample_ids, "outs")
>
> list.files(samples[1])
[1] "filtered_feature_bc_matrix" "spatial"
> list.files(file.path(samples[1], "spatial"))
[1] "aligned_fiducials.jpg" "barcode_fluorescence_intensity.csv"
[3] "detected_tissue_image.jpg" "scalefactors_json.json"
[5] "spatial_enrichment.csv" "tissue_hires_image.png"
[7] "tissue_lowres_image.png" "tissue_positions.csv"
> (sfe <- read10xVisiumSFE(dirs = samples, sample_id = sample_ids,
+ type = "sparse", data = "filtered",
+ load = FALSE
+ ))
Error in read10xVisiumSFE(dirs = samples, sample_id = sample_ids, type = "sparse", :
unused argument (load = FALSE)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
formatTxSpots 23.198 0.524 29.140
Img-set-SpatialExperiment-method 18.195 0.954 28.153
dimGeometries 7.335 0.215 13.045
findVisiumGraph 6.809 0.176 12.524
findSpatialNeighbors 6.454 0.167 12.582
cbind-SpatialFeatureExperiment-method 5.972 0.215 12.574
formatTxTech 5.371 0.357 8.819
getParams 4.375 0.151 7.835
getPixelSize 4.201 0.167 6.447
SFE-transform 3.856 0.252 6.655
crop 3.954 0.083 6.813
colFeatureData 3.836 0.177 6.796
changeSampleIDs 2.941 0.112 5.820
colGeometries 2.947 0.083 5.763
bbox-SpatialFeatureExperiment-method 2.838 0.135 5.485
annotSummary 2.801 0.155 5.654
annotOp 2.696 0.168 6.235
annotPred 2.728 0.108 5.574
SpatialFeatureExperiment-subset 2.507 0.132 5.828
annotGeometries 2.504 0.112 6.411
SFE-image 2.338 0.104 5.323
* 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:
`{ ... }` did not throw the expected message.
── Failure ('test-updateObject.R:18:5'): Update colFeatureData if present ──────
`df` (`actual`) not equal to `df2` (`expected`).
`actual` is an S4 object of class <DFrame>
`expected` is NULL
── Failure ('test-updateObject.R:19:5'): Update colFeatureData if present ──────
metadata(colData(sfe))$featureData is not NULL
`actual` is an S4 object of class <DFrame>
`expected` is NULL
[ FAIL 7 | WARN 10 | SKIP 10 | PASS 1217 ]
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: 2 ERRORs, 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** this is package ‘SpatialFeatureExperiment’ version ‘1.11.1’ ** 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 ‘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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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 3.13.1, GDAL 3.10.3, PROJ 9.6.0; 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
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following 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: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Some features are not enabled in this build of Arrow. Run `arrow_info()` for more information.
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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc77a0d134/xenium2
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc77a0d134/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`
>>> Must use gene symbols as row names when adding transcript spots.
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Reading transcript coordinates
>>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> 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 /home/biocbuild/bbs-3.22-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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc634237c4/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc634237c4/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc634237c4/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc781c80e7/vizgen_cellbound
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc781c80e7/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc781c80e7/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc48d9e5b2/vizgen_cellbound
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc18e71ebd/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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc614fbad8/xenium2
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
terra 1.8.60
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 object is masked from 'package:generics':
interpolate
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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc27c10fcc/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc4f941018/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, thresh, 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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1832dc6/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`
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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2e8a99d/xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dcb273bdc/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc13c82cb8/xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dcac81263/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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc6dde22ac/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/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
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: kidney
>>> 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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc3e26090/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc3e26090/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc3e26090/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2d80bfff/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2d80bfff/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2d80bfff/vizgen_cellbound/hdf5s_micron_space.parquet
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2e880f0d/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1f8791f1/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1c5587b4/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc547571c9/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc25b0bf6/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc25b0bf6/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc25b0bf6/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc5100dd9f/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1f365c5/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1f365c5/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1f365c5/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc5d27127b/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc5d27127b/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc5d27127b/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2afa9ccf/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2afa9ccf/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc2afa9ccf/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc57ea7638/vizgen_cellbound_Cellpose
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc57ea7638/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc57ea7638/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc3fa477d9/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc4a5f04ea/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc4a5f04ea/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc7d057bc7/vizgen_cellbound
>>> 1 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc7d057bc7/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc7d057bc7/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc29a59161/vizgen_cellbound
>>> 2 `.parquet` files exist:
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc29a59161/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc29a59161/vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc5100dd9f/vizgen_cellbound_Cellpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc57011e2e/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc6a0d0080/cosmx
>>> Constructing cell polygons
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc252caf41/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc27e37b69/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc194c4ba0/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc34636f23/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%
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|=================================== | 50%
|
|============================================ | 62%
|
|==================================================== | 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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc59ecb1c2/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc3c66ec72/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc5cf39252/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc322c18c9/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc24c00d85/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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc1481257a/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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc4d7b2063/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 0.8930166see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc61347750/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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc4c2a7d38/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 0.8930166see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc50bd09d1/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 0.8930166>>> 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
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/gtar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc48943f89/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
/usr/bin/gtar: kidney/outs/spatial.tar.gz: Cannot open: No such file or directory
/usr/bin/gtar: Error is not recoverable: exiting now
>>> 10X Visium data will be loaded: outs
>>> Converting pixels to microns
>>> Adding spatial neighborhood graph to ob
>>> 10X Visium data will be loaded: outs
[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 /home/biocbuild/tmp/Rtmpr8zW2W/file3f78dc3ea8c94c/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 7 | WARN 10 | SKIP 10 | PASS 1217 ]
══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test-read.R:692:5'
• 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-aggregate.R:75:5'): aggregateTxTech for Vizgen ───────────────
all(st_area(colGeometry(sfe)) == 400) is not TRUE
`actual`: FALSE
`expected`: TRUE
── 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
── Error ('test-subset.R:155:1'): (code run outside of `test_that()`) ──────────
Error in `.read10xVisium(dirs[i], sample_id[i], type, data, images, row.names = row.names,
flip = flip, VisiumHD = FALSE, unit = unit, zero.policy = zero.policy,
style = style)`: No matching files found for 'images=c("lowres", "hires")
Backtrace:
▆
1. └─SpatialFeatureExperiment::read10xVisiumSFE(...) at test-subset.R:155:1
2. └─base::lapply(...)
