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CHECK report for evaluomeR on tokay2

This page was generated on 2019-04-09 12:45:40 -0400 (Tue, 09 Apr 2019).

Package 513/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
evaluomeR 0.99.84
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: evaluomeR
Version: 0.99.84
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_0.99.84.tar.gz
StartedAt: 2019-04-09 02:37:12 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:41:08 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 235.8 seconds
RetCode: 0
Status:  OK  
CheckDir: evaluomeR.Rcheck
Warnings: 0

Command output

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###
### 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_0.99.84.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/evaluomeR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '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 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.

Installation output

evaluomeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/evaluomeR_0.99.84.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_0.99.84.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL evaluomeR_0.99.84.zip && rm evaluomeR_0.99.84.tar.gz evaluomeR_0.99.84.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 82635  100 82635    0     0   606k      0 --:--:-- --:--:-- --:--:--  645k

install for i386

* installing *source* package 'evaluomeR' ...
** 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_0.99.84.zip
* DONE (evaluomeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'evaluomeR' successfully unpacked and MD5 sums checked

Tests output

evaluomeR.Rcheck/tests_i386/testAll.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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, 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

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 
   7.01    0.70    7.70

evaluomeR.Rcheck/tests_x64/testAll.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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, 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

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"     "0.431069592245246" "0.803182811595014" "0.61712620192013"  
2 "DegFact" "0.728789163508571" "0.415236312384011" "0.630803897532146" 
  Cluster_1_Size Cluster_2_Size
1 "8"            "8"           
2 "11"           "5"           
> 
> 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 
   6.84    0.37    7.20

Example timings

evaluomeR.Rcheck/examples_i386/evaluomeR-Ex.timings

nameusersystemelapsed
getDataQualityRange0.500.110.61
metricsCorrelations0.030.010.05
quality0.410.030.44
qualityRange0.710.070.78
stability2.100.042.14
stabilityRange3.580.163.73

evaluomeR.Rcheck/examples_x64/evaluomeR-Ex.timings

nameusersystemelapsed
getDataQualityRange0.580.020.59
metricsCorrelations0.040.000.05
quality0.390.000.39
qualityRange1.160.001.16
stability2.230.042.26
stabilityRange3.640.003.64