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This page was generated on 2024-05-04 11:41:09 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2035/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialFeatureExperiment 1.6.0  (landing page)
Lambda Moses
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/SpatialFeatureExperiment
git_branch: RELEASE_3_19
git_last_commit: 57429f1
git_last_commit_date: 2024-04-30 11:45:09 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SpatialFeatureExperiment on kunpeng2


To the developers/maintainers of the SpatialFeatureExperiment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialFeatureExperiment.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SpatialFeatureExperiment
Version: 1.6.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SpatialFeatureExperiment_1.6.0.tar.gz
StartedAt: 2024-05-04 12:15:31 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:37:28 -0000 (Sat, 04 May 2024)
EllapsedTime: 1317.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SpatialFeatureExperiment.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:SpatialFeatureExperiment.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings SpatialFeatureExperiment_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.6.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘Biobase’
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
.seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to
  ‘assays_sfe_out’
.seu_to_sfe : <anonymous>: no visible binding for '<<-' assignment to
  ‘sfe_out’
.seu_to_sfe : <anonymous>: no visible global function definition for
  ‘reducedDim<-’
.seu_to_sfe : <anonymous>: no visible global function definition for
  ‘slot<-’
.seu_to_sfe : <anonymous>: no visible global function definition for
  ‘altExp<-’
.seu_to_sfe: no visible binding for '<<-' assignment to ‘obj_list_test’
reducedDimFeatureData<-: no visible global function definition for
  ‘reducedDim<-’
showAsCell,SpatRasterImage: no visible binding for global variable ‘d’
Undefined global functions or variables:
  altExp<- d reducedDim<- slot<-
Consider adding
  importFrom("methods", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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                                        20.987  1.263  26.859
removeEmptySpace                                      9.782  0.260  12.799
dimGeometries                                         8.372  0.175  13.128
spatialGraphs                                         7.196  0.120  11.876
findVisiumGraph                                       6.881  0.177  11.635
findSpatialNeighbors-SpatialFeatureExperiment-method  6.837  0.127  11.545
cbind-SpatialFeatureExperiment-method                 6.409  0.259  11.281
SFE-transform                                         5.382  0.526   8.224
crop                                                  5.355  0.147   7.782
readVizgen                                            5.185  0.058   7.526
SFE-image                                             4.919  0.160   9.020
readCosMX                                             4.370  0.087   7.202
getParams                                             3.829  0.075   6.646
colFeatureData                                        3.639  0.180   6.116
annotOp                                               2.567  0.655   5.502
SpatialFeatureExperiment-subset                       2.808  0.308   5.960
annotSummary                                          2.810  0.215   5.304
annotPred                                             2.599  0.391   5.267
annotGeometries                                       2.494  0.355   5.597
bbox-SpatialFeatureExperiment-method                  2.667  0.143   5.076
unit-SpatialFeatureExperiment-method                  2.723  0.047   5.037
show-SpatialFeatureExperiment-method                  2.554  0.068   5.894
sampleIDs                                             2.414  0.059   5.225
* 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:
  Backtrace:
      ▆
   1. ├─sfe1[, rep(FALSE, ncol(sfe1))] at test-subset.R:198:5
   2. └─sfe1[, rep(FALSE, ncol(sfe1))]
   3.   └─SpatialFeatureExperiment::`rowGeometries<-`(...)
   4.     └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
  ── Error ('test-utils.R:56:1'): (code run outside of `test_that()`) ────────────
  Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
  Backtrace:
      ▆
   1. └─SFEData::XeniumOutput("v1", file_path = "xenium_test") at test-utils.R:56:1
  
  [ FAIL 10 | WARN 0 | SKIP 2 | PASS 784 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.


Installation output

SpatialFeatureExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL SpatialFeatureExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)

Tests output

SpatialFeatureExperiment.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SpatialFeatureExperiment)

Attaching package: 'SpatialFeatureExperiment'

The following object is masked from 'package:base':

    scale

> 
> test_check("SpatialFeatureExperiment")
Linking to GEOS 3.9.0, GDAL 3.7.0, 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

Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'ggplot2'

The following object is masked from 'package:SpatialFeatureExperiment':

    unit

Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx 
>>> 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

