José Antonio Bernabé-Díaz
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/evaluomeR |
| Branch: RELEASE_3_10 |
| Last Commit: fa43266 |
| Last Changed Date: 2020-01-09 05:11:27 -0400 (Thu, 09 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:27 -0400 (Wed, 15 Apr 2020).
| Package 543/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| evaluomeR 1.2.41 José Antonio Bernabé-Díaz
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: evaluomeR |
| Version: 1.2.41 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings evaluomeR_1.2.41.tar.gz |
| StartedAt: 2020-04-15 06:24:02 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:28:26 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 264.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: evaluomeR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:evaluomeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings evaluomeR_1.2.41.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/evaluomeR.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (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 ‘1.2.41’ * 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 * 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 ‘/home/biocbuild/bbs-3.10-bioc/meat/evaluomeR.Rcheck/00check.log’ for details.
evaluomeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL evaluomeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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)
evaluomeR.Rcheck/tests/testAll.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
11.384 0.384 11.795
evaluomeR.Rcheck/tests/testAnalysis.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
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
11.768 0.396 12.202
evaluomeR.Rcheck/evaluomeR-Ex.timings
| name | user | system | elapsed | |
| getDataQualityRange | 0.800 | 0.012 | 0.838 | |
| getOptimalKValue | 0.460 | 0.000 | 0.465 | |
| metricsCorrelations | 0.048 | 0.004 | 0.049 | |
| plotMetricsBoxplot | 0.644 | 0.000 | 0.655 | |
| plotMetricsCluster | 0.296 | 0.000 | 0.297 | |
| plotMetricsClusterComparison | 1.136 | 0.000 | 1.187 | |
| plotMetricsMinMax | 0.456 | 0.000 | 0.472 | |
| plotMetricsViolin | 1.164 | 0.016 | 1.211 | |
| quality | 0.412 | 0.008 | 0.433 | |
| qualityRange | 0.392 | 0.000 | 0.393 | |
| qualitySet | 0.08 | 0.00 | 0.08 | |
| stability | 3.404 | 0.056 | 3.481 | |
| stabilityRange | 3.636 | 0.052 | 3.707 | |
| stabilitySet | 0.512 | 0.008 | 0.521 | |