3. └─SpatialFeatureExperiment (local) FUN(X[[i]], ...)
4. └─SpatialFeatureExperiment:::.read10xVisium(...)
── Failure ('test-updateObject.R:3:5'): SFEVersion of first version of SFE object should be NULL ──
SFEVersion(sfe) is not NULL
`actual` is an S3 object of class <package_version/numeric_version>, a list
`expected` is NULL
── Failure ('test-updateObject.R:8:5'): Add version in updateObject ────────────
`{ ... }` did not throw the expected message.
── Failure ('test-updateObject.R:18:5'): Update colFeatureData if present ──────
`df` (`actual`) not equal to `df2` (`expected`).
`actual` is an S4 object of class <DFrame>
`expected` is NULL
── Failure ('test-updateObject.R:19:5'): Update colFeatureData if present ──────
metadata(colData(sfe))$featureData is not NULL
`actual` is an S4 object of class <DFrame>
`expected` is NULL
[ FAIL 7 | WARN 10 | SKIP 10 | PASS 1217 ]
Error: Test failures
Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
| name | user | system | elapsed | |
| Img-set-SpatialExperiment-method | 18.195 | 0.954 | 28.153 | |
| SFE-image | 2.338 | 0.104 | 5.323 | |
| SFE-transform | 3.856 | 0.252 | 6.655 | |
| SpatRasterImage | 0 | 0 | 0 | |
| SpatialFeatureExperiment-coercion | 3.449 | 0.322 | 3.780 | |
| SpatialFeatureExperiment-subset | 2.507 | 0.132 | 5.828 | |
| SpatialFeatureExperiment | 0.659 | 0.044 | 0.705 | |
| addVisiumSpotPoly | 2.637 | 0.143 | 2.787 | |
| aggBboxes | 0 | 0 | 0 | |
| aggregate-SpatialFeatureExperiment-method | 0 | 0 | 0 | |
| annotGeometries | 2.504 | 0.112 | 6.411 | |
| annotOp | 2.696 | 0.168 | 6.235 | |
| annotPred | 2.728 | 0.108 | 5.574 | |
| annotSummary | 2.801 | 0.155 | 5.654 | |
| bbox-SpatialFeatureExperiment-method | 2.838 | 0.135 | 5.485 | |
| bbox_center | 0 | 0 | 0 | |
| cbind-SpatialFeatureExperiment-method | 5.972 | 0.215 | 12.574 | |
| changeSampleIDs | 2.941 | 0.112 | 5.820 | |
| colFeatureData | 3.836 | 0.177 | 6.796 | |
| colGeometries | 2.947 | 0.083 | 5.763 | |
| containsOutOfMemoryData-SpatialFeatureExperiment-method | 1.964 | 0.112 | 2.090 | |
| crop | 3.954 | 0.083 | 6.813 | |
| df2sf | 0.011 | 0.006 | 0.021 | |
| dimGeometries | 7.335 | 0.215 | 13.045 | |
| findSpatialNeighbors | 6.454 | 0.167 | 12.582 | |
| findVisiumGraph | 6.809 | 0.176 | 12.524 | |
| formatTxSpots | 23.198 | 0.524 | 29.140 | |
| formatTxTech | 5.371 | 0.357 | 8.819 | |
| gdalParquetAvailable | 0.000 | 0.003 | 0.003 | |
| getParams | 4.375 | 0.151 | 7.835 | |
| getPixelSize | 4.201 | 0.167 | 6.447 | |
| imageIDs | 0.755 | 0.008 | 0.733 | |
| localResults | 1.294 | 0.008 | 1.305 | |
| multi_listw2sparse | 0.000 | 0.000 | 0.001 | |