José Antonio Bernabé-Díaz
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/evaluomeR |
| Branch: master |
| Last Commit: fe3257d |
| Last Changed Date: 2019-03-31 14:04:56 -0400 (Sun, 31 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:22:05 -0400 (Tue, 09 Apr 2019).
| Package 513/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| evaluomeR 0.99.84 José Antonio Bernabé-Díaz
| malbec2 | Linux (Ubuntu 18.04.2 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: evaluomeR |
| Version: 0.99.84 |
| 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_0.99.84.tar.gz |
| StartedAt: 2019-04-09 01:47:50 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:52:08 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 258.2 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_0.99.84.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/evaluomeR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘0.99.84’
* 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 or elapsed time > 5s
user system elapsed
stabilityRange 5.401 0.157 5.564
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testAll.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-3.9-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/3.6/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) (2019-03-18 r76245) -- "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, colMeans, colSums, 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, rowMeans, rowSums,
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
>
> data("rnaMetrics")
>
>
> dataFrame <- stability(data=rnaMetrics, k=2, bs=20, 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(2,5), bs=20, getImages = FALSE)
Processing metric: RIN ( 1 )
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Calculation of k = 5
Processing metric: DegFact ( 2 )
Calculation of k = 2
Calculation of k = 3
Calculation of k = 4
Calculation of k = 5
>
> dataFrame <- quality(data=rnaMetrics, k=2, getImages = FALSE)
Processing metric: RIN ( 1 )
Calculation of k = 2
Processing metric: DegFact ( 2 )
Calculation of k = 2
> dataFrame <- qualityRange(data=rnaMetrics, k.range=c(2,3), getImages = FALSE)
Processing metric: RIN ( 1 )
Calculation of k = 2
Calculation of k = 3
Processing metric: DegFact ( 2 )
Calculation of k = 2
Calculation of k = 3
> assay(getDataQualityRange(dataFrame, 2), 1)
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"
>
> 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
9.955 1.028 10.933
evaluomeR.Rcheck/evaluomeR-Ex.timings
| name | user | system | elapsed | |
| getDataQualityRange | 0.948 | 0.078 | 1.026 | |
| metricsCorrelations | 0.041 | 0.005 | 0.047 | |
| quality | 1.222 | 0.066 | 1.294 | |
| qualityRange | 1.397 | 0.228 | 1.626 | |
| stability | 4.208 | 0.185 | 4.402 | |
| stabilityRange | 5.401 | 0.157 | 5.564 | |