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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 4.4.1 (2024-06-14 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                                        20.89   1.89   26.37
Img-set-SpatialExperiment-method                     18.60   3.20   22.97
removeEmptySpace                                      9.85   0.72   14.31
rowGeometries                                         9.49   0.84   10.86
readXenium                                            9.32   0.67   10.49
dimGeometries                                         7.70   0.68    8.71
spatialGraphs                                         7.64   0.67    8.50
findVisiumGraph                                       6.44   0.84    7.52
cbind-SpatialFeatureExperiment-method                 6.70   0.48    7.92
findSpatialNeighbors-SpatialFeatureExperiment-method  6.32   0.81    7.29
formatTxTech                                          6.11   0.42    6.83
getPixelSize                                          3.53   0.57    5.67
* 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:
   10.       └─arrow::ParquetFileReader$create(dsn, ...)
   11.         └─arrow:::parquet___arrow___FileReader__OpenFile(file, props, reader_props)
  ── Error ('test-read.R:640:5'): readXenium XOA v1 flip image ───────────────────
  Error: Invalid: Parquet magic bytes not found in footer. Either the file is corrupted or this is not a parquet file.
  Backtrace:
      ▆
   1. └─SpatialFeatureExperiment::readXenium(...) at test-read.R:640:5
   2.   └─base::lapply(fn_segs, sfarrow::st_read_parquet)
   3.     └─sfarrow (local) FUN(X[[i]], ...)
   4.       └─arrow::ParquetFileReader$create(dsn, ...)
   5.         └─arrow:::parquet___arrow___FileReader__OpenFile(file, props, reader_props)
  
  [ FAIL 19 | WARN 1 | SKIP 3 | PASS 1062 ]
  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.