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CHECK report for EDASeq on tokay2

This page was generated on 2019-04-09 11:59:44 -0400 (Tue, 09 Apr 2019).

Package 476/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDASeq 2.17.4
Davide Risso
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/EDASeq
Branch: master
Last Commit: a82a570
Last Changed Date: 2019-01-10 04:12:55 -0400 (Thu, 10 Jan 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: EDASeq
Version: 2.17.4
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EDASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EDASeq_2.17.4.tar.gz
StartedAt: 2019-04-09 02:29:26 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:36:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 421.9 seconds
RetCode: 0
Status:  OK  
CheckDir: EDASeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:EDASeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings EDASeq_2.17.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/EDASeq.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 'EDASeq/DESCRIPTION' ... OK
* this is package 'EDASeq' version '2.17.4'
* 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 'EDASeq' 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 ... OK
* 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 ... NOTE
plot,BamFileList-FastqFileList: no visible global function definition
  for 'elementMetadata'
plotQuality,BamFile: no visible global function definition for 'narrow'
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for 'narrow'
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for 'quality'
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for 'narrow'
Undefined global functions or variables:
  elementMetadata narrow quality
* 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
Examples with CPU or elapsed time > 5s
                          user system elapsed
getGeneLengthAndGCContent 7.06   0.17    12.7
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getGeneLengthAndGCContent 4.47   0.04    8.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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/EDASeq.Rcheck/00check.log'
for details.



Installation output

EDASeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/EDASeq_2.17.4.tar.gz && rm -rf EDASeq.buildbin-libdir && mkdir EDASeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=EDASeq.buildbin-libdir EDASeq_2.17.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL EDASeq_2.17.4.zip && rm EDASeq_2.17.4.tar.gz EDASeq_2.17.4.zip
###
##############################################################################
##############################################################################


  % 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  121k  100  121k    0     0   772k      0 --:--:-- --:--:-- --:--:--  807k

install for i386

* installing *source* package 'EDASeq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'EDASeq'
    finding HTML links ... done
    EDASeq-package                          html  
    finding level-2 HTML links ... done

    MDPlot-methods                          html  
    SeqExpressionSet-class                  html  
    barplot-methods                         html  
    betweenLaneNormalization-methods        html  
    biasBoxplot-methods                     html  
    biasPlot-methods                        html  
    boxplot-methods                         html  
    getGeneLengthAndGCContent               html  
    meanVarPlot-methods                     html  
    newSeqExpressionSet                     html  
    plot-methods                            html  
    plotNtFrequency-methods                 html  
    plotPCA-methods                         html  
    plotQuality-methods                     html  
    plotRLE-methods                         html  
    withinLaneNormalization-methods         html  
    yeastGC                                 html  
    yeastLength                             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 'EDASeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'EDASeq' as EDASeq_2.17.4.zip
* DONE (EDASeq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'EDASeq' successfully unpacked and MD5 sums checked

Tests output

EDASeq.Rcheck/tests_i386/testthat.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(testthat)
> library(EDASeq)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:Biostrings':

    type

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> 
> test_check("EDASeq")
== testthat results  ===========================================================
OK: 19 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  27.64    1.64   35.15 

EDASeq.Rcheck/tests_x64/testthat.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(testthat)
> library(EDASeq)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:Biostrings':

    type

The following objects are masked from 'package:base':

    aperm, apply, rowsum

> 
> test_check("EDASeq")
== testthat results  ===========================================================
OK: 19 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  18.90    0.46   24.53 

Example timings

EDASeq.Rcheck/examples_i386/EDASeq-Ex.timings

nameusersystemelapsed
MDPlot-methods0.280.030.33
SeqExpressionSet-class0.120.000.12
betweenLaneNormalization-methods0.080.000.08
biasBoxplot-methods0.070.010.09
biasPlot-methods0.190.020.21
getGeneLengthAndGCContent 7.06 0.1712.70
newSeqExpressionSet0.030.000.04
plotPCA-methods0.720.200.92
plotRLE-methods0.360.280.64
withinLaneNormalization-methods0.160.020.17

EDASeq.Rcheck/examples_x64/EDASeq-Ex.timings

nameusersystemelapsed
MDPlot-methods0.590.040.65
SeqExpressionSet-class0.220.000.22
betweenLaneNormalization-methods0.060.050.11
biasBoxplot-methods1.160.051.20
biasPlot-methods0.250.030.28
getGeneLengthAndGCContent4.470.048.88
newSeqExpressionSet0.040.000.05
plotPCA-methods1.180.001.17
plotRLE-methods0.730.020.75
withinLaneNormalization-methods0.230.020.25