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CHECK report for systemPipeR on tokay1

This page was generated on 2020-04-15 12:23:39 -0400 (Wed, 15 Apr 2020).

Package 1702/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 1.20.0
Thomas Girke
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/systemPipeR
Branch: RELEASE_3_10
Last Commit: 70b884d
Last Changed Date: 2019-10-29 13:09:04 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: systemPipeR
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings systemPipeR_1.20.0.tar.gz
StartedAt: 2020-04-15 07:02:21 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:13:22 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 661.5 seconds
RetCode: 0
Status:  OK  
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings systemPipeR_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/systemPipeR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'systemPipeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'systemPipeR' version '1.20.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.batchtools.conf.R
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'systemPipeR' 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 ... NOTE
Namespace in Imports field not imported from: 'BiocGenerics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.AffyID2GeneID: no visible global function definition for 'read.delim'
.readGOorg: no visible global function definition for 'read.delim'
.readGOorg: no visible global function definition for 'na.omit'
.resizeFeature: no visible global function definition for 'DataFrame'
.sampleDFgene2GO: no visible global function definition for 'na.omit'
.subsetReadsByMappingRegion: no visible global function definition for
  'IRanges'
.subsetReadsByMappingRegion: no visible global function definition for
  'seqlengths'
.subsetReadsByMappingRegion: no visible global function definition for
  'readGAlignments'
GOHyperGAll: no visible global function definition for 'phyper'
GOHyperGAll_Simplify: no visible global function definition for
  'na.omit'
GOHyperGAll_Subset: no visible binding for global variable
  'test_sample'
assembleCommandlineList: no visible binding for global variable 'WF'
combineVarReports: no visible global function definition for
  'read.delim'
countRangeset: no visible global function definition for 'read.delim'
countRangeset: no visible global function definition for 'import.bed'
countRangeset: no visible global function definition for
  'summarizeOverlaps'
countRangeset: no visible global function definition for 'write.table'
createWF: no visible global function definition for 'read.delim'
featureCoverage: no visible global function definition for
  'readGAlignments'
featureCoverage: no visible global function definition for 'qwidth'
featureCoverage: no visible global function definition for
  'subsetByOverlaps'
featureCoverage: no visible global function definition for 'Rle'
featureCoverage: no visible global function definition for 'na.omit'
featureCoverage: no visible global function definition for
  'write.table'
featuretypeCounts: no visible global function definition for
  'readGAlignments'
featuretypeCounts: no visible global function definition for
  'readGAlignmentPairs'
featuretypeCounts: no visible global function definition for
  'subsetByOverlaps'
featuretypeCounts: no visible global function definition for 'qwidth'
featuretypeCounts: no visible global function definition for 'last'
featuretypeCounts: no visible global function definition for 'first'
filterDEGs: no visible binding for global variable 'Comparisons'
filterDEGs: no visible binding for global variable 'Counts'
filterDEGs: no visible binding for global variable 'Type'
findBestMatch: no visible global function definition for 'setNames'
genFeatures: no visible global function definition for 'DataFrame'
genFeatures: no visible global function definition for 'seqlengths<-'
getQsubargs: no visible binding for global variable 'tophatargs'
goBarplot: no visible binding for global variable 'SampleMatch'
goBarplot: no visible binding for global variable 'Sample'
loadWF: no visible global function definition for 'read.delim'
loadWorkflow: no visible global function definition for 'read.delim'
olBarplot: no visible binding for global variable 'Intersect_Sets'
olBarplot: no visible binding for global variable 'Counts'
olBarplot: no visible binding for global variable 'Level'
olRanges: no visible global function definition for 'seqlengths<-'
olRanges: no visible global function definition for 'seqlengths'
olRanges: no visible global function definition for 'Rle'
olRanges: no visible global function definition for 'IRanges'
overLapper : <anonymous>: no visible global function definition for
  'combn'
plotfeatureCoverage: no visible global function definition for
  'aggregate'
plotfeatureCoverage: no visible binding for global variable 'Coverage'
plotfeatureCoverage: no visible binding for global variable 'Strand'
plotfeaturetypeCounts: no visible binding for global variable 'Feature'
plotfeaturetypeCounts: no visible binding for global variable 'Counts'
plotfeaturetypeCounts: no visible binding for global variable 'Strand'
plotfeaturetypeCounts: no visible global function definition for
  'dev.off'
plotfeaturetypeCounts: no visible binding for global variable 'Length'
predORF : .predORF: no visible global function definition for 'na.omit'
predORF : .predORF: no visible global function definition for 'IRanges'
readComp: no visible binding for global variable 'args_bam'
readComp: no visible global function definition for 'read.delim'
readComp: no visible global function definition for 'combn'
renderInputs: no visible binding for global variable 'WF'
renderOutputs: no visible binding for global variable 'WF'
runDiff: no visible global function definition for 'read.delim'
runDiff: no visible global function definition for 'write.table'
runDiff: no visible global function definition for 'pdf'
runDiff: no visible global function definition for 'dev.off'
run_edgeR: no visible global function definition for 'model.matrix'
run_edgeR: no visible global function definition for 'pdf'
run_edgeR: no visible global function definition for 'dev.off'
scaleRanges : .scaleRanges: no visible global function definition for
  'IRanges'
scaleRanges: no visible global function definition for 'DataFrame'
seeFastq : seeFastqSingle: no visible global function definition for
  'boxplot'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'Cycle'
seeFastqPlot : fastqPlot: no visible binding for global variable 'low'
seeFastqPlot : fastqPlot: no visible binding for global variable 'mid'
seeFastqPlot : fastqPlot: no visible binding for global variable 'top'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'Frequency'
seeFastqPlot : fastqPlot: no visible binding for global variable 'Base'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'Quality'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'RelDiv'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'Method'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'minQuality'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'Percent'
seeFastqPlot : fastqPlot: no visible binding for global variable
  'Outliers'
systemArgs: no visible global function definition for 'read.delim'
varSummary: no visible global function definition for 'read.delim'
variantReport: no visible global function definition for 'write.table'
vennPlot: no visible global function definition for 'symbols'
vennPlot: no visible global function definition for 'text'
vennPlot : plotellipse: no visible global function definition for
  'plot'
vennPlot : ellipseVenn: no visible global function definition for
  'split.screen'
vennPlot : ellipseVenn: no visible global function definition for
  'screen'
vennPlot : ellipseVenn: no visible global function definition for
  'text'
vennPlot : ellipseVenn: no visible global function definition for
  'close.screen'
writeTargetsRef: no visible global function definition for 'read.delim'
modules,SYSargs2: no visible global function definition for 'setNames'
Undefined global functions or variables:
  Base Comparisons Counts Coverage Cycle DataFrame Feature Frequency
  IRanges Intersect_Sets Length Level Method Outliers Percent Quality
  RelDiv Rle Sample SampleMatch Strand Type WF aggregate args_bam
  boxplot close.screen combn dev.off first import.bed last low mid
  minQuality model.matrix na.omit pdf phyper plot qwidth read.delim
  readGAlignmentPairs readGAlignments screen seqlengths seqlengths<-
  setNames split.screen subsetByOverlaps summarizeOverlaps symbols
  test_sample text top tophatargs write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "boxplot", "close.screen", "plot", "screen",
             "split.screen", "symbols", "text")
  importFrom("stats", "aggregate", "model.matrix", "na.omit", "phyper",
             "setNames")
  importFrom("utils", "combn", "read.delim", "write.table")
to your NAMESPACE file.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 28.31   3.32   31.65
run_DESeq2  13.84   0.00   13.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
genFeatures          29.16   0.46   29.62
run_DESeq2           13.80   0.12   13.92
SYSargs2Pipe-methods  5.61   0.00    5.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/systemPipeR.Rcheck/00check.log'
for details.



