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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MatrixQCvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MatrixQCvis_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MatrixQCvis.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MatrixQCvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MatrixQCvis’ version ‘1.4.0’
* 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 ‘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:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MatrixQCvis
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘MatrixQCvis’ ...
** using staged installation
** R
** 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 (MatrixQCvis)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
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 0.0003020955 
... Procrustes: rmse 0.0568434  max resid 0.07508257 
*** Best solution was not repeated -- 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 9.767372e-05 
... Procrustes: rmse 0.003267177  max resid 0.004039734 
... 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 0.0002348296 
... Procrustes: rmse 0.003606683  max resid 0.004441825 
... 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 9.86778e-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 9.894488e-05 
... Procrustes: rmse 0.008297871  max resid 0.009269218 
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 
*** Best solution was not repeated -- 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 456 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 456 ]
> 
> proc.time()
   user  system elapsed 
 57.325   1.426  58.822