##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CATALYST_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.28.0’
* 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 ‘CATALYST’ 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 ... 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 ... NOTE
checkRd: (-1) plotDiffHeatmap.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotDiffHeatmap.Rd:88: Lost braces in \itemize; meant \describe ?
* 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 LazyData ... 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
plotDR           13.723  0.686  14.491
plotMultiHeatmap 12.036  1.111  13.158
plotDiffHeatmap  11.676  1.355  13.134
plotPbExprs      12.127  0.415  12.552
sce2fcs          10.204  0.716  10.937
plotExprHeatmap   9.862  0.912  10.784
SCE-accessors     7.879  0.880   8.815
pbMDS             7.771  0.509   8.307
plotClusterExprs  7.828  0.432   8.267
plotCodes         7.056  0.640   7.731
plotAbundances    6.877  0.434   7.332
runDR             7.156  0.070   7.228
clrDR             6.351  0.361   6.725
plotMahal         6.465  0.202   6.686
filterSCE         5.970  0.499   6.473
plotFreqHeatmap   5.717  0.619   6.341
plotScatter       5.970  0.147   6.124
compCytof         5.692  0.346   6.041
cluster           5.348  0.612   6.000
mergeClusters     5.617  0.291   5.951
extractClusters   5.404  0.361   5.783
computeSpillmat   4.889  0.215   5.106
* 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:
  c(y) not identical to c(ms).
  Objects equal but not identical
  ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ──
  p@ht_list[[i + 1]]@matrix not identical to meds[[i]].
  Objects equal but not identical
  ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ──
  p@ht_list[[i + 1]]@matrix not identical to meds[[i]].
  Objects equal but not identical
  ── Failure ('test_plotMultiHeatmap.R:58:9'): plotMultiHeatmap() - hm2 = specific state markers ──
  p@ht_list[[i + 1]]@matrix not identical to meds[[i]].
  Objects equal but not identical
  
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 740 ]
  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-3.19-bioc/meat/CATALYST.Rcheck/00check.log’
for details.