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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialFeatureExperiment.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SpatialFeatureExperiment_1.6.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SpatialFeatureExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SpatialFeatureExperiment' version '1.6.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SpatialFeatureExperiment' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::disableValidity' 'SpatialExperiment:::.get_img_idx'
  'spdep:::minmax.listw'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.no_raw_bytes: no visible binding for global variable 'xoa_version'
.no_raw_bytes: no visible binding for global variable 'major_version'
.no_raw_bytes: no visible binding for global variable 'minor_version'
.no_raw_bytes: no visible binding for global variable
  'instrument_version'
addTxTech: no visible binding for global variable 'gene_col'
addTxTech: no visible binding for global variable 'cell_col'
addTxTech: no visible binding for global variable 'fn'
formatTxTech: no visible binding for global variable 'gene_col'
formatTxTech: no visible binding for global variable 'cell_col'
formatTxTech: no visible binding for global variable 'fn'
readXenium: no visible binding for global variable 'xoa_version'
readXenium: no visible binding for global variable 'major_version'
readXenium: no visible binding for global variable 'minor_version'
readXenium: no visible binding for global variable 'instrument_version'
Undefined global functions or variables:
  cell_col fn gene_col instrument_version major_version minor_version
  xoa_version
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                      user system elapsed
formatTxSpots                                        21.20   1.96   25.45
Img-set-SpatialExperiment-method                     17.39   3.02   21.48
readXenium                                           10.54   0.69   11.68
removeEmptySpace                                     10.00   0.74   14.24
rowGeometries                                         9.46   0.64   10.75
findVisiumGraph                                       8.23   0.40    8.78
dimGeometries                                         7.75   0.69    8.54
spatialGraphs                                         6.97   0.64    7.73
findSpatialNeighbors-SpatialFeatureExperiment-method  6.82   0.53    7.50
cbind-SpatialFeatureExperiment-method                 5.93   0.59    7.00
readVizgen                                            4.53   0.29    5.04
getPixelSize                                          3.56   0.50    5.39
* 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:
  
  ── Failure ('test-read.R:535:5'): readCosMX, split z, split cell compartments ──
  time_note > time_check is not TRUE
  
  `actual`:   <NA>
  `expected`: TRUE
  ── Failure ('test-read.R:536:5'): readCosMX, split z, split cell compartments ──
  rowGeometryNames(sfe) (`actual`) and rgns[1:4] (`expected`) don't have the same values.
  * Only in `expected`: "txSpots"
  * Only in `actual`: "Nuclear_z0", "None_z0", "Membrane_z0", "Cytoplasm_z0"
  
  
  [ FAIL 17 | WARN 1 | SKIP 3 | PASS 1065 ]
  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
  'F:/biocbuild/bbs-3.19-bioc/meat/SpatialFeatureExperiment.Rcheck/00check.log'
for details.