José Antonio Bernabé-Díaz
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/evaluomeR |
| Branch: RELEASE_3_9 |
| Last Commit: 1212878 |
| Last Changed Date: 2019-09-26 17:00:06 -0400 (Thu, 26 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:43:50 -0400 (Wed, 16 Oct 2019).
| Package 522/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| evaluomeR 1.0.63 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 | |
| Package: evaluomeR |
| Version: 1.0.63 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:evaluomeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings evaluomeR_1.0.63.tar.gz |
| StartedAt: 2019-10-16 03:36:12 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:40:00 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 227.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: evaluomeR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:evaluomeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings evaluomeR_1.0.63.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/evaluomeR.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.0.63' * 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 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testAll.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.9-bioc/meat/evaluomeR.Rcheck/00check.log' for details.
evaluomeR.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/evaluomeR_1.0.63.tar.gz && rm -rf evaluomeR.buildbin-libdir && mkdir evaluomeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=evaluomeR.buildbin-libdir evaluomeR_1.0.63.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL evaluomeR_1.0.63.zip && rm evaluomeR_1.0.63.tar.gz evaluomeR_1.0.63.zip
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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
metricsCorrelations html
ontMetrics html
quality html
qualityRange html
rnaMetrics html
stability html
stabilityRange 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_1.0.63.zip
* DONE (evaluomeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'evaluomeR' successfully unpacked and MD5 sums checked
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evaluomeR.Rcheck/tests_i386/testAll.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
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" "0.728789163508571" "0.415236312384011" "0.630803897532146"
Cluster_1_Size Cluster_2_Size
1 "5" "11"
2 "11" "5"
>
> 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
8.09 0.59 8.67
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evaluomeR.Rcheck/tests_x64/testAll.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
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" "0.728789163508571" "0.415236312384011" "0.630803897532146"
Cluster_1_Size Cluster_2_Size
1 "5" "11"
2 "11" "5"
>
> 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
6.20 0.29 6.48
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evaluomeR.Rcheck/examples_i386/evaluomeR-Ex.timings
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evaluomeR.Rcheck/examples_x64/evaluomeR-Ex.timings
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