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx 
>>> 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`
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
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
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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> Reading '.hdf5' files..
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/hdf5s_micron_space.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> Reading '.hdf5' files..
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/multi/vizgen_cellbound/cell_boundaries.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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/small/vizgen_cellbound/cell_boundaries.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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/polyT/vizgen_cellbound/cell_boundaries.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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound_Cellpose 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound_Cellpose/Cellpose/cellpose_micron_space.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/empty/vizgen_cellbound/cell_boundaries.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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> 2 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cell_boundaries.parquet
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound/cool_cell_boundaries.parquet
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/test_spots/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
>>> Total of 26 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
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound 
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/vizgen_test/vizgen_cellbound 
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/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 /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx 
>>> 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`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx 
>>> 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 no transcript detected or `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 no transcript detected or `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`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx 
>>> 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
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx 
>>> 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 no transcript detected or `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 no transcript detected or `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 no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx 
>>> 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
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
[ FAIL 10 | WARN 0 | SKIP 2 | PASS 784 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test-read.R:627:5'
• empty test (1): 'test-read.R:637:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-geometry_operation.R:139:5'): When a sample is removed by cropping ──
Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object.
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-geometry_operation.R:139:5
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. └─SpatialFeatureExperiment::crop(sfe_visium, m)
  8.   ├─x[, preds]
  9.   └─x[, preds]
 10.     └─SpatialFeatureExperiment::`rowGeometries<-`(...)
 11.       └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
── Error ('test-geometry_operation.R:319:5'): bbox when 0 rows or columns ──────
Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object.
Backtrace:
    ▆
 1. ├─sfe_visium[, logical(0)] at test-geometry_operation.R:319:5
 2. └─sfe_visium[, logical(0)]
 3.   └─SpatialFeatureExperiment::`rowGeometries<-`(...)
 4.     └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
── Error ('test-geometry_operation.R:531:5'): When no cells/spots left after cropping ──
Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object.
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test-geometry_operation.R:531:5
  2. │ └─testthat:::expect_condition_matching(...)
  3. │   └─testthat:::quasi_capture(...)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  7. └─SpatialFeatureExperiment::crop(sfe, bbox0)
  8.   ├─x[, preds]
  9.   └─x[, preds]
 10.     └─SpatialFeatureExperiment::`rowGeometries<-`(...)
 11.       └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
── Error ('test-geometry_operation.R:869:1'): (code run outside of `test_that()`) ──
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
    ▆
 1. └─SFEData::XeniumOutput(file_path = "xenium_test") at test-geometry_operation.R:869:1
── Error ('test-image.R:16:1'): (code run outside of `test_that()`) ────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
    ▆
 1. └─SFEData::XeniumOutput("v1", file_path = "xenium_test") at test-image.R:16:1
── Error ('test-read.R:434:5'): Format MERFISH transcript spots for colGeometries ──
<Rcpp::exception/C++Error/error/condition>
Error: Cannot open "/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cg_vizgen/vizgen_cellbound/tx_in_cells/NCAM1_spots.parquet"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
Backtrace:
    ▆
 1. ├─sf::st_read(fn) at test-read.R:434:5
 2. └─sf:::st_read.character(fn)
 3.   └─sf:::CPL_read_ogr(...)
── Error ('test-read.R:606:5'): Format CosMX spots for colGeometry, multiple z-planes ──
<Rcpp::exception/C++Error/error/condition>
Error: Cannot open "/home/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/cosmx_test/cosmx/tx_spots/6330403K07Rik_spots_z0.parquet"; The source could be corrupt or not supported. See `st_drivers()` for a list of supported formats.
Backtrace:
    ▆
 1. ├─sf::st_read(fn) at test-read.R:606:5
 2. └─sf:::st_read.character(fn)
 3.   └─sf:::CPL_read_ogr(...)
── Error ('test-subset.R:186:5'): Returning 0 columns ──────────────────────────
Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object.
Backtrace:
    ▆
 1. ├─sfe1[, integer(0)] at test-subset.R:186:5
 2. └─sfe1[, integer(0)]
 3.   └─SpatialFeatureExperiment::`rowGeometries<-`(...)
 4.     └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
── Error ('test-subset.R:198:5'): Still works when using logical vector of all FALSE ──
Error in `.check_sample_id(x, sample_id, one = FALSE)`: None of the samples are present in the SFE object.
Backtrace:
    ▆
 1. ├─sfe1[, rep(FALSE, ncol(sfe1))] at test-subset.R:198:5
 2. └─sfe1[, rep(FALSE, ncol(sfe1))]
 3.   └─SpatialFeatureExperiment::`rowGeometries<-`(...)
 4.     └─SpatialFeatureExperiment::.check_sample_id(x, sample_id, one = FALSE)
── Error ('test-utils.R:56:1'): (code run outside of `test_that()`) ────────────
Error in `names(fn) <- datasets`: 'names' attribute [2] must be the same length as the vector [1]
Backtrace:
    ▆
 1. └─SFEData::XeniumOutput("v1", file_path = "xenium_test") at test-utils.R:56:1

[ FAIL 10 | WARN 0 | SKIP 2 | PASS 784 ]
Error: Test failures
Execution halted

Example timings

SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings

nameusersystemelapsed
SFE-image4.9190.1609.020
SFE-transform5.3820.5268.224
SpatRasterImage000
SpatialFeatureExperiment-coercion3.9100.1904.108
SpatialFeatureExperiment-subset2.8080.3085.960
SpatialFeatureExperiment0.9920.0781.073
addVisiumSpotPoly3.7260.1523.886
annotGeometries2.4940.3555.597
annotOp2.5670.6555.502
annotPred2.5990.3915.267
annotSummary2.8100.2155.304
bbox-SpatialFeatureExperiment-method2.6670.1435.076
bbox_center000
cbind-SpatialFeatureExperiment-method 6.409 0.25911.281
changeSampleIDs2.5760.1244.971
colFeatureData3.6390.1806.116
colGeometries2.5800.0724.932
crop5.3550.1477.782
df2sf0.0130.0090.024
dimGeometries 8.372 0.17513.128
findSpatialNeighbors-SpatialFeatureExperiment-method 6.837 0.12711.545
findVisiumGraph 6.881 0.17711.635
formatTxSpots20.987 1.26326.859
getParams3.8290.0756.646
localResults1.9210.0001.926
read10xVisiumSFE3.8170.0123.850
readCosMX4.3700.0877.202
readVizgen5.1850.0587.526
readXenium000
removeEmptySpace 9.782 0.26012.799
rowGeometries000
sampleIDs2.4140.0595.225
saveRDS-SpatialFeatureExperiment-method3.3750.0233.404
show-SpatialFeatureExperiment-method2.5540.0685.894
spatialGraphs 7.196 0.12011.876
st_any_pred0.0340.0000.034
unit-SpatialFeatureExperiment-method2.7230.0475.037
updateObject2.5760.0284.871