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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:microSTASIS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings microSTASIS_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/microSTASIS.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘microSTASIS/DESCRIPTION’ ... OK
* this is package ‘microSTASIS’ version ‘1.10.0’
* 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 ‘microSTASIS’ 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
Namespace in Imports field not imported from: ‘TreeSummarizedExperiment’
  All declared Imports should be used.
* 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 ... NOTE
Rd files without \alias:
  ‘microSTASIS.Rd’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
mSerrorCV             43.367  2.283  32.617
plotmSlinesCV         42.808  2.745  31.081
iterativeClusteringCV 40.689  2.235  29.206
plotmSdynamics        18.635  1.360  15.048
plotmSscatter         17.889  1.168  14.432
plotmSheatmap         17.502  1.427  14.052
iterativeClustering   17.002  0.955  13.512
mSpreviz              16.602  1.345  12.986
mSmetadataGroups      16.498  1.296  13.359
* 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:
  Actual type: "object"
  ── Failure ('test-plotmSheatmap.R:3:3'): plotmSheatmap output is a list for plotting a ggplot object ──
  Expected `plotmSheatmap(...)` to have type "list".
  Actual type: "object"
  ── Failure ('test-plotmSlinesCV.R:3:3'): plotmSlineCV output is a list for plotting a ggplot object ──
  Expected `plotmSlinesCV(...)` to have type "list".
  Actual type: "object"
  ── Failure ('test-plotmSscatter.R:3:3'): plotmSscater output is a list for plotting a ggplot with ggside extension ──
  Expected `plotmSscatter(...)` to have type "list".
  Actual type: "object"
  
  [ FAIL 4 | WARN 21 | SKIP 0 | PASS 16 ]
  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-3.22-bioc/meat/microSTASIS.Rcheck/00check.log’
for details.