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### Running command:
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###   /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_1.8.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpatialFeatureExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SpatialFeatureExperiment’ version ‘1.8.6’
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::disableValidity’ ‘spdep:::minmax.listw’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.seu_to_sfe: warning in do.call(setdiff, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe: warning in do.call(intersect, arg = assays_n): partial
  argument match of 'arg' to 'args'
.seu_to_sfe : <anonymous>: warning in do.call(setdiff, arg = assays_n):
  partial argument match of 'arg' to 'args'
.filter_polygons: no visible binding for global variable ‘ID_row’
.no_raw_bytes: no visible binding for global variable ‘xoa_version’
.no_raw_bytes: no visible binding for global variable ‘major_version’
.no_raw_bytes: no visible binding for global variable ‘minor_version’
.no_raw_bytes: no visible binding for global variable
  ‘instrument_version’
.read10xVisium: no visible global function definition for
  ‘spatialCoordsNames<-’
addTxTech: no visible binding for global variable ‘gene_col’
addTxTech: no visible binding for global variable ‘cell_col’
addTxTech: no visible binding for global variable ‘fn’
aggregateTx: no visible global function definition for ‘tail’
aggregateTxTech: no visible binding for global variable ‘gene_col’
aggregateTxTech: no visible binding for global variable ‘cell_col’
aggregateTxTech: no visible binding for global variable ‘fn’
aggregateTxTech: no visible binding for global variable ‘xoa_version’
aggregateTxTech: no visible binding for global variable ‘major_version’
aggregateTxTech: no visible binding for global variable ‘minor_version’
aggregateTxTech: no visible binding for global variable
  ‘instrument_version’
findVisiumHDGraph: no visible binding for global variable ‘..cols’
formatTxTech: no visible binding for global variable ‘gene_col’
formatTxTech: no visible binding for global variable ‘cell_col’
formatTxTech: no visible binding for global variable ‘fn’
readVizgen: no visible binding for global variable ‘img_df’
readXenium: no visible binding for global variable ‘xoa_version’
readXenium: no visible binding for global variable ‘major_version’
readXenium: no visible binding for global variable ‘minor_version’
readXenium: no visible binding for global variable ‘instrument_version’
readXenium: no visible binding for global variable ‘img_df’
Undefined global functions or variables:
  ..cols ID_row cell_col fn gene_col img_df instrument_version
  major_version minor_version spatialCoordsNames<- tail xoa_version
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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                                        22.337  1.317  25.388
Img-set-SpatialExperiment-method                     19.684  1.747  21.239
readXenium                                           15.507  0.717  15.835
rowGeometries                                        12.494  0.680  13.755
removeEmptySpace                                     10.920  0.402  12.335
spatialGraphs                                        10.176  0.371  12.154
dimGeometries                                         9.522  0.381  11.595
cbind-SpatialFeatureExperiment-method                 9.483  0.398  11.444
findVisiumGraph                                       7.810  0.386   9.980
formatTxTech                                          7.316  0.515   7.699
findSpatialNeighbors-SpatialFeatureExperiment-method  7.163  0.404   9.166
getPixelSize                                          6.210  0.350   6.840
crop                                                  5.917  0.218   6.954
readVizgen                                            5.694  0.266   6.243
SFE-transform                                         5.542  0.212   6.548
updateObject                                          5.285  0.185   6.265
annotSummary                                          4.535  0.185   5.516
bbox-SpatialFeatureExperiment-method                  4.255  0.185   5.236
annotPred                                             4.241  0.185   5.190
annotOp                                               4.207  0.178   5.141
getParams                                             4.085  0.246   5.498
changeSampleIDs                                       4.142  0.187   5.092
* 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:
    'test-read.R:158:5', 'test-read.R:168:5', 'test-read.R:175:5',
    'test-read.R:187:5'
  • gdalParquetAvailable() is not TRUE (3): 'test-formatTxSpots.R:113:5',
    'test-formatTxSpots.R:140:5', 'test-formatTxSpots.R:157:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-formatTxSpots.R:13:5'): Read MERFISH transcript spots into rowGeometries ──
  sum(v$mosaic_PolyT_z3 < 30, na.rm = TRUE) < 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 1256 ]
  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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log’
for details.