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This page was generated on 2025-09-04 11:40 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 2061/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialFeatureExperiment 1.10.1  (landing page)
Lambda Moses
Snapshot Date: 2025-09-01 13:40 -0400 (Mon, 01 Sep 2025)
git_url: https://git.bioconductor.org/packages/SpatialFeatureExperiment
git_branch: RELEASE_3_21
git_last_commit: 0098d43
git_last_commit_date: 2025-05-08 12:30:20 -0400 (Thu, 08 May 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    TIMEOUT    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for SpatialFeatureExperiment on merida1

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.

raw results


Summary

Package: SpatialFeatureExperiment
Version: 1.10.1
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_1.10.1.tar.gz
StartedAt: 2025-09-02 10:52:07 -0400 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 11:32:08 -0400 (Tue, 02 Sep 2025)
EllapsedTime: 2400.7 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: SpatialFeatureExperiment.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.10.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpatialFeatureExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.seu_to_sfe: warning in do.call(setdiff, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe: warning in do.call(intersect, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe : <anonymous>: warning in do.call(setdiff, arg = assays_n):
  partial argument match of 'arg' to 'args'
.filter_polygons: no visible binding for global variable ‘gmax’
.filter_polygons: no visible binding for global variable ‘area’
.filter_polygons: no visible binding for global variable ‘name’
.filter_polygons: no visible binding for global variable ‘gi’
.filter_polygons: no visible binding for global variable ‘.N’
.filter_polygons: no visible binding for global variable ‘i’
.filter_polygons: no visible binding for global variable ‘.I’
.filter_polygons: no visible binding for global variable ‘ID_row’
findVisiumHDGraph: no visible binding for global variable ‘..cols’
Undefined global functions or variables:
  ..cols .I .N ID_row area gi gmax i name
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SpatialFeatureExperiment-coercion.Rd: DataFrame
  SpatialFeatureExperiment.Rd: DataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                          user system elapsed
Img-set-SpatialExperiment-method                        31.010  3.038  34.545
formatTxSpots                                           27.704  1.754 174.413
readXenium                                              16.538  0.818  32.164
removeEmptySpace                                        10.438  0.491 176.849
rowGeometries                                           10.261  0.614  38.057
cbind-SpatialFeatureExperiment-method                    7.354  0.446  15.315
findSpatialNeighbors-SpatialFeatureExperiment-method     7.070  0.401   8.329
findVisiumGraph                                          6.340  0.408   7.361
spatialGraphs                                            6.270  0.328   7.071
SFE-transform                                            6.192  0.392   6.910
formatTxTech                                             5.320  0.525  13.343
dimGeometries                                            5.474  0.260   6.107
readVizgen                                               4.940  0.279  14.420
colFeatureData                                           4.763  0.320  36.438
getPixelSize                                             4.424  0.476 107.215
annotPred                                                4.564  0.248   5.188
getParams                                                4.341  0.277   5.267
readCosMX                                                3.743  0.243   5.834
containsOutOfMemoryData-SpatialFeatureExperiment-method  1.739  0.036  12.071
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

SpatialFeatureExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpatialFeatureExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SpatialFeatureExperiment’ ...
** this is package ‘SpatialFeatureExperiment’ version ‘1.10.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘toSpatialFeatureExperiment’ with signature ‘"Seurat"’: no definition for class “Seurat”
Creating a generic function for ‘NROW’ from package ‘base’ in package ‘SpatialFeatureExperiment’
Creating a generic function for ‘NCOL’ from package ‘base’ in package ‘SpatialFeatureExperiment’
Creating a generic function for ‘readRDS’ from package ‘base’ in package ‘SpatialFeatureExperiment’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialFeatureExperiment)

Tests output

SpatialFeatureExperiment.Rcheck/tests/testthat.Rout


R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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 3.13.0, GDAL 3.8.5, PROJ 9.5.1; 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'arrow'

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

    type

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

    matches

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

    timestamp

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c1361cb52b/xenium2 
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c1361cb52b/vizgen_cellbound_Cellpose 
>>> Must use gene symbols as row names when adding transcript spots.
>>> Cell segmentations are found in `.parquet` file(s)
>>> Reading cell and nucleus segmentations
>>> Making MULTIPOLYGON nuclei geometries
>>> Making POLYGON cell geometries
Sanity checks on cell segmentation polygons:
>>> ..found 132 cells with (nested) polygon lists
>>> ..applying filtering
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
>>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> Must use gene symbols as row names when adding transcript spots.
>>> Preprocessed sf segmentations found
>>> Reading cell and nucleus segmentations
>>> Reading cell metadata -> `cells.parquet`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 6272 cells with counts > 0
>>> filtering nucSeg geometries to match 6158 cells with counts > 0
>>> Reading transcript coordinates
>>> Total of 116 features/genes with no transcript detected or `min_phred` < 20 are removed from SFE object
>>> To keep all features -> set `min_phred = NULL`
>>> 10X Visium data will be loaded: outs

