| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-03 12:37 -0500 (Mon, 03 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4704 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4467 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4478 |
| 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 2016/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.9.7 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
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: 1.9.7 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SpatialFeatureExperiment_1.9.7.tar.gz |
| StartedAt: 2025-02-03 02:44:17 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 03:05:17 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 1259.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpatialFeatureExperiment.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SpatialFeatureExperiment_1.9.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.9.7’
* 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 ‘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 global function definition for ‘tail’
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 ID_row cell_col fn gene_col img_df instrument_version
major_version minor_version spatialCoordsNames<- tail xoa_version
Consider adding
importFrom("utils", "tail")
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:
BioFormatsImage.Rd: Image
ExtImage.Rd: Image
Img-set-SpatialExperiment-method.Rd: addImg
SpatRasterImage.Rd: rast, SpatRaster
SpatialFeatureExperiment-class.Rd: SpatialExperiment,
SingleCellExperiment
SpatialFeatureExperiment-coercion.Rd: SpatialExperiment, DataFrame
SpatialFeatureExperiment.Rd: DataFrame, SpatialExperiment,
SingleCellExperiment
aggregate-SpatialFeatureExperiment-method.Rd: BiocParallelParam
annotOp.Rd: st_intersection
annotPred.Rd: st_intersects
annotSummary.Rd: st_intersects
colFeatureData.Rd: reducedDimNames
crop.Rd: st_intersection, st_difference
findSpatialNeighbors-SpatialFeatureExperiment-method.Rd: nb2listw,
BiocParallelParam, BiocNeighborParam, KmknnParam, VptreeParam
formatTxSpots.Rd: BiocParallelParam
formatTxTech.Rd: BiocParallelParam
getParams.Rd: reducedDimNames
readCosMX.Rd: BiocParallelParam
readVizgen.Rd: SpatRaster, BiocParallelParam
readXenium.Rd: BiocParallelParam
saveRDS-SpatialFeatureExperiment-method.Rd: wrap
spatialGraphs.Rd: SpatialExperiment
st_any_pred.Rd: st_intersects
updateObject.Rd: objectVersion
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 17.486 1.770 16.749
formatTxSpots 16.698 0.784 17.865
readXenium 10.248 0.705 10.417
rowGeometries 9.621 0.353 9.610
dimGeometries 6.435 1.374 8.272
findSpatialNeighbors-SpatialFeatureExperiment-method 6.352 1.367 8.183
cbind-SpatialFeatureExperiment-method 6.269 0.980 7.713
removeEmptySpace 6.302 0.146 6.681
spatialGraphs 5.633 0.215 6.324
findVisiumGraph 4.769 0.532 5.765
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** this is package ‘SpatialFeatureExperiment’ version ‘1.9.7’ ** 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
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 3.12.1, GDAL 3.8.4, PROJ 9.4.0; 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 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, 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: 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
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c5611f3768/xenium2
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c5611f3768/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-3.21-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 /tmp/RtmpjeEvPm/file17e3c53b3b60f5/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c53b3b60f5/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c53b3b60f5/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 /tmp/RtmpjeEvPm/file17e3c5696df438/vizgen_cellbound
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c5696df438/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c5696df438/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
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>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c5675d6c8a/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/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c56d357b2c/xenium2
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
terra 1.8.15
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 /tmp/RtmpjeEvPm/file17e3c53ea39289/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 /tmp/RtmpjeEvPm/file17e3c537beba67/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 /tmp/RtmpjeEvPm/file17e3c57772cd39/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 /tmp/RtmpjeEvPm/file17e3c53cac830b/xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c5286ba1bd/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c52c7f4d6c/xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c515cd8dff/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/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c57355cb5b/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 /tmp/RtmpjeEvPm/file17e3c556ee7916/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c556ee7916/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c556ee7916/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 /tmp/RtmpjeEvPm/file17e3c56dc639de/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c56dc639de/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c56dc639de/vizgen_cellbound/hdf5s_micron_space.parquet
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c549afa8e9/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c53842de50/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c52439d1e0/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c53ec76fd2/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 /tmp/RtmpjeEvPm/file17e3c54b4cd3fe/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c54b4cd3fe/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c54b4cd3fe/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 /tmp/RtmpjeEvPm/file17e3c56a20fbf9/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c5c440e6c/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c5c440e6c/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c5c440e6c/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 /tmp/RtmpjeEvPm/file17e3c53b2a8e1e/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c53b2a8e1e/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c53b2a8e1e/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 /tmp/RtmpjeEvPm/file17e3c574810223/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c574810223/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c574810223/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 /tmp/RtmpjeEvPm/file17e3c5249aa2c1/vizgen_cellbound_Cellpose
