##############################################################################
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###
### 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CATALYST.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.24.0’
* 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 R 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.cluster_cols’
* 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 ... 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
plotPbExprs      15.770  0.267  20.982
plotMultiHeatmap 15.290  0.220  22.837
plotDiffHeatmap  14.855  0.321  23.255
plotDR           12.689  0.203  19.575
sce2fcs          12.040  0.327  19.027
plotExprHeatmap  10.994  0.220  17.207
plotClusterExprs  8.412  0.167  12.780
pbMDS             7.909  0.199  12.089
plotAbundances    7.671  0.136  11.497
plotFreqHeatmap   7.473  0.162  11.930
plotCodes         7.430  0.148  11.604
mergeClusters     7.092  0.167  11.018
clrDR             7.003  0.171  10.932
SCE-accessors     6.690  0.259  10.691
compCytof         6.629  0.161  10.176
plotMahal         6.316  0.108  10.209
filterSCE         6.041  0.150   9.330
cluster           5.808  0.149   8.780
extractClusters   5.381  0.167   8.381
plotSpillmat      5.364  0.122   8.373
plotScatter       5.147  0.134   8.069
runDR             5.035  0.056   7.869
estCutoffs        4.812  0.091   6.376
plotYields        4.740  0.086   7.419
adaptSpillmat     4.664  0.142   7.454
plotExprs         4.563  0.070   7.122
computeSpillmat   4.449  0.105   5.898
applyCutoffs      3.772  0.070   5.878
* 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 735 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/meat/CATALYST.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CATALYST
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘CATALYST’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (CATALYST)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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.

> library(testthat)
> library(CATALYST)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("CATALYST")
[ FAIL 6 | WARN 1 | SKIP 0 | PASS 735 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plotDiffHeatmap.R:36:5'): plotDiffHeatmap() - DA ─────────────
all(colSums(y) == 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_plotMultiHeatmap.R:26:5'): plotMultiHeatmap() - hm2 = 'abundances' ──
all(colSums(y) == 1) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Failure ('test_plotMultiHeatmap.R:43:5'): plotMultiHeatmap() - hm2 = 'state' ──
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 735 ]
Error: Test failures
Execution halted