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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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CATALYST.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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           15.196  1.077  16.913
plotMultiHeatmap 14.901  0.837  18.213
plotPbExprs      14.636  0.823  17.599
plotDiffHeatmap  12.702  0.869  15.589
sce2fcs          11.139  1.028  13.786
plotExprHeatmap  10.926  0.818  13.366
SCE-accessors     8.435  1.273  10.036
plotClusterExprs  8.031  1.383   9.673
plotFreqHeatmap   7.554  1.152   9.792
clrDR             6.802  1.126   8.353
runDR             7.220  0.059   8.200
plotCodes         6.183  0.958   7.369
cluster           5.915  0.948   7.113
mergeClusters     6.113  0.709   7.016
plotAbundances    6.324  0.491   7.030
extractClusters   5.468  1.251   6.977
pbMDS             6.062  0.599   6.795
compCytof         5.976  0.329   6.497
filterSCE         5.007  0.967   6.162
plotMahal         5.706  0.116   6.624
estCutoffs        5.494  0.188   5.918
plotScatter       4.999  0.155   5.808
plotSpillmat      4.777  0.227   5.761
plotYields        4.372  0.195   5.156
* 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.

##############################################################################
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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/4.4-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> 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, 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 740 ]

══ 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 740 ]
Error: Test failures
Execution halted