| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-18 18:00 -0400 (Tue, 18 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 2035/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.6.1 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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: 1.6.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.6.1.tar.gz |
| StartedAt: 2024-06-17 12:37:18 -0400 (Mon, 17 Jun 2024) |
| EndedAt: 2024-06-17 13:17:19 -0400 (Mon, 17 Jun 2024) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: SpatialFeatureExperiment.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialFeatureExperiment_1.6.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialFeatureExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘S4Vectors:::disableValidity’ ‘SpatialExperiment:::.get_img_idx’
‘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
.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’
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’
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’
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’
Undefined global functions or variables:
cell_col fn gene_col instrument_version major_version minor_version
xoa_version
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
formatTxSpots 33.231 1.835 38.893
Img-set-SpatialExperiment-method 27.138 2.779 30.208
rowGeometries 18.297 0.830 20.560
readXenium 15.134 0.657 17.104
removeEmptySpace 13.400 0.541 15.253
dimGeometries 12.000 0.493 13.959
spatialGraphs 10.440 0.473 12.124
findSpatialNeighbors-SpatialFeatureExperiment-method 9.675 0.459 11.283
cbind-SpatialFeatureExperiment-method 9.473 0.468 11.182
findVisiumGraph 8.936 0.470 10.749
readVizgen 6.405 0.288 7.338
getParams 6.122 0.349 7.261
SpatialFeatureExperiment-coercion 6.225 0.234 6.981
SFE-transform 6.065 0.328 7.063
addVisiumSpotPoly 6.095 0.154 6.825
crop 5.821 0.289 6.740
read10xVisiumSFE 6.021 0.064 6.565
formatTxTech 5.457 0.525 6.519
saveRDS-SpatialFeatureExperiment-method 5.891 0.062 6.496
colFeatureData 5.331 0.330 6.317
getPixelSize 5.057 0.454 5.169
readCosMX 4.849 0.254 5.510
annotOp 4.717 0.242 5.530
annotSummary 4.592 0.238 5.376
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘toSpatialFeatureExperiment’ with signature ‘"Seurat"’: no definition for class “Seurat” Creating a generic function for ‘NROW’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘NCOL’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘saveRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ Creating a generic function for ‘readRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpatialFeatureExperiment)
SpatialFeatureExperiment.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpatialFeatureExperiment)
Attaching package: 'SpatialFeatureExperiment'
The following object is masked from 'package:base':
scale
>
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.11.0, GDAL 3.5.3, PROJ 9.1.0; sf_use_s2() is TRUE
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
expand, unname
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: scuttle
Loading required package: ggplot2
Attaching package: 'ggplot2'
The following object is masked from 'package:SpatialFeatureExperiment':
unit
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium2
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> 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
terra 1.7.78
Attaching package: 'terra'
The following objects are masked from 'package:SummarizedExperiment':
distance, nearest, shift, trim, values, values<-, width
The following objects are masked from 'package:GenomicRanges':
distance, gaps, nearest, shift, trim, values, values<-, width
The following objects are masked from 'package:IRanges':
distance, gaps, nearest, shift, trim, width
The following objects are masked from 'package:S4Vectors':
values, values<-, width
The following object is masked from 'package:BiocGenerics':
width
The following objects are masked from 'package:SpatialFeatureExperiment':
centroids, crop, origin, rotate
The following objects are masked from 'package:testthat':
compare, describe
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
BioFormats library version 7.3.0
Attaching package: 'EBImage'
The following objects are masked from 'package:terra':
flip, rotate
The following object is masked from 'package:SummarizedExperiment':
resize
The following object is masked from 'package:Biobase':
channel
The following objects are masked from 'package:GenomicRanges':
resize, tile
The following objects are masked from 'package:IRanges':
resize, tile
The following objects are masked from 'package:SpatialFeatureExperiment':
affine, rotate, translate, transpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
Error in .jcall(.jcall("RBioFormats", "Lloci/formats/meta/MetadataStore;", :
java.lang.NullPointerException: Cannot invoke "loci.formats.DimensionSwapper.setMetadataFiltered(boolean)" because "RBioFormats.reader" is null
>>> 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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
Testing dist_type none style W
Testing dist_type idw style W
Testing dist_type exp style W
Testing dist_type dpd style W
Testing dist_type idw style raw
Testing dist_type idw style W
Testing dist_type idw style B
Testing dist_type idw style C
Testing dist_type idw style U
Testing dist_type idw style minmax
Testing dist_type idw style S
Testing dist_type none style W
Testing dist_type idw style W
Testing dist_type exp style W
Testing dist_type dpd style W
Testing dist_type idw style raw
Testing dist_type idw style W
Testing dist_type idw style B
Testing dist_type idw style C
Testing dist_type idw style U
Testing dist_type idw style minmax
Testing dist_type idw style S
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium2
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
>>> 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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium2
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
>>> 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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet
Removing 3 cells with area less than 15
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> Reading '.hdf5' files..