Installation output

systemPipeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/systemPipeR_1.20.0.tar.gz && rm -rf systemPipeR.buildbin-libdir && mkdir systemPipeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=systemPipeR.buildbin-libdir systemPipeR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL systemPipeR_1.20.0.zip && rm systemPipeR_1.20.0.tar.gz systemPipeR_1.20.0.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  993k  100  993k    0     0  3007k      0 --:--:-- --:--:-- --:--:-- 3047k

install for i386

* installing *source* package 'systemPipeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'systemPipeR'
    finding HTML links ... done
    GOHyperGAll                             html  
    INTERSECTset-class                      html  
    SYSargs-class                           html  
    SYSargs2-class                          html  
    SYSargs2Pipe-class                      html  
    SYSargs2Pipe-methods                    html  
    SYSargs2list-methods                    html  
    VENNset-class                           html  
    alignStats                              html  
    catDB-class                             html  
    catmap                                  html  
    clusterRun                              html  
    countRangeset                           html  
    createWF                                html  
    featureCoverage                         html  
    featuretypeCounts                       html  
    filterDEGs                              html  
    filterVars                              html  
    genFeatures                             html  
    getQsubargs                             html  
    loadWorkflow                            html  
    mergeBamByFactor                        html  
    module                                  html  
    moduleload                              html  
    olBarplot                               html  
    olRanges                                html  
    output_update                           html  
    overLapper                              html  
    plotfeatureCoverage                     html  
    plotfeaturetypeCounts                   html  
    predORF                                 html  
    preprocessReads                         html  
    qsubRun                                 html  
    readComp                                html  
    renderWF                                html  
    returnRPKM                              html  
    runCommandline                          html  
    runDiff                                 html  
    run_DESeq2                              html  
    run_edgeR                               html  
    run_track                               html  
    scaleRanges                             html  
    seeFastq                                html  
    subsetWF                                html  
    symLink2bam                             html  
    sysargs                                 html  
    systemArgs                              html  
    targets.as.df                           html  
    variantReport                           html  
    vennPlot                                html  
    writeTargetsRef                         html  
    writeTargetsout                         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 'systemPipeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeR' as systemPipeR_1.20.0.zip
* DONE (systemPipeR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'systemPipeR' successfully unpacked and MD5 sums checked

