R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 446 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 446 ]
> 
> proc.time()
   user  system elapsed 
  35.04    1.60   36.62 

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 446 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 446 ]
> 
> proc.time()
   user  system elapsed 
  38.54    0.75   39.32