| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:37:08 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 2008/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpatialFeatureExperiment 1.5.2 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the SpatialFeatureExperiment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialFeatureExperiment.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SpatialFeatureExperiment |
| Version: 1.5.2 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialFeatureExperiment_1.5.2.tar.gz |
| StartedAt: 2024-03-28 02:56:47 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:09:07 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 739.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpatialFeatureExperiment.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SpatialFeatureExperiment_1.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.5.2’
* 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 ... NOTE
Found the following non-portable file path:
SpatialFeatureExperiment/inst/extdata/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialFeatureExperiment’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.3Mb
sub-directories of 1Mb or more:
R 1.2Mb
extdata 5.7Mb
* 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 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 ... OK
* 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 12.131 1.135 13.248
removeEmptySpace 5.994 0.721 7.013
dimGeometries 5.915 0.583 7.044
SFE-image 5.336 0.712 6.520
spatialGraphs 5.303 0.549 6.360
cbind-SpatialFeatureExperiment-method 5.084 0.692 6.277
findVisiumGraph 4.932 0.612 6.069
findSpatialNeighbors-SpatialFeatureExperiment-method 4.689 0.583 5.779
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 771 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On Bioconductor (5): 'test-image.R:40:5', 'test-image.R:65:5',
'test-image.R:99:5', 'test-image.R:134:5', 'test-read.R:658:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-image.R:263:1'): (code run outside of `test_that()`) ───────────
<NullPointerException/RuntimeException/Exception/Throwable/Object/error/condition>
Error in `.jcall(.jcall("RBioFormats", "Lloci/formats/meta/MetadataStore;",
"getOMEXML"), "S", "dumpXML")`: java.lang.NullPointerException
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 771 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.
SpatialFeatureExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SpatialFeatureExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SpatialFeatureExperiment’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘saveRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpatialFeatureExperiment)
SpatialFeatureExperiment.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 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)
>
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following 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
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 212 features/genes with `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
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 1.7.71
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
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 212 features/genes with `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
BioFormats library version 6.12.0
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':
rotate, translate, transpose
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/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
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 1023 cells with counts > 0
>>> Reading '.hdf5' files..
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/detected_transcripts.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/hdf5s_micron_space.parquet
Removing 3 cells with area less than 15
>>> Reading '.hdf5' files..
>>> Reading '.hdf5' files..
>>> Reading '.hdf5' files..
>>> Reading '.hdf5' files..
>>> Reading '.hdf5' files..
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 3 cells with counts > 0
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/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
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> Cell segmentations are found in `.parquet` file
>>> filtering geometries to match 1023 cells with counts > 0
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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
>>> 3 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/cool_cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_cellbound/detected_transcripts.parquet
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/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
>>> Total of 26 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Converting transcript spots to geometry
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/R/site-library/SpatialFeatureExperiment/extdata/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/R/site-library/SpatialFeatureExperiment/extdata/vizgen_cellbound/detected_transcripts.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/R/site-library/SpatialFeatureExperiment/extdata/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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>>> Converting transcript spots to geometry
>>> Constructing cell polygons
>>> File cell_boundaries_sf.parquet found
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 258 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> Total of 258 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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>>> Total of 212 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> Total of 212 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> Total of 576 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 212 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Constructing cell polygons
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
|
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>>> Total of 212 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> Total of 212 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> File cell_boundaries_sf.parquet found
>>> Reading transcript coordinates
>>> Total of 576 features/genes with `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
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[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
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 771 ]
══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• On Bioconductor (5): 'test-image.R:40:5', 'test-image.R:65:5',
'test-image.R:99:5', 'test-image.R:134:5', 'test-read.R:658:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-image.R:263:1'): (code run outside of `test_that()`) ───────────
<NullPointerException/RuntimeException/Exception/Throwable/Object/error/condition>
Error in `.jcall(.jcall("RBioFormats", "Lloci/formats/meta/MetadataStore;",
"getOMEXML"), "S", "dumpXML")`: java.lang.NullPointerException
[ FAIL 1 | WARN 0 | SKIP 5 | PASS 771 ]
Error: Test failures
Execution halted
SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings
| name | user | system | elapsed | |
| SFE-image | 5.336 | 0.712 | 6.520 | |
| SFE-transform | 3.312 | 0.415 | 3.983 | |
| SpatRasterImage | 0.001 | 0.000 | 0.000 | |
| SpatialFeatureExperiment-coercion | 2.680 | 0.168 | 2.849 | |
| SpatialFeatureExperiment-subset | 2.196 | 0.213 | 2.691 | |
| SpatialFeatureExperiment | 0.612 | 0.032 | 0.646 | |
| addVisiumSpotPoly | 2.504 | 0.084 | 2.588 | |
| annotGeometries | 1.938 | 0.217 | 2.428 | |
| annotOp | 2.146 | 0.200 | 2.657 | |
| annotPred | 2.083 | 0.257 | 2.650 | |
| annotSummary | 2.043 | 0.278 | 2.578 | |
| bbox-SpatialFeatureExperiment-method | 2.057 | 0.269 | 2.625 | |
| bbox_center | 0.001 | 0.000 | 0.001 | |
| callMeta | 2.305 | 0.308 | 2.869 | |
| cbind-SpatialFeatureExperiment-method | 5.084 | 0.692 | 6.277 | |
| changeSampleIDs | 2.083 | 0.224 | 2.559 | |
| colGeometries | 2.218 | 0.243 | 2.728 | |
| crop | 3.150 | 0.413 | 3.817 | |
| df2sf | 0.014 | 0.004 | 0.019 | |
| dimGeometries | 5.915 | 0.583 | 7.044 | |
| findSpatialNeighbors-SpatialFeatureExperiment-method | 4.689 | 0.583 | 5.779 | |
| findVisiumGraph | 4.932 | 0.612 | 6.069 | |
| formatTxSpots | 12.131 | 1.135 | 13.248 | |
| localResults | 1.250 | 0.036 | 1.287 | |
| read10xVisiumSFE | 1.860 | 0.092 | 1.956 | |
| readCosMX | 1.060 | 0.013 | 1.061 | |
| readVizgen | 1.741 | 0.018 | 1.749 | |
| readXenium | 0.001 | 0.000 | 0.001 | |
| removeEmptySpace | 5.994 | 0.721 | 7.013 | |
| rowGeometries | 0 | 0 | 0 | |
| sampleIDs | 1.947 | 0.292 | 2.516 | |
| saveRDS-SpatialFeatureExperiment-method | 1.917 | 0.276 | 2.193 | |
| show-SpatialFeatureExperiment-method | 1.964 | 0.188 | 2.400 | |
| spatialGraphs | 5.303 | 0.549 | 6.360 | |
| st_any_pred | 0.019 | 0.016 | 0.034 | |
| unit-SpatialFeatureExperiment-method | 3.050 | 0.448 | 3.750 | |
| updateObject | 2.180 | 0.215 | 2.656 | |