Multiple platform build/check report for BioC 3.11 - CHECK report for evaluomeR on tokay2

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CHECK report for evaluomeR on tokay2

This page was generated on 2020-10-17 11:56:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE evaluomeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.

evaluomeR 1.4.0
José Antonio Bernabé-Díaz

Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)

URL: https://git.bioconductor.org/packages/evaluomeR

Branch: RELEASE_3_11

Last Commit: 6d2d310

Last Changed Date: 2020-04-27 15:25:05 -0400 (Mon, 27 Apr 2020)

malbec2

Linux (Ubuntu 18.04.4 LTS) / x86_64

tokay2

Windows Server 2012 R2 Standard / x64

[ OK ]

machv2

macOS 10.14.6 Mojave / x86_64

Summary

Package: evaluomeR

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:evaluomeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings evaluomeR_1.4.0.tar.gz

StartedAt: 2020-10-17 03:55:49 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:01:54 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 365.0 seconds

RetCode: 0

Status: OK

CheckDir: evaluomeR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:evaluomeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings evaluomeR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/evaluomeR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'evaluomeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'evaluomeR' 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 whether package 'evaluomeR' 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
stabilityRange  4.2   0.28    5.02
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
stabilityRange 4.04   0.16   10.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testAll.R'
  Running 'testAnalysis.R'
 OK
** running tests for arch 'x64' ...
  Running 'testAll.R'
  Running 'testAnalysis.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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/evaluomeR.Rcheck/00check.log'
for details.

Installation output

evaluomeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/evaluomeR_1.4.0.tar.gz && rm -rf evaluomeR.buildbin-libdir && mkdir evaluomeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=evaluomeR.buildbin-libdir evaluomeR_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL evaluomeR_1.4.0.zip && rm evaluomeR_1.4.0.tar.gz evaluomeR_1.4.0.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 94634  100 94634    0     0  1457k      0 --:--:-- --:--:-- --:--:-- 1621k

install for i386

* installing *source* package 'evaluomeR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
Loading required namespace: evaluomeR
*** installing help indices
  converting help for package 'evaluomeR'
    finding HTML links ... done
    bioMetrics                              html  
    getDataQualityRange                     html  
    finding level-2 HTML links ... done

    getOptimalKValue                        html  
    metricsCorrelations                     html  
    ontMetrics                              html  
    plotMetricsBoxplot                      html  
    plotMetricsCluster                      html  
    plotMetricsClusterComparison            html  
    plotMetricsMinMax                       html  
    plotMetricsViolin                       html  
    quality                                 html  
    qualityRange                            html  
    qualitySet                              html  
    rnaMetrics                              html  
    stability                               html  
    stabilityRange                          html  
    stabilitySet                            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 'evaluomeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'evaluomeR' as evaluomeR_1.4.0.zip
* DONE (evaluomeR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'evaluomeR' successfully unpacked and MD5 sums checked

Tests output

evaluomeR.Rcheck/tests_i386/testAll.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
> 
> data("rnaMetrics")
> 
> dataFrame <- stability(data=rnaMetrics, k=2, bs=100, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,4), bs=20, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> dataFrame <- stabilitySet(data=rnaMetrics, k.set=c(2,3,4), bs=20, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> 
> dataFrame <- quality(data=rnaMetrics, k=3, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 3
Processing metric: DegFact(2)
	Calculation of k = 3
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,4), getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> assay(getDataQualityRange(dataFrame, 2), 1)
  Metric    Cluster_1_SilScore  Cluster_2_SilScore  Avg_Silhouette_Width
1 "RIN"     "0.431069592245246" "0.803182811595014" "0.61712620192013"  
2 "DegFact" "0.728789163508571" "0.415236312384011" "0.630803897532146" 
  Cluster_1_Size Cluster_2_Size
1 "8"            "8"           
2 "11"           "5"           
> dataFrame1 <- qualitySet(data=rnaMetrics, k.set=c(2,3,4), getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> 
> 
> dataFrame <- metricsCorrelations(data=rnaMetrics, getImages = FALSE, margins = c(4,4,11,10))
> assay(dataFrame, 1)
               RIN    DegFact
RIN      1.0000000 -0.9744685
DegFact -0.9744685  1.0000000
> 
> 
> proc.time()
   user  system elapsed 
   9.06    0.81   11.31

