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CHECK report for systemPipeR on tokay1

This page was generated on 2019-04-13 11:24:19 -0400 (Sat, 13 Apr 2019).

Package 1541/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
systemPipeR 1.16.1
Thomas Girke
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/systemPipeR
Branch: RELEASE_3_8
Last Commit: 6f1a478
Last Changed Date: 2019-01-04 13:07:22 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
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: 1.16.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings systemPipeR_1.16.1.tar.gz
StartedAt: 2019-04-13 05:52:12 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:00:35 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 503.3 seconds
RetCode: 0
Status:  OK  
CheckDir: systemPipeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings systemPipeR_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/systemPipeR.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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/.BatchJobs.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
Namespaces in Imports field not imported from:
  'BiocGenerics' 'VariantAnnotation'
  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'
clusterRun: no visible global function definition for 'chunk'
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'
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'
filterVars: no visible global function definition for 'readVcf'
filterVars: no visible global function definition for 'totalDepth<-'
filterVars: no visible global function definition for 'refDepth<-'
filterVars: no visible global function definition for 'altDepth<-'
filterVars: no visible global function definition for 'asVCF'
filterVars: no visible global function definition for 'writeVcf'
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'
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'
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 global function definition for 'read.delim'
readComp: no visible global function definition for 'combn'
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 'readVcf'
variantReport: no visible global function definition for
  'locateVariants'
variantReport: no visible global function definition for 'AllVariants'
variantReport: no visible global function definition for
  'predictCoding'
variantReport: no visible global function definition for 'ref'
variantReport: no visible global function definition for 'alt'
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'
show,INTERSECTset: no visible binding for global variable 'vennset'
Undefined global functions or variables:
  AllVariants Base Comparisons Counts Coverage Cycle DataFrame Feature
  Frequency IRanges Intersect_Sets Length Level Method Outliers Percent
  Quality RelDiv Rle Sample SampleMatch Strand Type aggregate alt
  altDepth<- asVCF boxplot chunk close.screen combn dev.off first
  import.bed last locateVariants low mid minQuality model.matrix
  na.omit pdf phyper plot predictCoding qwidth read.delim
  readGAlignmentPairs readGAlignments readVcf ref refDepth<- screen
  seqlengths seqlengths<- split.screen subsetByOverlaps
  summarizeOverlaps symbols test_sample text top tophatargs
  totalDepth<- vennset write.table writeVcf
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")
  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 16.64   1.65   18.29
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
genFeatures 22.56   0.33   22.89
run_DESeq2   5.80   0.07    5.86
* 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-3.8-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/3.8/bioc/src/contrib/systemPipeR_1.16.1.tar.gz && rm -rf systemPipeR.buildbin-libdir && mkdir systemPipeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=systemPipeR.buildbin-libdir systemPipeR_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL systemPipeR_1.16.1.zip && rm systemPipeR_1.16.1.tar.gz systemPipeR_1.16.1.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
 23 2206k   23  512k    0     0   530k      0  0:00:04 --:--:--  0:00:04  532k
100 2206k  100 2206k    0     0  1994k      0  0:00:01  0:00:01 --:--:-- 2002k

install for i386

* installing *source* package 'systemPipeR' ...
** 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  
    VENNset-class                           html  
    alignStats                              html  
    catDB-class                             html  
    catmap                                  html  
    clusterRun                              html  
    countRangeset                           html  
    featureCoverage                         html  
    featuretypeCounts                       html  
    filterDEGs                              html  
    filterVars                              html  
    genFeatures                             html  
    getQsubargs                             html  
    mergeBamByFactor                        html  
    moduleload                              html  
    olBarplot                               html  
    overLapper                              html  
    plotfeatureCoverage                     html  
    plotfeaturetypeCounts                   html  
    predORF                                 html  
    preprocessReads                         html  
    qsubRun                                 html  
    readComp                                html  
    returnRPKM                              html  
    runCommandline                          html  
    runDiff                                 html  
    run_DESeq2                              html  
    run_edgeR                               html  
    scaleRanges                             html  
    seeFastq                                html  
    symLink2bam                             html  
    sysargs                                 html  
    systemArgs                              html  
    variantReport                           html  
    vennPlot                                html  
    writeTargetsRef                         html  
    writeTargetsout                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'systemPipeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeR' as systemPipeR_1.16.1.zip
* DONE (systemPipeR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'systemPipeR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

systemPipeR.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, 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


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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply




RUNIT TEST PROTOCOL -- Sat Apr 13 06:00:14 2019 
*********************************************** 
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 
  10.53    0.90   11.43 

systemPipeR.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, 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


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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply




RUNIT TEST PROTOCOL -- Sat Apr 13 06:00:27 2019 
*********************************************** 
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 
  12.15    0.43   12.57 

Example timings

systemPipeR.Rcheck/examples_i386/systemPipeR-Ex.timings

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class000
SYSargs-class0.000.040.05
VENNset-class000
alignStats0.010.000.01
catDB-class000
catmap000
clusterRun0.020.000.02
countRangeset0.090.000.09
featureCoverage000
featuretypeCounts0.020.000.02
filterDEGs0.920.031.00
filterVars0.030.000.05
genFeatures16.64 1.6518.29
getQsubargs0.000.020.02
mergeBamByFactor0.020.000.03
moduleload000
olBarplot1.950.001.95
overLapper0.80.00.8
plotfeatureCoverage0.010.000.01
plotfeaturetypeCounts0.020.000.02
predORF0.200.050.25
preprocessReads0.020.000.05
qsubRun0.010.000.01
readComp0.020.000.02
returnRPKM000
runCommandline0.010.000.01
runDiff0.040.000.04
run_DESeq23.590.514.10
run_edgeR1.080.521.60
scaleRanges0.180.010.20
seeFastq000
symLink2bam0.020.000.01
sysargs0.010.000.02
systemArgs0.020.000.01
variantReport0.010.000.02
vennPlot0.440.160.59
writeTargetsRef000
writeTargetsout000

systemPipeR.Rcheck/examples_x64/systemPipeR-Ex.timings

nameusersystemelapsed
GOHyperGAll000
INTERSECTset-class0.020.000.01
SYSargs-class0.020.000.02
VENNset-class0.010.000.01
alignStats0.020.000.02
catDB-class000
catmap000
clusterRun0.010.000.01
countRangeset0.070.000.07
featureCoverage000
featuretypeCounts0.020.000.02
filterDEGs0.940.020.95
filterVars000
genFeatures22.56 0.3322.89
getQsubargs0.020.000.02
mergeBamByFactor0.020.000.01
moduleload000
olBarplot0.790.020.82
overLapper0.670.000.67
plotfeatureCoverage0.020.000.01
plotfeaturetypeCounts000
predORF0.230.010.25
preprocessReads0.040.000.03
qsubRun0.010.000.02
readComp0.020.000.02
returnRPKM000
runCommandline0.010.000.01
runDiff0.050.000.05
run_DESeq25.800.075.86
run_edgeR1.570.011.59
scaleRanges0.250.000.25
seeFastq000
symLink2bam0.020.000.01
sysargs0.010.000.02
systemArgs0.020.000.01
variantReport0.010.000.02
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