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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:alabaster.sfe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings alabaster.sfe_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/alabaster.sfe.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alabaster.sfe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘alabaster.sfe’ version ‘1.1.0’
* 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 ‘alabaster.sfe’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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:
  readBioFormatsImage.Rd: BioFormatsImage
  readExtImage.Rd: readImage, ExtImage
  readSpatRaster.Rd: SpatRasterImage
  saveObject-ExtImage-method.Rd: writeImage
  saveObject-SpatRaster-method.Rd: writeRaster
  saveObject-SpatialFeatureExperiment-method.Rd: colFeatureData,
    getParams
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
readBioFormatsImage 7.817  0.778   8.187
* 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:
  >>> filtering nucSeg geometries to match 16324 cells with counts > 0
  Resolution subscript out of bound, reading the lowest resolution
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.R:113:5'): Save and read single file BioFormatsImage ─────────
  imgSource(bfi2) (`actual`) not equal to normalizePath(file.path(fsave, "image.ome.tif")) (`expected`).
  
  actual vs expected
  - "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpaAJMQ9/file1c5c690a9508/bfi1/image.ome.tif"
  + "/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpaAJMQ9/file1c5c690a9508/bfi1/image.ome.tif"
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 38 ]
  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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/alabaster.sfe.Rcheck/00check.log’
for details.