evaluomeR.Rcheck/tests_x64/testAll.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
> 
> data("rnaMetrics")
> 
> dataFrame <- stability(data=rnaMetrics, k=2, bs=100, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,4), bs=20, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> dataFrame <- stabilitySet(data=rnaMetrics, k.set=c(2,3,4), bs=20, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> 
> dataFrame <- quality(data=rnaMetrics, k=3, getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 3
Processing metric: DegFact(2)
	Calculation of k = 3
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,4), getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> assay(getDataQualityRange(dataFrame, 2), 1)
  Metric    Cluster_1_SilScore  Cluster_2_SilScore  Avg_Silhouette_Width
1 "RIN"     "0.431069592245246" "0.803182811595014" "0.61712620192013"  
2 "DegFact" "0.728789163508571" "0.415236312384011" "0.630803897532146" 
  Cluster_1_Size Cluster_2_Size
1 "8"            "8"           
2 "11"           "5"           
> dataFrame1 <- qualitySet(data=rnaMetrics, k.set=c(2,3,4), getImages = FALSE)
Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
> 
> 
> dataFrame <- metricsCorrelations(data=rnaMetrics, getImages = FALSE, margins = c(4,4,11,10))
> assay(dataFrame, 1)
               RIN    DegFact
RIN      1.0000000 -0.9744685
DegFact -0.9744685  1.0000000
> 
> 
> proc.time()
   user  system elapsed 
   9.25    0.42   11.01

evaluomeR.Rcheck/tests_i386/testAnalysis.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
> 
> data("rnaMetrics")
> plotMetricsMinMax(rnaMetrics)
There were 17 warnings (use warnings() to see them)
> plotMetricsBoxplot(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged. Use `variable` instead. 
2: Use of `data.melt$value` is discouraged. Use `value` instead. 
> plotMetricsCluster(rnaMetrics)
> plotMetricsViolin(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged. Use `variable` instead. 
2: Use of `data.melt$value` is discouraged. Use `value` instead. 
3: Use of `data.melt$variable` is discouraged. Use `variable` instead. 
4: Use of `data.melt$value` is discouraged. Use `value` instead. 
> 
> stabilityData <- stabilityRange(data=rnaMetrics, k.range=c(3,4), bs=20, getImages = FALSE, seed=100)
Processing metric: RIN(1)
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 3
	Calculation of k = 4
> qualityData <- qualityRange(data=rnaMetrics, k.range=c(3,4), getImages = FALSE, seed=100)
Processing metric: RIN(1)
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 3
	Calculation of k = 4
> 
> kOptTable <- getOptimalKValue(stabilityData, qualityData, k.range=c(3,4))
Processing metric:  RIN 
	Maximum stability and quality values matches the same K value: ' 3 '
Processing metric:  DegFact 
	Maximum stability and quality values matches the same K value: ' 3 '
> kOptTable
        Stability_max_k Stability_max_k_stab Stability_max_k_qual Quality_max_k
RIN                   3            0.8901389            0.6278294             3
DegFact               3            1.0000000            0.7371912             3
        Quality_max_k_stab Quality_max_k_qual Global_optimal_k
RIN              0.8901389          0.6278294                3
DegFact          1.0000000          0.7371912                3
> 
> 
> df = assay(rnaMetrics)
> k.vector1=rep(5,length(colnames(df))-1)
> k.vector2=rep(2,length(colnames(df))-1)
> plotMetricsClusterComparison(df, k.vector1, k.vector2)
> 
> proc.time()
   user  system elapsed 
   8.93    0.84   10.17

