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CHECK report for IsoformSwitchAnalyzeR on riesling1

This page was generated on 2020-10-24 11:05:43 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IsoformSwitchAnalyzeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 920/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 1.11.11
Kristoffer Vitting-Seerup
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
Branch: master
Last Commit: 83fbe04
Last Changed Date: 2020-10-13 08:25:03 -0400 (Tue, 13 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IsoformSwitchAnalyzeR
Version: 1.11.11
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.11.11.tar.gz
StartedAt: 2020-10-24 02:54:53 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 03:10:09 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 916.4 seconds
RetCode: 0
Status:  OK  
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.11.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/IsoformSwitchAnalyzeR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IsoformSwitchAnalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IsoformSwitchAnalyzeR' version '1.11.11'
* 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 'IsoformSwitchAnalyzeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
analyzeIUPred2A: no visible global function definition for 'queryHits'
analyzeIUPred2A: no visible global function definition for
  'subjectHits'
compareAnnotationOfTwoIsoforms: no visible global function definition
  for 'queryHits'
compareAnnotationOfTwoIsoforms: no visible global function definition
  for 'subjectHits'
createSwitchAnalyzeRlist: no visible global function definition for
  'package.version'
expressionAnalysisPlot: no visible binding for global variable
  'Condition'
expressionAnalysisPlot: no visible binding for global variable
  'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
  'CI_down'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
  'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceEnrichment: no visible binding for global variable
  'feature2'
extractConsequenceEnrichment: no visible binding for global variable
  'propOfRelevantEvents'
extractConsequenceEnrichment: no visible binding for global variable
  'Significant'
extractConsequenceEnrichment: no visible binding for global variable
  'propCiLo'
extractConsequenceEnrichment: no visible binding for global variable
  'propCiHi'
extractConsequenceEnrichment: no visible binding for global variable
  'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'Comparison'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propOfRelevantEvents'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'Significant'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'nTot'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propCiHi'
extractConsequenceEnrichmentComparison: no visible binding for global
  variable 'propCiLo'
extractConsequenceGenomeWide: no visible binding for global variable
  'isoform_feature'
extractConsequenceGenomeWide: no visible binding for global variable
  'value'
extractConsequenceGenomeWide: no visible binding for global variable
  'variable'
extractConsequenceGenomeWide: no visible binding for global variable
  'ymax'
extractConsequenceGenomeWide: no visible binding for global variable
  'significance'
extractConsequenceGenomeWide: no visible binding for global variable
  'idNr'
extractConsequenceSummary: no visible binding for global variable
  'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
  'geneFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
  'isoFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractSplicingEnrichment: no visible binding for global variable
  'AStype'
extractSplicingEnrichment: no visible binding for global variable
  'propUp'
extractSplicingEnrichment: no visible binding for global variable
  'Significant'
extractSplicingEnrichment: no visible binding for global variable
  'nTot'
extractSplicingEnrichment: no visible binding for global variable
  'propUpCiHi'
extractSplicingEnrichment: no visible binding for global variable
  'propUpCiLo'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'Comparison'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUp'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'Significant'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'nTot'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUpCiHi'
extractSplicingEnrichmentComparison: no visible binding for global
  variable 'propUpCiLo'
extractSplicingGenomeWide: no visible binding for global variable
  'isoform_feature'
extractSplicingGenomeWide: no visible binding for global variable
  'value'
extractSplicingGenomeWide: no visible binding for global variable
  'variable'
extractSplicingGenomeWide: no visible binding for global variable
  'ymax'
