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CHECK report for transcriptR on tokay1

This page was generated on 2020-04-15 12:25:52 -0400 (Wed, 15 Apr 2020).

Package 1745/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.14.0
Armen R. Karapetyan
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/transcriptR
Branch: RELEASE_3_10
Last Commit: 894be86
Last Changed Date: 2019-10-29 13:09:31 -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 [ WARNINGS ] 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: transcriptR
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings transcriptR_1.14.0.tar.gz
StartedAt: 2020-04-15 07:10:53 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 07:22:09 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 676.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: transcriptR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings transcriptR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/transcriptR.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 'transcriptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'transcriptR' version '1.14.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'transcriptR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/ChipDataSet-class.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/ChipDataSet-class.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:26: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:29: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/annotateTranscripts-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/annotateTranscripts-methods.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:22: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:44: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructTDS.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructTDS.Rd:29: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructTDS.Rd:49: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/detectTranscripts-methods.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/detectTranscripts-methods.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/estimateGapDistance-methods.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/getPeaks-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/getTranscripts-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/transcriptR.Rcheck/00install.out' for details.
* 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 ... 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
Examples with CPU or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 10.47   1.00   13.63
predictStrand-methods            5.57   0.15    5.72
peaksToBed-methods               4.86   0.15    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
breakTranscriptsByPeaks-methods 8.11   0.33    8.44
peaksToBed-methods              6.72   0.14    6.86
predictStrand-methods           5.45   0.15    5.71
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/transcriptR.Rcheck/00check.log'
for details.



Installation output

transcriptR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/transcriptR_1.14.0.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.14.0.zip && rm transcriptR_1.14.0.tar.gz transcriptR_1.14.0.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 2472k  100 2472k    0     0  13.2M      0 --:--:-- --:--:-- --:--:-- 13.4M

install for i386

* installing *source* package 'transcriptR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'transcriptR'
    finding HTML links ... done
    ChipDataSet-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/ChipDataSet-class.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/ChipDataSet-class.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    TranscriptionDataSet-class              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:26: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:29: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/TranscriptionDataSet-class.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    addFeature-methods                      html  
    annot                                   html  
    finding level-2 HTML links ... done

    annotateTranscripts-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/annotateTranscripts-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/annotateTranscripts-methods.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    breakTranscriptsByPeaks-methods         html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    cds                                     html  
    constructCDS                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:22: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:44: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructCDS.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    constructTDS                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructTDS.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructTDS.Rd:29: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/constructTDS.Rd:49: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    detectTranscripts-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/detectTranscripts-methods.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/detectTranscripts-methods.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    estimateBackground-methods              html  
    estimateGapDistance-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/estimateGapDistance-methods.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    exportCoverage-methods                  html  
    getConfusionMatrix-methods              html  
    getGenomicAnnot-methods                 html  
    getPeaks-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/getPeaks-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    getPredictorSignificance-methods        html  
    getProbTreshold-methods                 html  
    getQuadProb-methods                     html  
    getTestedGapDistances-methods           html  
    getTranscripts-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpuAYumc/R.INSTALL2008225251d6/transcriptR/man/getTranscripts-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    peaksToBed-methods                      html  
    plotErrorRate-methods                   html  
    plotFeatures-methods                    html  
    plotGenomicAnnot-methods                html  
    plotROC-methods                         html  
    predictStrand-methods                   html  
    predictTssOverlap-methods               html  
    show                                    html  
    tds                                     html  
    transcriptsToBed-methods                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 'transcriptR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptR' as transcriptR_1.14.0.zip
* DONE (transcriptR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'transcriptR' successfully unpacked and MD5 sums checked

Tests output

transcriptR.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(transcriptR)
> 
> test_check("transcriptR")
== testthat results  ===========================================================
[ OK: 87 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  62.60    3.28   66.93 

transcriptR.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(transcriptR)
> 
> test_check("transcriptR")
== testthat results  ===========================================================
[ OK: 87 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  65.84    1.96   67.79 

Example timings

transcriptR.Rcheck/examples_i386/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.130.080.20
annotateTranscripts-methods3.530.143.68
breakTranscriptsByPeaks-methods10.47 1.0013.63
constructCDS000
constructTDS0.260.030.30
detectTranscripts-methods1.240.041.28
estimateBackground-methods0.530.000.53
estimateGapDistance-methods1.170.041.21
exportCoverage-methods0.270.010.28
getConfusionMatrix-methods000
getGenomicAnnot-methods0.020.000.02
getPeaks-methods0.030.000.03
getPredictorSignificance-methods000
getProbTreshold-methods0.010.000.01
getQuadProb-methods0.430.020.52
getTestedGapDistances-methods0.430.030.47
getTranscripts-methods0.440.000.47
peaksToBed-methods4.860.155.08
plotErrorRate-methods0.940.071.00
plotFeatures-methods1.790.011.81
plotGenomicAnnot-methods0.360.000.36
plotROC-methods2.220.132.34
predictStrand-methods5.570.155.72
predictTssOverlap-methods1.860.021.87
show0.320.000.33
transcriptsToBed-methods1.910.032.27

transcriptR.Rcheck/examples_x64/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.110.000.11
annotateTranscripts-methods3.350.053.39
breakTranscriptsByPeaks-methods8.110.338.44
constructCDS000
constructTDS0.180.030.22
detectTranscripts-methods1.280.061.35
estimateBackground-methods0.430.080.50
estimateGapDistance-methods1.970.032.00
exportCoverage-methods0.260.020.28
getConfusionMatrix-methods0.000.010.01
getGenomicAnnot-methods000
getPeaks-methods0.030.000.04
getPredictorSignificance-methods000
getProbTreshold-methods0.000.020.01
getQuadProb-methods0.30.00.3
getTestedGapDistances-methods0.200.040.25
getTranscripts-methods0.220.020.23
peaksToBed-methods6.720.146.86
plotErrorRate-methods1.020.001.02
plotFeatures-methods1.920.021.93
plotGenomicAnnot-methods0.430.010.46
plotROC-methods1.820.021.83
predictStrand-methods5.450.155.71
predictTssOverlap-methods2.640.022.66
show0.350.020.41
transcriptsToBed-methods1.610.031.69