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c5249aa2c1/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c5249aa2c1/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 /tmp/RtmpjeEvPm/file17e3c566e9a1a/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c541154ccd/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c541154ccd/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 /tmp/RtmpjeEvPm/file17e3c536427da5/vizgen_cellbound
>>> 1 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c536427da5/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /tmp/RtmpjeEvPm/file17e3c536427da5/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 /tmp/RtmpjeEvPm/file17e3c5272a49db/vizgen_cellbound
>>> 2 `.parquet` files exist:
/tmp/RtmpjeEvPm/file17e3c5272a49db/vizgen_cellbound/cell_boundaries.parquet
/tmp/RtmpjeEvPm/file17e3c5272a49db/vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c56a20fbf9/vizgen_cellbound_Cellpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c54661450b/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 /tmp/RtmpjeEvPm/file17e3c54ef1bd3d/cosmx
>>> Constructing cell polygons
>>> Checking polygon validity
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c551834c81/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 /tmp/RtmpjeEvPm/file17e3c52fb9fc55/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 /tmp/RtmpjeEvPm/file17e3c55a314d5b/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 /tmp/RtmpjeEvPm/file17e3c538082c62/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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|========= | 12%
|
|================== | 25%
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|========================== | 38%
|
|=================================== | 50%
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|============================================ | 62%
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|==================================================== | 75%
|
|============================================================= | 88%
|
|======================================================================| 100%
>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Checking polygon validity
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c559ea5199/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 /tmp/RtmpjeEvPm/file17e3c56f7e0efa/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 /tmp/RtmpjeEvPm/file17e3c57c42ae7e/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 /tmp/RtmpjeEvPm/file17e3c529a32929/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 /tmp/RtmpjeEvPm/file17e3c5316fdc2b/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 /tmp/RtmpjeEvPm/file17e3c545aeb930/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/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c58f394d5/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
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c522706328/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/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c55a48aadf/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
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c51c7216d0/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
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
/usr/bin/tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.provenance'
The downloaded files are in /tmp/RtmpjeEvPm/file17e3c5512bad3c/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 /tmp/RtmpjeEvPm/file17e3c55309b5c8/xenium_lr
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 1257 ]
══ 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'
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 1257 ]
>
> proc.time()
user system elapsed
621.005 36.689 654.401
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
| name | user | system | elapsed | |
| Img-set-SpatialExperiment-method | 17.486 | 1.770 | 16.749 | |
| SFE-image | 2.037 | 0.132 | 2.411 | |
| SFE-transform | 3.328 | 0.462 | 4.021 | |
| SpatRasterImage | 0 | 0 | 0 | |
| SpatialFeatureExperiment-coercion | 1.787 | 0.226 | 2.012 | |
| SpatialFeatureExperiment-subset | 2.335 | 0.287 | 2.854 | |
| SpatialFeatureExperiment | 0.427 | 0.036 | 0.463 | |
| addVisiumSpotPoly | 1.756 | 0.212 | 1.966 | |
| aggBboxes | 0.001 | 0.000 | 0.000 | |
| aggregate-SpatialFeatureExperiment-method | 0.000 | 0.000 | 0.001 | |
| annotGeometries | 2.56 | 0.62 | 3.46 | |
| annotOp | 2.178 | 0.368 | 2.779 | |
| annotPred | 3.245 | 0.318 | 3.795 | |
| annotSummary | 2.193 | 0.292 | 2.719 | |
| bbox-SpatialFeatureExperiment-method | 2.854 | 0.413 | 3.498 | |
| bbox_center | 0 | 0 | 0 | |
| cbind-SpatialFeatureExperiment-method | 6.269 | 0.980 | 7.713 | |
| changeSampleIDs | 2.421 | 0.499 | 3.154 | |
| colFeatureData | 3.278 | 0.477 | 3.996 | |
| colGeometries | 2.551 | 0.297 | 3.098 | |
| crop | 3.511 | 0.326 | 4.100 | |
| df2sf | 0.011 | 0.003 | 0.015 | |
| dimGeometries | 6.435 | 1.374 | 8.272 | |
| findSpatialNeighbors-SpatialFeatureExperiment-method | 6.352 | 1.367 | 8.183 | |
| findVisiumGraph | 4.769 | 0.532 | 5.765 | |
| formatTxSpots | 16.698 | 0.784 | 17.865 | |
| formatTxTech | 3.831 | 0.445 | 4.013 | |
| gdalParquetAvailable | 0.001 | 0.002 | 0.003 | |
| getParams | 2.781 | 0.173 | 3.188 | |
| getPixelSize | 3.702 | 0.329 | 3.689 | |
| imageIDs | 0.559 | 0.014 | 0.573 | |
| listw2sparse | 2.178 | 0.100 | 2.531 | |
| localResults | 0.959 | 0.008 | 0.966 | |
| multi_listw2sparse | 0.001 | 0.000 | 0.000 | |
| read10xVisiumSFE | 1.350 | 0.015 | 1.365 | |
| readCosMX | 2.534 | 0.144 | 2.897 | |
| readSelectTx | 0.017 | 0.002 | 0.019 | |
| readVisiumHD | 0 | 0 | 0 | |
| readVizgen | 3.135 | 0.167 | 3.512 | |
| readXenium | 10.248 | 0.705 | 10.417 | |
| removeEmptySpace | 6.302 | 0.146 | 6.681 | |
| rowGeometries | 9.621 | 0.353 | 9.610 | |
| sampleIDs | 2.079 | 0.112 | 2.425 | |
| saveRDS-SpatialFeatureExperiment-method | 2.576 | 0.008 | 2.590 | |
| show-SpatialFeatureExperiment-method | 2.093 | 0.119 | 2.448 | |
| spatialGraphs | 5.633 | 0.215 | 6.324 | |
| splitByCol | 0 | 0 | 0 | |
| st_any_pred | 0.021 | 0.002 | 0.023 | |
| unit-SpatialFeatureExperiment-method | 2.092 | 0.116 | 2.442 | |
| updateObject | 3.216 | 0.097 | 3.543 | |