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###
### Running command:
###
###   /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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/microSTASIS.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.8.0’
* 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             43.398  2.275  30.911
plotmSlinesCV         42.054  2.549  30.624
iterativeClusteringCV 40.439  2.242  27.649
plotmSdynamics        18.812  1.547  15.394
plotmSscatter         17.793  1.128  14.445
iterativeClustering   17.249  1.090  13.550
plotmSheatmap         17.032  1.103  13.501
mSmetadataGroups      16.727  1.331  13.346
mSpreviz              16.732  1.320  13.169
* 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:
  [ FAIL 4 | WARN 21 | SKIP 0 | PASS 16 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plotmSdynamics.R:3:3'): plotmSdynamics output is a list for plotting a ggplot object ──
  plotmSdynamics(...) has type 'object', not 'list'.
  ── Failure ('test-plotmSheatmap.R:3:3'): plotmSheatmap output is a list for plotting a ggplot object ──
  plotmSheatmap(...) has type 'object', not 'list'.
  ── Failure ('test-plotmSlinesCV.R:3:3'): plotmSlineCV output is a list for plotting a ggplot object ──
  plotmSlinesCV(...) has type 'object', not 'list'.
  ── Failure ('test-plotmSscatter.R:3:3'): plotmSscater output is a list for plotting a ggplot with ggside extension ──
  plotmSscatter(...) has type 'object', not 'list'.
  
  [ 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-3.21-bioc/meat/microSTASIS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL microSTASIS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘microSTASIS’ ...
** this is package ‘microSTASIS’ version ‘1.8.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘pairedTimes’ with signature ‘"TreeSummarizedExperiment"’: no definition for class “TreeSummarizedExperiment”
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (microSTASIS)

R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(microSTASIS)
> 
> test_check("microSTASIS")
[ FAIL 4 | WARN 21 | SKIP 0 | PASS 16 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotmSdynamics.R:3:3'): plotmSdynamics output is a list for plotting a ggplot object ──
plotmSdynamics(...) has type 'object', not 'list'.
── Failure ('test-plotmSheatmap.R:3:3'): plotmSheatmap output is a list for plotting a ggplot object ──
plotmSheatmap(...) has type 'object', not 'list'.
── Failure ('test-plotmSlinesCV.R:3:3'): plotmSlineCV output is a list for plotting a ggplot object ──
plotmSlinesCV(...) has type 'object', not 'list'.
── Failure ('test-plotmSscatter.R:3:3'): plotmSscater output is a list for plotting a ggplot with ggside extension ──
plotmSscatter(...) has type 'object', not 'list'.

[ FAIL 4 | WARN 21 | SKIP 0 | PASS 16 ]
Error: Test failures
Execution halted