>>> Adding spatial neighborhood graph to sample01

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /Users/biocbuild/bbs-3.21-bioc/meat/SpatialFeatureExperiment.Rcheck/tests/testthat/xenium_lr 
>>> Cell segmentations are found in `.csv` file(s)
>>> Reading cell and nucleus segmentations
>>> Making POLYGON geometries
>>> Checking polygon validity
>>> Saving geometries to parquet files
>>> Reading cell metadata -> `cells.csv`
>>> Reading h5 gene count matrix
>>> filtering cellSeg geometries to match 16324 cells with counts > 0
>>> filtering nucSeg geometries to match 16324 cells with counts > 0
Loading required package: scuttle
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    unit

Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c1127af42a/vizgen_cellbound 
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp8TmYap/file148c1127af42a/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp8TmYap/file148c1127af42a/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c115fe3faa/vizgen_cellbound 
>>> Converting transcript spots to geometry
>>> 1 `.parquet` files exist:
/private/tmp/Rtmp8TmYap/file148c115fe3faa/vizgen_cellbound/cell_boundaries.parquet
>>> using -> /private/tmp/Rtmp8TmYap/file148c115fe3faa/vizgen_cellbound/cell_boundaries.parquet
>>> Cell segmentations are found in `.parquet` file
>>> Checking polygon validity
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk

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see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c162724c74/vizgen_cellbound 
>>> Converting transcript spots to geometry
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c15958b46a/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/Rtmp8TmYap/file148c1743abe09/xenium2 
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
terra 1.8.60

Attaching package: 'terra'

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

    buffer

The following objects are masked from 'package:SummarizedExperiment':

    distance, nearest, shift, trim, values, values<-, width

The following objects are masked from 'package:GenomicRanges':

    distance, gaps, nearest, shift, trim, values, values<-, width

The following objects are masked from 'package:IRanges':

    distance, gaps, nearest, shift, trim, width

The following objects are masked from 'package:S4Vectors':

    values, values<-, width

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

    width

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

    interpolate

The following objects are masked from 'package:SpatialFeatureExperiment':

    centroids, crop, origin, rotate

The following objects are masked from 'package:testthat':

    compare, describe

see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
The downloaded files are in /private/tmp/Rtmp8TmYap/file148c11783c3ae/cosmx 
>>> Constructing cell polygons
>>> Checking polygon validity
>>> Reading transcript coordinates
>>> Converting transcript spots to geometry
>>> Writing reformatted transcript spots to disk
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache
see ?SFEData and browseVignettes('SFEData') for documentation
loading from cache

Example timings

SpatialFeatureExperiment.Rcheck/SpatialFeatureExperiment-Ex.timings

nameusersystemelapsed
Img-set-SpatialExperiment-method31.010 3.03834.545
SFE-image3.4860.2544.121
SFE-transform6.1920.3926.910
SpatRasterImage0.0000.0010.000
SpatialFeatureExperiment-coercion4.0300.1924.370
SpatialFeatureExperiment-subset3.7380.2804.560
SpatialFeatureExperiment0.9750.0171.172
addVisiumSpotPoly4.0600.1064.211
aggBboxes0.0000.0010.000
aggregate-SpatialFeatureExperiment-method0.0000.0010.001
annotGeometries3.4440.2593.956
annotOp3.6390.2334.116
annotPred4.5640.2485.188
annotSummary3.2640.2163.661
bbox-SpatialFeatureExperiment-method4.1630.2384.840
bbox_center0.0000.0000.001
cbind-SpatialFeatureExperiment-method 7.354 0.44615.315
changeSampleIDs3.3280.2163.912
colFeatureData 4.763 0.32036.438
colGeometries3.2070.2133.607
containsOutOfMemoryData-SpatialFeatureExperiment-method 1.739 0.03612.071
crop3.2070.1303.536
df2sf0.0160.0053.989
dimGeometries5.4740.2606.107
findSpatialNeighbors-SpatialFeatureExperiment-method7.0700.4018.329
findVisiumGraph6.3400.4087.361
formatTxSpots 27.704 1.754174.413
formatTxTech 5.320 0.52513.343
gdalParquetAvailable0.0020.0010.447
getParams4.3410.2775.267
getPixelSize 4.424 0.476107.215
imageIDs1.0600.0161.079
listw2sparse3.2980.2223.735
localResults2.0200.0402.199
multi_listw2sparse0.0000.0000.001
read10xVisiumSFE2.6760.0492.739
readCosMX3.7430.2435.834
readSelectTx0.0260.0020.027
readVisiumHD0.0000.0000.001
readVizgen 4.940 0.27914.420
readXenium16.538 0.81832.164
removeEmptySpace 10.438 0.491176.849
rowGeometries10.261 0.61438.057
sampleIDs1.9110.1193.058
saveRDS-SpatialFeatureExperiment-method1.8860.0313.991
show-SpatialFeatureExperiment-method2.5800.1772.978
spatialGraphs6.2700.3287.071
splitByCol0.0000.0000.001
st_any_pred0.0290.0021.830
unit-SpatialFeatureExperiment-method2.0960.1402.451
updateObject2.0270.1272.328