evaluomeR.Rcheck/tests_x64/testAnalysis.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(evaluomeR)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Loading required package: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
> 
> data("rnaMetrics")
> plotMetricsMinMax(rnaMetrics)
There were 17 warnings (use warnings() to see them)
> plotMetricsBoxplot(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged. Use `variable` instead. 
2: Use of `data.melt$value` is discouraged. Use `value` instead. 
> plotMetricsCluster(rnaMetrics)
> plotMetricsViolin(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged. Use `variable` instead. 
2: Use of `data.melt$value` is discouraged. Use `value` instead. 
3: Use of `data.melt$variable` is discouraged. Use `variable` instead. 
4: Use of `data.melt$value` is discouraged. Use `value` instead. 
> 
> stabilityData <- stabilityRange(data=rnaMetrics, k.range=c(3,4), bs=20, getImages = FALSE, seed=100)
Processing metric: RIN(1)
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 3
	Calculation of k = 4
> qualityData <- qualityRange(data=rnaMetrics, k.range=c(3,4), getImages = FALSE, seed=100)
Processing metric: RIN(1)
	Calculation of k = 3
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 3
	Calculation of k = 4
> 
> kOptTable <- getOptimalKValue(stabilityData, qualityData, k.range=c(3,4))
Processing metric:  RIN 
	Maximum stability and quality values matches the same K value: ' 3 '
Processing metric:  DegFact 
	Maximum stability and quality values matches the same K value: ' 3 '
> kOptTable
        Stability_max_k Stability_max_k_stab Stability_max_k_qual Quality_max_k
RIN                   3            0.8901389            0.6278294             3
DegFact               3            1.0000000            0.7371912             3
        Quality_max_k_stab Quality_max_k_qual Global_optimal_k
RIN              0.8901389          0.6278294                3
DegFact          1.0000000          0.7371912                3
> 
> 
> df = assay(rnaMetrics)
> k.vector1=rep(5,length(colnames(df))-1)
> k.vector2=rep(2,length(colnames(df))-1)
> plotMetricsClusterComparison(df, k.vector1, k.vector2)
> 
> proc.time()
   user  system elapsed 
  12.40    0.60   13.28

Example timings

evaluomeR.Rcheck/examples_i386/evaluomeR-Ex.timings

name	user	system	elapsed
getDataQualityRange	0.87	0.08	0.95
getOptimalKValue	0.61	0.11	0.77
metricsCorrelations	0.06	0.00	0.06
plotMetricsBoxplot	0.69	0.02	0.70
plotMetricsCluster	0.33	0.00	0.33
plotMetricsClusterComparison	0.51	0.03	0.55
plotMetricsMinMax	0.47	0.00	0.47
plotMetricsViolin	1.81	0.06	1.87
quality	0.45	0.02	0.47
qualityRange	0.47	0.01	0.49
qualitySet	0.09	0.00	0.09
stability	4.08	0.24	4.61
stabilityRange	4.20	0.28	5.02
stabilitySet	0.63	0.01	0.64

evaluomeR.Rcheck/examples_x64/evaluomeR-Ex.timings

name	user	system	elapsed
getDataQualityRange	0.60	0.01	0.61
getOptimalKValue	0.59	0.02	0.78
metricsCorrelations	0.07	0.00	0.08
plotMetricsBoxplot	0.93	0.01	0.94
plotMetricsCluster	0.32	0.00	0.33
plotMetricsClusterComparison	1.24	0.02	1.25
plotMetricsMinMax	0.42	0.00	0.42
plotMetricsViolin	1.08	0.02	1.09
quality	0.42	0.06	0.49
qualityRange	0.42	0.00	0.42
qualitySet	0.10	0.01	0.11
stability	3.06	0.08	3.42
stabilityRange	4.04	0.16	10.58
stabilitySet	0.77	0.00	0.77