Tests output

systemPipeR.Rcheck/tests_i386/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("systemPipeR")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

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


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 objects are masked from 'package:base':

    aperm, apply, rowsum




RUNIT TEST PROTOCOL -- Wed Apr 15 07:12:56 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="SRR446027_1.fastq": The system cannot find the file specified
2: In normalizePath(path.expand(path), winslash, mustWork) :
  path[2]="SRR446028_1.fastq": The system cannot find the file specified
3: In normalizePath(path.expand(path), winslash, mustWork) :
  path[3]="SRR446029_1.fastq": The system cannot find the file specified
4: In normalizePath(path.expand(path), winslash, mustWork) :
  path[4]="SRR446030_1.fastq": The system cannot find the file specified
> 
> proc.time()
   user  system elapsed 
  13.35    1.23   14.57 

systemPipeR.Rcheck/tests_x64/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> BiocGenerics:::testPackage("systemPipeR")

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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows


Attaching package: 'Biostrings'

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

    strsplit

Welcome to Bioconductor

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


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 objects are masked from 'package:base':

    aperm, apply, rowsum




RUNIT TEST PROTOCOL -- Wed Apr 15 07:13:13 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeR RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="SRR446027_1.fastq": The system cannot find the file specified
2: In normalizePath(path.expand(path), winslash, mustWork) :
  path[2]="SRR446028_1.fastq": The system cannot find the file specified
3: In normalizePath(path.expand(path), winslash, mustWork) :
  path[3]="SRR446029_1.fastq": The system cannot find the file specified
4: In normalizePath(path.expand(path), winslash, mustWork) :
  path[4]="SRR446030_1.fastq": The system cannot find the file specified
> 
> proc.time()
   user  system elapsed 
  15.20    0.65   15.84 

Example timings

systemPipeR.Rcheck/examples_i386/systemPipeR-Ex.timings

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class000
SYSargs-class0.030.010.06
SYSargs2-class1.380.441.83
SYSargs2Pipe-class1.220.021.24
SYSargs2Pipe-methods3.290.003.31
SYSargs2list-methods1.990.001.98
VENNset-class000
alignStats1.950.011.97
catDB-class000
catmap000
clusterRun1.920.001.92
countRangeset0.080.020.10
createWF000
featureCoverage0.000.010.01
featuretypeCounts0.020.000.02
filterDEGs1.260.461.75
filterVars0.020.000.04
genFeatures28.31 3.3231.65
getQsubargs000
loadWorkflow1.330.051.37
mergeBamByFactor0.030.000.05
module000
moduleload000
olBarplot0.440.050.48
olRanges0.120.010.14
output_update1.910.021.92
overLapper0.390.000.39
plotfeatureCoverage000
plotfeaturetypeCounts000
predORF0.140.090.23
preprocessReads0.010.000.02
qsubRun0.020.000.02
readComp0.000.020.01
renderWF1.340.001.35
returnRPKM000
runCommandline1.280.011.29
runDiff0.020.020.03
run_DESeq213.84 0.0013.85
run_edgeR1.080.311.39
run_track3.440.003.44
scaleRanges0.160.000.16
seeFastq000
subsetWF1.480.001.48
symLink2bam000
sysargs0.000.020.02
systemArgs0.020.000.01
targets.as.df1.310.001.32
variantReport0.020.000.01
vennPlot0.530.000.53
writeTargetsRef000
writeTargetsout1.250.011.27

systemPipeR.Rcheck/examples_x64/systemPipeR-Ex.timings

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class0.020.000.01
SYSargs-class0.030.000.03
SYSargs2-class2.470.112.58
SYSargs2Pipe-class2.220.002.21
SYSargs2Pipe-methods5.610.005.61
SYSargs2list-methods2.750.002.91
VENNset-class0.010.000.02
alignStats2.680.002.68
catDB-class000
catmap000
clusterRun2.230.012.35
countRangeset0.110.000.11
createWF000
featureCoverage0.010.000.01
featuretypeCounts0.020.000.02
filterDEGs1.310.001.31
filterVars0.000.010.02
genFeatures29.16 0.4629.62
getQsubargs0.010.000.02
loadWorkflow2.080.012.09
mergeBamByFactor0.020.000.02
module000
moduleload000
olBarplot0.570.020.59
olRanges0.180.010.19
output_update4.920.024.94
overLapper0.590.010.61
plotfeatureCoverage000
plotfeaturetypeCounts0.010.000.01
predORF0.250.000.25
preprocessReads0.020.000.02
qsubRun0.010.000.01
readComp0.010.000.01
renderWF1.80.01.8
returnRPKM000
runCommandline2.190.022.20
runDiff0.050.000.05
run_DESeq213.80 0.1213.92
run_edgeR101
run_track3.690.023.70
scaleRanges0.180.000.19
seeFastq000
subsetWF1.520.001.52
symLink2bam000
sysargs000
systemArgs0.020.000.02
targets.as.df1.630.001.62
variantReport0.010.000.02
vennPlot0.410.010.42
writeTargetsRef000
writeTargetsout1.640.021.66