Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:50 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MatrixQCvis on tokay2


To the developers/maintainers of the MatrixQCvis package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MatrixQCvis.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1058/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MatrixQCvis 1.2.4  (landing page)
Thomas Naake
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MatrixQCvis
git_branch: RELEASE_3_14
git_last_commit: 9cccc5b
git_last_commit_date: 2022-04-09 05:14:53 -0400 (Sat, 09 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MatrixQCvis
Version: 1.2.4
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MatrixQCvis.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MatrixQCvis_1.2.4.tar.gz
StartedAt: 2022-04-12 22:18:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 22:24:24 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 354.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MatrixQCvis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MatrixQCvis.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MatrixQCvis_1.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MatrixQCvis.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.2.4'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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


Installation output

MatrixQCvis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MatrixQCvis_1.2.4.tar.gz && rm -rf MatrixQCvis.buildbin-libdir && mkdir MatrixQCvis.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MatrixQCvis.buildbin-libdir MatrixQCvis_1.2.4.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MatrixQCvis_1.2.4.zip && rm MatrixQCvis_1.2.4.tar.gz MatrixQCvis_1.2.4.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   99k  100   99k    0     0   517k      0 --:--:-- --:--:-- --:--:--  521k

install for i386

* 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  
    barplot_samples_memi                    html  
    batchCorrectionAssay                    html  
    biocrates                               html  
    createDfFeature                         html  
    create_boxplot                          html  
    cv                                      html  
    cvFeaturePlot                           html  
    distSample                              html  
    distShiny                               html  
    driftPlot                               html  
    explVar                                 html  
    extractComb                             html  
    featurePlot                             html  
    hist_feature                            html  
    hist_feature_category                   html  
    hist_sample                             html  
    hist_sample_num                         html  
    hoeffDPlot                              html  
    hoeffDValues                            html  
    imputeAssay                             html  
    maxQuant                                html  
    measured_category                       html  
    mosaic                                  html  
    normalizeAssay                          html  
    ordination                              html  
    ordinationPlot                          html  
    permuteExplVar                          html  
    plotCV                                  html  
    plotPCALoadings                         html  
    plotPCAVar                              html  
    plotPCAVarPvalue                        html  
    samples_memi                            html  
    shinyQC                                 html  
    sumDistSample                           html  
    tblPCALoadings                          html  
    transformAssay                          html  
    upset_category                          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

install for x64

* installing *source* package 'MatrixQCvis' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MatrixQCvis' as MatrixQCvis_1.2.4.zip
* DONE (MatrixQCvis)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MatrixQCvis' successfully unpacked and MD5 sums checked

Tests output

MatrixQCvis.Rcheck/tests_i386/testthat.Rout


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 

MatrixQCvis.Rcheck/tests_x64/testthat.Rout


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 

Example timings

MatrixQCvis.Rcheck/examples_i386/MatrixQCvis-Ex.timings

nameusersystemelapsed
ECDF0.330.000.33
MAplot0.860.020.88
MAvalues0.610.020.63
barplot_samples_memi0.370.030.40
batchCorrectionAssay0.050.000.05
biocrates000
createDfFeature000
create_boxplot0.440.000.44
cv000
cvFeaturePlot0.450.050.50
distSample0.940.040.98
distShiny000
driftPlot0.390.050.44
explVar000
extractComb0.060.000.06
featurePlot0.30.00.3
hist_feature0.120.050.17
hist_feature_category0.270.030.31
hist_sample0.160.030.19
hist_sample_num0.030.000.03
hoeffDPlot1.080.091.24
hoeffDValues0.280.000.28
imputeAssay000
maxQuant000
measured_category0.030.000.04
mosaic0.320.000.31
normalizeAssay000
ordination2.570.022.60
ordinationPlot0.160.010.17
permuteExplVar0.020.000.02
plotCV0.180.000.18
plotPCALoadings0.180.020.19
plotPCAVar0.20.00.2
plotPCAVarPvalue0.170.010.19
samples_memi0.050.000.05
shinyQC0.060.000.06
sumDistSample0.110.030.14
tblPCALoadings0.120.000.13
transformAssay0.110.000.11
upset_category0.360.000.35
volcanoPlot0.160.070.25

MatrixQCvis.Rcheck/examples_x64/MatrixQCvis-Ex.timings

nameusersystemelapsed
ECDF0.280.030.31
MAplot1.610.001.61
MAvalues0.070.010.10
barplot_samples_memi0.430.070.48
batchCorrectionAssay0.100.010.11
biocrates000
createDfFeature000
create_boxplot0.410.000.41
cv000
cvFeaturePlot0.330.030.36
distSample0.930.050.98
distShiny000
driftPlot0.420.080.50
explVar0.020.000.02
extractComb0.030.000.03
featurePlot0.20.00.2
hist_feature0.130.010.14
hist_feature_category0.270.020.28
hist_sample0.120.010.16
hist_sample_num0.030.000.03
hoeffDPlot0.880.050.92
hoeffDValues0.250.000.25
imputeAssay000
maxQuant000
measured_category0.040.000.05
mosaic0.330.000.33
normalizeAssay000
ordination3.110.003.11
ordinationPlot0.170.020.19
permuteExplVar000
plotCV0.190.000.18
plotPCALoadings0.160.030.19
plotPCAVar0.180.050.24
plotPCAVarPvalue0.180.000.17
samples_memi0.040.000.04
shinyQC0.030.000.04
sumDistSample0.140.010.15
tblPCALoadings0.130.000.13
transformAssay0.090.000.09
upset_category0.390.000.39
volcanoPlot0.180.020.20