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/multi/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/multi/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/multi/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 3 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/small/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/small/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/small/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/image/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/image/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/image/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cellpose/vizgen_cellbound_Cellpose
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/cellpose/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /private/tmp/RtmpSKw7m0/cellpose/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/empty/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/empty/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/empty/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 34 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/all/vizgen_cellbound
>>> 1 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/all/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/RtmpSKw7m0/all/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
Removing 35 cells with area less than 15
>>> filtering geometries to match 1023 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound
>>> 2 `.parquet` files exist:
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
/private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/vizgen_test/vizgen_cellbound_Cellpose
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> File cell_boundaries_sf.parquet found
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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|
|=================================== | 50%
|
|======================================================================| 100%
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/cosmx_test/cosmx
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
| | 0%
|
|========= | 12%
|
|================== | 25%
|
|========================== | 38%
|
|=================================== | 50%
|
|============================================ | 62%
|
|==================================================== | 75%
|
|============================================================= | 88%
|
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>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 484 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 484 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Converting columns with raw bytes (ie 'arrow_binary') to character
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 163 cells with counts > 0
>>> filtering nucSeg geometries to match 163 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium_lr
>>> 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`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/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
>>> 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`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium2
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
>>> 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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/xenium2
>>> Must use gene symbols as row names when adding transcript spots.
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
>>> 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`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/RtmpSKw7m0/xenium_test/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
>>> 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`
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> 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
[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
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
| name | user | system | elapsed | |
| Img-set-SpatialExperiment-method | 27.138 | 2.779 | 30.208 | |
| SFE-image | 3.459 | 0.253 | 4.552 | |
| SFE-transform | 6.065 | 0.328 | 7.063 | |
| SpatRasterImage | 0 | 0 | 0 | |
| SpatialFeatureExperiment-coercion | 6.225 | 0.234 | 6.981 | |
| SpatialFeatureExperiment-subset | 3.829 | 0.255 | 4.644 | |
| SpatialFeatureExperiment | 2.817 | 0.066 | 3.235 | |
| addVisiumSpotPoly | 6.095 | 0.154 | 6.825 | |
| aggBboxes | 0.001 | 0.000 | 0.001 | |
| annotGeometries | 3.418 | 0.242 | 4.108 | |
| annotOp | 4.717 | 0.242 | 5.530 | |
| annotPred | 3.429 | 0.220 | 4.188 | |
| annotSummary | 4.592 | 0.238 | 5.376 | |
| bbox-SpatialFeatureExperiment-method | 3.328 | 0.217 | 1.834 | |
| bbox_center | 0.000 | 0.001 | 0.001 | |
| cbind-SpatialFeatureExperiment-method | 9.473 | 0.468 | 11.182 | |
| changeSampleIDs | 3.757 | 0.225 | 4.480 | |
| colFeatureData | 5.331 | 0.330 | 6.317 | |
| colGeometries | 3.790 | 0.232 | 4.518 | |
| crop | 5.821 | 0.289 | 6.740 | |
| df2sf | 0.025 | 0.006 | 0.036 | |
| dimGeometries | 12.000 | 0.493 | 13.959 | |
| findSpatialNeighbors-SpatialFeatureExperiment-method | 9.675 | 0.459 | 11.283 | |
| findVisiumGraph | 8.936 | 0.470 | 10.749 | |
| formatTxSpots | 33.231 | 1.835 | 38.893 | |
| formatTxTech | 5.457 | 0.525 | 6.519 | |
| gdalParquetAvailable | 0.003 | 0.001 | 0.005 | |
| getParams | 6.122 | 0.349 | 7.261 | |
| getPixelSize | 5.057 | 0.454 | 5.169 | |
| imageIDs | 2.002 | 0.024 | 2.223 | |
| localResults | 3.145 | 0.034 | 3.454 | |
| read10xVisiumSFE | 6.021 | 0.064 | 6.565 | |
| readCosMX | 4.849 | 0.254 | 5.510 | |
| readSelectTx | 0.029 | 0.002 | 0.034 | |
| readVizgen | 6.405 | 0.288 | 7.338 | |
| readXenium | 15.134 | 0.657 | 17.104 | |
| removeEmptySpace | 13.400 | 0.541 | 15.253 | |
| rowGeometries | 18.297 | 0.830 | 20.560 | |
| sampleIDs | 3.344 | 0.236 | 4.414 | |
| saveRDS-SpatialFeatureExperiment-method | 5.891 | 0.062 | 6.496 | |
| show-SpatialFeatureExperiment-method | 3.662 | 0.237 | 4.455 | |
| spatialGraphs | 10.440 | 0.473 | 12.124 | |
| st_any_pred | 0.044 | 0.003 | 0.050 | |
| unit-SpatialFeatureExperiment-method | 3.353 | 0.220 | 4.020 | |
| updateObject | 3.975 | 0.231 | 4.684 | |