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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MatrixQCvis.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MatrixQCvis_1.3.4.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MatrixQCvis.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MatrixQCvis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MatrixQCvis' version '1.3.4'
* 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 whether package 'MatrixQCvis' 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 ... 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 ... 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 files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: OK

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MatrixQCvis
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MatrixQCvis' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MatrixQCvis'
    finding HTML links ... done
    ECDF                                    html  
    MAplot                                  html  
    MAvalues                                html  
    barplotSamplesMeasuredMissing           html  
    batchCorrectionAssay                    html  
    biocrates                               html  
    createBoxplot                           html  
    createDfFeature                         html  
    cv                                      html  
    cvFeaturePlot                           html  
    distSample                              html  
    distShiny                               html  
    driftPlot                               html  
    explVar                                 html  
    extractComb                             html  
    featurePlot                             html  
    histFeature                             html  
    histFeatureCategory                     html  
    hist_sample                             html  
    hist_sample_num                         html  
    hoeffDPlot                              html  
    hoeffDValues                            html  
    imputeAssay                             html  
    maxQuant                                html  
    measuredCategory                        html  
    mosaic                                  html  
    normalizeAssay                          html  
    ordination                              html  
    ordinationPlot                          html  
    permuteExplVar                          html  
    plotCV                                  html  
    plotPCALoadings                         html  
    plotPCAVar                              html  
    plotPCAVarPvalue                        html  
    samplesMeasuredMissing                  html  
    shinyQC                                 html  
    spectronaut                             html  
    sumDistSample                           html  
    tblPCALoadings                          html  
    transformAssay                          html  
    upsetCategory                           html  
    volcanoPlot                             html  
** 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 (MatrixQCvis)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ToxicoGx' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(MatrixQCvis)
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, 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 objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

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

Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    slice

The following object is masked from 'package:S4Vectors':

    rename

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

    filter

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

    layout

Loading required package: shiny
> testthat::test_check("MatrixQCvis")
Run 0 stress 8.265989e-05 
Run 1 stress 0.169102 
Run 2 stress 8.992935e-05 
... Procrustes: rmse 0.00239228  max resid 0.003134234 
... Similar to previous best
Run 3 stress 9.700943e-05 
... Procrustes: rmse 0.05868483  max resid 0.07203161 
Run 4 stress 0.0001436887 
... Procrustes: rmse 0.005626332  max resid 0.007460659 
Run 5 stress 0.0001062862 
... Procrustes: rmse 0.007305057  max resid 0.009562478 
Run 6 stress 9.877636e-05 
... Procrustes: rmse 0.02888586  max resid 0.02977172 
Run 7 stress 0.0001982466 
... Procrustes: rmse 0.007573268  max resid 0.009738113 
Run 8 stress 0.0002680068 
... Procrustes: rmse 0.002687366  max resid 0.003711859 
... Similar to previous best
Run 9 stress 0.0003167605 
... Procrustes: rmse 0.004636575  max resid 0.006328334 
... Similar to previous best
Run 10 stress 0.0002987005 
... Procrustes: rmse 0.004408102  max resid 0.005943395 
... Similar to previous best
Run 11 stress 9.790087e-05 
... Procrustes: rmse 0.007593141  max resid 0.009525576 
Run 12 stress 0.0001818735 
... Procrustes: rmse 0.004827114  max resid 0.006366064 
... Similar to previous best
Run 13 stress 0.0002314656 
... Procrustes: rmse 0.002967181  max resid 0.004197936 
... Similar to previous best
Run 14 stress 7.9935e-05 
... New best solution
... Procrustes: rmse 0.05869899  max resid 0.07201246 
Run 15 stress 8.631928e-05 
... Procrustes: rmse 0.05902824  max resid 0.07539873 
Run 16 stress 9.957121e-05 
... Procrustes: rmse 0.05775399  max resid 0.07410335 
Run 17 stress 0.000272693 
... Procrustes: rmse 0.05773292  max resid 0.07502263 
Run 18 stress 9.846488e-05 
... Procrustes: rmse 0.06236186  max resid 0.09219349 
Run 19 stress 9.59976e-05 
... Procrustes: rmse 0.05841065  max resid 0.07896578 
Run 20 stress 0.0003066203 
... Procrustes: rmse 0.05683508  max resid 0.07507448 
*** No convergence -- monoMDS stopping criteria:
     1: no. of iterations >= maxit
     9: stress < smin
    10: scale factor of the gradient < sfgrmin
Run 0 stress 8.265989e-05 
Run 1 stress 0.169102 
Run 2 stress 0.0003007226 
... Procrustes: rmse 0.005074216  max resid 0.006885082 
Run 3 stress 9.531511e-05 
... Procrustes: rmse 0.003267165  max resid 0.004039282 
... Similar to previous best
Run 4 stress 0.0001911927 
... Procrustes: rmse 0.002441307  max resid 0.003514601 
... Similar to previous best
Run 5 stress 0.0002105326 
... Procrustes: rmse 0.00521649  max resid 0.00695519 
Run 6 stress 8.128315e-05 
... New best solution
... Procrustes: rmse 0.002638155  max resid 0.003297701 
... Similar to previous best
Run 7 stress 0.0001050818 
... Procrustes: rmse 0.006610891  max resid 0.008523544 
Run 8 stress 0.0002020997 
... Procrustes: rmse 0.006494124  max resid 0.00840103 
Run 9 stress 9.387056e-05 
... Procrustes: rmse 0.00700665  max resid 0.009042353 
Run 10 stress 0.0002430134 
... Procrustes: rmse 0.005659323  max resid 0.007186489 
Run 11 stress 0.0001936404 
... Procrustes: rmse 0.005619137  max resid 0.007215792 
Run 12 stress 0.0002397795 
... Procrustes: rmse 0.003609393  max resid 0.004453447 
... Similar to previous best
Run 13 stress 0.000268075 
... Procrustes: rmse 0.004634287  max resid 0.006037192 
... Similar to previous best
Run 14 stress 0.0001703978 
... Procrustes: rmse 0.00636042  max resid 0.008340336 
Run 15 stress 9.867777e-05 
... Procrustes: rmse 0.006722358  max resid 0.008694583 
Run 16 stress 0.0001456857 
... Procrustes: rmse 0.002822979  max resid 0.003860954 
... Similar to previous best
Run 17 stress 9.894459e-05 
... Procrustes: rmse 0.008297871  max resid 0.009269219 
Run 18 stress 8.097499e-05 
... New best solution
... Procrustes: rmse 0.05520127  max resid 0.06685365 
Run 19 stress 9.611423e-05 
... Procrustes: rmse 0.05373027  max resid 0.06966406 
Run 20 stress 9.998435e-05 
... Procrustes: rmse 0.05314911  max resid 0.06979144 
*** No convergence -- monoMDS stopping criteria:
     2: no. of iterations >= maxit
     8: stress < smin
    10: scale factor of the gradient < sfgrmin
[1] 302.7832
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 457 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 457 ]
> 
> proc.time()
   user  system elapsed 
  26.96    1.28   28.23