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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings CATALYST_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CATALYST.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.25.0’
* 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 loading without being on the library search path ... 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
plotMultiHeatmap 20.141  0.124  20.297
plotPbExprs      19.143  0.068  19.241
plotDiffHeatmap  16.797  0.159  16.997
sce2fcs          16.062  0.068  16.159
plotDR           15.725  0.084  15.836
plotExprHeatmap  14.388  0.032  14.447
plotCodes        10.094  0.020  10.135
plotAbundances    9.867  0.048   9.936
plotClusterExprs  9.815  0.048   9.881
mergeClusters     9.757  0.044   9.827
plotFreqHeatmap   9.601  0.008   9.629
clrDR             9.396  0.060   9.475
SCE-accessors     9.252  0.143   9.416
pbMDS             9.228  0.056   9.302
filterSCE         8.439  0.027   8.486
cluster           7.917  0.044   7.977
plotMahal         7.459  0.040   7.513
compCytof         7.323  0.044   7.381
extractClusters   6.840  0.008   6.862
plotYields        6.696  0.012   6.720
estCutoffs        6.583  0.069   6.666
plotSpillmat      6.508  0.012   6.532
computeSpillmat   6.389  0.041   6.444
runDR             5.993  0.004   6.004
plotScatter       5.782  0.023   5.817
adaptSpillmat     5.670  0.088   5.769
plotExprs         5.188  0.000   5.198
* 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:
      anyMissing, rowMedians
  
  > 
  > test_check("CATALYST")
  [ FAIL 2 | WARN 20 | SKIP 0 | PASS 739 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plotting-differential.R:84:5'): pbMDS() - by = 'sample_id' ───
  `p <- pbMDS(filterSCE(x0, !sample_id %in% s))` produced warnings.
  ── Failure ('test_plotting-differential.R:97:5'): pbMDS() - by = 'cluster_id' ──
  `p <- pbMDS(y, by = "cluster_id", k = k)` produced warnings.
  
  [ FAIL 2 | WARN 20 | SKIP 0 | PASS 739 ]
  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 ...
  ‘differential.Rmd’ using ‘UTF-8’... OK
  ‘preprocessing.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/CATALYST.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL CATALYST
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 2 | WARN 20 | SKIP 0 | PASS 739 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plotting-differential.R:84:5'): pbMDS() - by = 'sample_id' ───
`p <- pbMDS(filterSCE(x0, !sample_id %in% s))` produced warnings.
── Failure ('test_plotting-differential.R:97:5'): pbMDS() - by = 'cluster_id' ──
`p <- pbMDS(y, by = "cluster_id", k = k)` produced warnings.

[ FAIL 2 | WARN 20 | SKIP 0 | PASS 739 ]
Error: Test failures
Execution halted