José Antonio Bernabé-Díaz
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/evaluomeR |
| Branch: master |
| Last Commit: 120cc8d |
| Last Changed Date: 2020-01-07 07:25:05 -0500 (Tue, 07 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:53:48 -0500 (Thu, 16 Jan 2020).
| Package 544/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| evaluomeR 1.3.41 José Antonio Bernabé-Díaz
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: evaluomeR |
| Version: 1.3.41 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings evaluomeR_1.3.41.tar.gz |
| StartedAt: 2020-01-16 04:17:59 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 04:24:37 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 397.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: evaluomeR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings evaluomeR_1.3.41.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/evaluomeR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘evaluomeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘evaluomeR’ version ‘1.3.41’
* 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 ‘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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
stabilityRange 6.014 0.350 6.381
stability 5.224 0.337 5.562
* 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 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
‘/Users/biocbuild/bbs-3.11-bioc/meat/evaluomeR.Rcheck/00check.log’
for details.
evaluomeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL evaluomeR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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)
evaluomeR.Rcheck/tests/testAll.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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
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
Loading required package: BiocParallel
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
16.513 1.357 17.826
evaluomeR.Rcheck/tests/testAnalysis.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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
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
Loading required package: BiocParallel
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)
> plotMetricsBoxplot(rnaMetrics)
> plotMetricsCluster(rnaMetrics)
> plotMetricsViolin(rnaMetrics)
>
> 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
17.261 1.456 18.683
evaluomeR.Rcheck/evaluomeR-Ex.timings
| name | user | system | elapsed | |
| getDataQualityRange | 1.118 | 0.197 | 1.315 | |
| getOptimalKValue | 0.678 | 0.014 | 0.697 | |
| metricsCorrelations | 0.063 | 0.007 | 0.069 | |
| plotMetricsBoxplot | 0.854 | 0.082 | 0.937 | |
| plotMetricsCluster | 0.570 | 0.108 | 0.679 | |
| plotMetricsClusterComparison | 0.704 | 0.056 | 0.760 | |
| plotMetricsMinMax | 0.605 | 0.005 | 0.610 | |
| plotMetricsViolin | 2.020 | 0.073 | 2.093 | |
| quality | 0.492 | 0.027 | 0.526 | |
| qualityRange | 0.523 | 0.011 | 0.534 | |
| qualitySet | 0.114 | 0.008 | 0.123 | |
| stability | 5.224 | 0.337 | 5.562 | |
| stabilityRange | 6.014 | 0.350 | 6.381 | |
| stabilitySet | 0.769 | 0.029 | 0.801 | |