Multiple platform build/check report for BioC 3.20 - CHECK results for evaluomeR on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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 evaluomeR on palomino4

To the developers/maintainers of the evaluomeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/evaluomeR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: evaluomeR

Version: 1.21.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:evaluomeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings evaluomeR_1.21.0.tar.gz

StartedAt: 2024-06-10 02:33:06 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 02:39:52 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 405.2 seconds

RetCode: 0

Status: OK

CheckDir: evaluomeR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:evaluomeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings evaluomeR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/evaluomeR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'evaluomeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'evaluomeR' version '1.21.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'SummarizedExperiment', 'MultiAssayExperiment', 'cluster', 'fpc',
  'randomForest', 'flexmix'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 code 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 ... NOTE
Namespace in Imports field not imported from: 'kableExtra'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'flexmix' 'randomForest'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
flemixModel: no visible global function definition for 'FLXMRglm'
flemixModel: no visible global function definition for 'stepFlexmix'
flemixModel: no visible global function definition for 'getModel'
globalMetric: no visible global function definition for 'prior'
metrics_pca: no visible global function definition for 'prcomp'
metrics_randomforest: no visible global function definition for
  'randomForest'
metrics_randomforest: no visible global function definition for 'head'
speccCBI: no visible global function definition for 'specc'
Undefined global functions or variables:
  FLXMRglm getModel head prcomp prior randomForest specc stepFlexmix
Consider adding
  importFrom("stats", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testAll.R'
  Running 'testAnalysis.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/evaluomeR.Rcheck/00check.log'
for details.

Installation output

evaluomeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL evaluomeR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* 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
** 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 (evaluomeR)

Tests output

evaluomeR.Rcheck/tests/testAll.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: 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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
Loading required package: randomForest
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    combine

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

    combine

Loading required package: flexmix
Loading required package: lattice
> 
> data("rnaMetrics")
> 
> dataFrame <- stability(data=rnaMetrics, k=4, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 4
Processing metric: DegFact(2)
	Calculation of k = 4
> dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,4), bs=20, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


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(dataFrame)
     Metric    Mean_stability_k_2  Mean_stability_k_3  Mean_stability_k_4 
[1,] "RIN"     "0.825833333333333" "0.778412698412698" "0.69625"          
[2,] "DegFact" "0.955595238095238" "0.977777777777778" "0.820833333333333"
> # Metric    Mean_stability_k_2  Mean_stability_k_3  Mean_stability_k_4
> # [1,] "RIN"     "0.825833333333333" "0.778412698412698" "0.69625"
> # [2,] "DegFact" "0.955595238095238" "0.977777777777778" "0.820833333333333"
> dataFrame <- stabilitySet(data=rnaMetrics, k.set=c(2,3,4), bs=20, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


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, cbi="kmeans", k=3, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 3
Processing metric: DegFact(2)
	Calculation of k = 3
> assay(dataFrame)
     Metric    Cluster_1_SilScore  Cluster_2_SilScore  Cluster_3_SilScore 
[1,] "RIN"     "0.420502645502646" "0.724044583696066" "0.68338517747747" 
[2,] "DegFact" "0.876516605981734" "0.643613928123002" "0.521618857725795"
     Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
[1,] "0.627829396038413"  "4"            "4"            "8"           
[2,] "0.737191191352892"  "8"            "5"            "3"           
> # Metric    Cluster_1_SilScore  Cluster_2_SilScore  Cluster_3_SilScore
> # [1,] "RIN"     "0.420502645502646" "0.724044583696066" "0.68338517747747"
> # [2,] "DegFact" "0.876516605981734" "0.643613928123002" "0.521618857725795"
> # Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
> # [1,] "0.627829396038413"  "4"            "4"            "8"
> # [2,] "0.737191191352892"  "8"            "5"            "3"
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,4), seed = 20, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


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))
  Metric    Cluster_1_SilScore  Cluster_2_SilScore  Avg_Silhouette_Width
1 "RIN"     "0.583166775069983" "0.619872562681118" "0.608402004052639" 
2 "DegFact" "0.664573423022171" "0.675315791048653" "0.666587617027136" 
  Cluster_1_Size Cluster_2_Size
1 "5"            "11"          
2 "13"           "3"           
> # Metric    Cluster_1_SilScore  Cluster_2_SilScore  Avg_Silhouette_Width Cluster_1_Size
> # 1 "RIN"     "0.583166775069983" "0.619872562681118" "0.608402004052639"  "5"
> # 2 "DegFact" "0.664573423022171" "0.675315791048653" "0.666587617027136"  "13"
> # Cluster_2_Size
> # 1 "11"
> # 2 "3"
> assay(getDataQualityRange(dataFrame, 4))
  Metric    Cluster_1_SilScore  Cluster_2_SilScore  Cluster_3_SilScore 
1 "RIN"     "0.420502645502646" "0.674226581940152" "0.433333333333333"
2 "DegFact" "0.759196481622952" "0.59496499852177"  "0.600198799385732"
  Cluster_4_SilScore  Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size
1 "0.348714574898785" "0.463905611516569"  "4"            "4"           
2 "0.521618857725795" "0.634170498361632"  "5"            "3"           
  Cluster_3_Size Cluster_4_Size
1 "3"            "5"           
2 "5"            "3"           
> # Metric    Cluster_1_SilScore  Cluster_2_SilScore  Cluster_3_SilScore
> # 1 "RIN"     "0.420502645502646" "0.674226581940152" "0.433333333333333"
> # 2 "DegFact" "0.759196481622952" "0.59496499852177"  "0.600198799385732"
> # Cluster_4_SilScore  Avg_Silhouette_Width Cluster_1_Size Cluster_2_Size Cluster_3_Size
> # 1 "0.348714574898785" "0.463905611516569"  "4"            "4"            "3"
> # 2 "0.521618857725795" "0.634170498361632"  "5"            "3"            "5"
> # Cluster_4_Size
> # 1 "5"
> # 2 "3"
> dataFrame1 <- qualitySet(data=rnaMetrics, k.set=c(2,3,4), getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


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))

Data loaded.
Number of rows: 16
Number of columns: 3


> assay(dataFrame, 1)
               RIN    DegFact
RIN      1.0000000 -0.9744685
DegFact -0.9744685  1.0000000
> 
> 
> dataFrame <- stability(data=rnaMetrics, cbi="kmeans", k=2, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="clara", k=2, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="clara_pam", k=2, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="hclust", k=2, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="pamk", k=2, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> dataFrame <- stability(data=rnaMetrics, cbi="pamk_pam", k=2, bs=100, getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
Processing metric: DegFact(2)
	Calculation of k = 2
> 
> # Supported CBIs:
> evaluomeRSupportedCBI()
[1] "kmeans"    "clara"     "clara_pam" "hclust"    "pamk"      "pamk_pam" 
> 
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,10), getImages = FALSE)

Data loaded.
Number of rows: 16
Number of columns: 3


Processing metric: RIN(1)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
	Calculation of k = 5
	Calculation of k = 6
	Calculation of k = 7
	Calculation of k = 8
	Calculation of k = 9
	Calculation of k = 10
Processing metric: DegFact(2)
	Calculation of k = 2
	Calculation of k = 3
	Calculation of k = 4
	Calculation of k = 5
	Calculation of k = 6
	Calculation of k = 7
	Calculation of k = 8
	Calculation of k = 9
	Calculation of k = 10
> dataFrame
ExperimentList class object of length 9:
 [1] k_2: SummarizedExperiment with 2 rows and 6 columns
 [2] k_3: SummarizedExperiment with 2 rows and 8 columns
 [3] k_4: SummarizedExperiment with 2 rows and 10 columns
 [4] k_5: SummarizedExperiment with 2 rows and 12 columns
 [5] k_6: SummarizedExperiment with 2 rows and 14 columns
 [6] k_7: SummarizedExperiment with 2 rows and 16 columns
 [7] k_8: SummarizedExperiment with 2 rows and 18 columns
 [8] k_9: SummarizedExperiment with 2 rows and 20 columns
 [9] k_10: SummarizedExperiment with 2 rows and 22 columns
> 
> #dataFrame <- stabilityRange(data=rnaMetrics, k.range=c(2,8), bs=20, getImages = FALSE)
> #assay(dataFrame)
> 
> proc.time()
   user  system elapsed 
  11.15    4.73   15.84

evaluomeR.Rcheck/tests/testAnalysis.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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: 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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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: MultiAssayExperiment
Loading required package: cluster
Loading required package: fpc
Loading required package: randomForest
randomForest 4.7-1.1
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    combine

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

    combine

Loading required package: flexmix
Loading required package: lattice
> 
> data("rnaMetrics")
> plotMetricsMinMax(rnaMetrics)
There were 17 warnings (use warnings() to see them)
> plotMetricsBoxplot(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged.
ℹ Use `variable` instead. 
2: Use of `data.melt$value` is discouraged.
ℹ Use `value` instead. 
> cluster = plotMetricsCluster(ontMetrics, scale = TRUE)
> plotMetricsViolin(rnaMetrics)
Warning messages:
1: Use of `data.melt$variable` is discouraged.
ℹ Use `variable` instead. 
2: Use of `data.melt$value` is discouraged.
ℹ Use `value` instead. 
3: Use of `data.melt$variable` is discouraged.
ℹ Use `variable` instead. 
4: Use of `data.melt$value` is discouraged.
ℹ Use `value` instead. 
> 
> stabilityData <- stabilityRange(data=rnaMetrics, k.range=c(3,4), bs=20, getImages = FALSE, seed=100)

Data loaded.
Number of rows: 16
Number of columns: 3


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)

Data loaded.
Number of rows: 16
Number of columns: 3


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
   Metric Stability_max_k Stability_max_k_stab Stability_max_k_qual
1     RIN               3            0.8901389            0.6278294
2 DegFact               3            1.0000000            0.7371912
  Quality_max_k Quality_max_k_stab Quality_max_k_qual Global_optimal_k
1             3          0.8901389          0.6278294                3
2             3          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(rnaMetrics, k.vector1=k.vector1, k.vector2=k.vector2)
> plotMetricsClusterComparison(rnaMetrics, k.vector1=3, k.vector2=c(2,5))
> 
> 
> proc.time()
   user  system elapsed 
   9.89    4.78   16.04

Example timings

evaluomeR.Rcheck/evaluomeR-Ex.timings

name	user	system	elapsed
evaluomeRSupportedCBI	0	0	0
getDataQualityRange	0.44	0.08	0.53
getOptimalKValue	0.44	0.03	0.48
globalMetric	1.42	0.02	1.44
metricsCorrelations	0.05	0.01	0.06
plotMetricsBoxplot	0.86	0.03	0.89
plotMetricsCluster	0.17	0.02	0.19
plotMetricsClusterComparison	1.02	0.04	1.06
plotMetricsMinMax	0.82	0.04	0.86
plotMetricsViolin	0.96	0.04	1.00
quality	0.36	0.08	0.44
qualityRange	0.28	0.06	0.34
qualitySet	0.06	0.00	0.07
stability	1.92	0.12	2.05
stabilityRange	2.70	0.13	2.83
stabilitySet	0.45	0.01	0.47