extractSplicingGenomeWide: no visible binding for global variable
  'significance'
extractSplicingGenomeWide: no visible binding for global variable
  'idNr'
extractSplicingSummary: no visible binding for global variable
  'splicingResult'
extractSplicingSummary: no visible binding for global variable
  'geneFraction'
extractSplicingSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractSplicingSummary: no visible binding for global variable
  'isoFraction'
extractSplicingSummary: no visible binding for global variable
  'nrIsoWithConsequences'
grangesFracOverlap: no visible global function definition for
  'queryHits'
grangesFracOverlap: no visible global function definition for
  'subjectHits'
importGTF: no visible binding for global variable 'gene_id'
importGTF: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'isoform_id'
importRdata: no visible binding for global variable 'gene_id'
importRdata: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'n_gene_names'
importRdata: no visible binding for global variable 'n_iso_na'
importRdata: no visible global function definition for 'queryHits'
importRdata: no visible global function definition for 'subjectHits'
importRdata: no visible binding for global variable 'novel_iso'
importRdata: no visible binding for global variable 'known_gene_name'
importRdata: no visible binding for global variable 'nt_overlap'
importRdata: no visible binding for global variable 'frac_overlap'
importRdata: no visible binding for global variable
  'log2_overlap_ratio'
importRdata: no visible binding for global variable 'has_gene_name'
importRdata: no visible binding for global variable 'has_novel_iso'
importSalmonData: no visible global function definition for 'metadata'
importSalmonData: no visible global function definition for 'assay'
isoformToGeneExp: no visible binding for global variable 'gene_id'
isoformToGeneExp: no visible binding for global variable 'gene_name'
isoformToGeneExp: no visible binding for global variable 'isoform_id'
preFilter: no visible global function definition for 'setdff'
switchPlotTranscript: no visible global function definition for
  'queryHits'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
Undefined global functions or variables:
  AStype CI_down CI_hi CI_low CI_up Comparison Condition Domain IF
  Significant assay feature2 frac_overlap geneFraction gene_expression
  gene_id gene_name has_gene_name has_novel_iso idNr isoFraction
  isoform_feature isoform_id known_gene_name log2_overlap_ratio
  metadata nTot n_gene_names n_iso_na novel_iso nrGenesWithConsequences
  nrIsoWithConsequences nt_overlap package.version propCiHi propCiLo
  propOfRelevantEvents propUp propUpCiHi propUpCiLo queryHits setdff
  sigEval sigLevel sigLevelPos significance splicingResult subjectHits
  switchConsequence value variable x xmax xmin y yend ymax ymin
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.12-bioc/R/library/IsoformSwitchAnalyzeR/libs/i386/IsoformSwitchAnalyzeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbuild/bbs-3.12-bioc/R/library/IsoformSwitchAnalyzeR/libs/x64/IsoformSwitchAnalyzeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
importSalmonData              31.81   1.04   41.11
IsoformSwitchTestDEXSeq       26.21   0.20   31.72
importCufflinksGalaxyData     20.57   0.03   20.59
IsoformSwitchTestDRIMSeq      13.57   0.02   18.89
prepareSalmonFilesDataFrame   12.15   0.18   16.28
isoformSwitchAnalysisCombined  9.16   0.11    9.27
isoformSwitchAnalysisPart1     6.58   0.02    6.59
extractSequence                6.53   0.04    6.56
analyzeORF                     6.11   0.01    6.12
extractTopSwitches             5.81   0.02    5.83
isoformSwitchAnalysisPart2     5.76   0.04    5.81
extractSwitchSummary           5.56   0.01    5.58
isoformToGeneExp               1.92   0.00    9.86
importRdata                    0.97   0.02    6.23
switchAnalyzeRlist             0.94   0.00    6.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
importSalmonData              36.64   1.17   48.08
IsoformSwitchTestDEXSeq       36.61   0.36   42.27
importCufflinksGalaxyData     25.30   0.11   25.41
IsoformSwitchTestDRIMSeq      20.86   0.05   26.20
prepareSalmonFilesDataFrame   15.25   0.34   20.75
isoformSwitchAnalysisCombined 11.22   0.10   11.31
extractSequence                9.68   0.05    9.74
extractTopSwitches             9.36   0.00    9.36
extractSwitchSummary           8.75   0.00    8.80
isoformSwitchAnalysisPart1     8.06   0.06    8.12
analyzeORF                     7.40   0.02    7.42
analyzeAlternativSplicing      6.53   0.02    6.55
isoformToGeneExp               2.07   0.03    9.97
importRdata                    1.50   0.06    6.85
switchAnalyzeRlist             1.33   0.02    6.67
* 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.12-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log'
for details.



Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/IsoformSwitchAnalyzeR_1.11.11.tar.gz && rm -rf IsoformSwitchAnalyzeR.buildbin-libdir && mkdir IsoformSwitchAnalyzeR.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR_1.11.11.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR_1.11.11.zip && rm IsoformSwitchAnalyzeR_1.11.11.tar.gz IsoformSwitchAnalyzeR_1.11.11.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
 76 2904k   76 2221k    0     0  27.8M      0 --:--:-- --:--:-- --:--:-- 27.4M
100 2904k  100 2904k    0     0  33.7M      0 --:--:-- --:--:-- --:--:-- 33.3M

install for i386

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/IsoformSwitchAnalyzeR.buildbin-libdir/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IsoformSwitchAnalyzeR'
    finding HTML links ... done
    CDSSet                                  html  
    IsoformSwitchTestDEXSeq                 html  
    IsoformSwitchTestDRIMSeq                html  
    finding level-2 HTML links ... done

    analyzeAlternativSplicing               html  
    analyzeCPAT                             html  
    analyzeCPC2                             html  
    analyzeIUPred2A                         html  
    analyzeNetSurf2                         html  
    analyzeORF                              html  
    analyzePFAM                             html  
    analyzeSignalP                          html  
    analyzeSwitchConsequences               html  
    expressionAnalysisPlots                 html  
    extractConsequenceEnrichment            html  
    extractConsequenceEnrichmentComparison
                                            html  
    extractConsequenceSummary               html  
    extractGeneExpression                   html  
    extractGenomeWideAnalysis               html  
    extractGenomeWideSplicingAnalysis       html  
    extractSequence                         html  
    extractSplicingEnrichment               html  
    extractSplicingEnrichmentComparison     html  
    extractSplicingSummary                  html  
    extractSwitchOverlap                    html  
    extractSwitchSummary                    html  
    extractTopSwitches                      html  
    getCDS                                  html  
    importCufflinksGalaxyData               html  
    importGTF                               html  
    importIsoformExpression                 html  
    importRdata                             html  
    importSalmonData                        html  
    isoformSwitchAnalysisCombined           html  
    isoformSwitchAnalysisPart1              html  
    isoformSwitchAnalysisPart2              html  
    isoformToGeneExp                        html  
    isoformToIsoformFraction                html  
    preFilter                               html  
    prepareSalmonFilesDataFrame             html  
    subsetSwitchAnalyzeRlist                html  
    switchAnalyzeRlist                      html  
    switchPlot                              html  
    switchPlotTopSwitches                   html  
    switchPlotTranscript                    html  
    testData                                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 'IsoformSwitchAnalyzeR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o IsoformSwitchAnalyzeR.dll tmp.def utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.12-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.12-bioc/meat/IsoformSwitchAnalyzeR.buildbin-libdir/IsoformSwitchAnalyzeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IsoformSwitchAnalyzeR' as IsoformSwitchAnalyzeR_1.11.11.zip
* DONE (IsoformSwitchAnalyzeR)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'IsoformSwitchAnalyzeR' successfully unpacked and MD5 sums checked

Tests output


Example timings

IsoformSwitchAnalyzeR.Rcheck/examples_i386/IsoformSwitchAnalyzeR-Ex.timings

nameusersystemelapsed
IsoformSwitchTestDEXSeq26.21 0.2031.72
IsoformSwitchTestDRIMSeq13.57 0.0218.89
analyzeAlternativSplicing4.160.014.18
analyzeCPAT0.040.000.05
analyzeCPC20.050.000.05
analyzeIUPred2A1.550.021.56
analyzeORF6.110.016.12
analyzePFAM0.290.020.32
analyzeSignalP0.070.000.06
analyzeSwitchConsequences0.620.020.64
expressionAnalysisPlots0.580.010.63
extractConsequenceEnrichment0.360.000.36
extractConsequenceEnrichmentComparison0.470.000.50
extractConsequenceSummary0.480.000.48
extractGeneExpression0.050.000.05
extractGenomeWideAnalysis2.230.032.26
extractGenomeWideSplicingAnalysis1.580.011.64
extractSequence6.530.046.56
extractSplicingEnrichment0.770.000.77
extractSplicingEnrichmentComparison0.790.030.82
extractSplicingSummary0.610.010.65
extractSwitchOverlap0.350.020.36
extractSwitchSummary5.560.015.58
extractTopSwitches5.810.025.83
getCDS000
importCufflinksGalaxyData20.57 0.0320.59
importGTF0.590.003.24
importIsoformExpression0.390.003.05
importRdata0.970.026.23
importSalmonData31.81 1.0441.11
isoformSwitchAnalysisCombined9.160.119.27
isoformSwitchAnalysisPart16.580.026.59
isoformSwitchAnalysisPart25.760.045.81
isoformToGeneExp1.920.009.86
isoformToIsoformFraction0.190.040.24
preFilter0.020.000.01
prepareSalmonFilesDataFrame12.15 0.1816.28
subsetSwitchAnalyzeRlist0.030.000.03
switchAnalyzeRlist0.940.006.27
switchPlot1.940.001.94
switchPlotTranscript1.260.001.27
testData0.020.000.02

IsoformSwitchAnalyzeR.Rcheck/examples_x64/IsoformSwitchAnalyzeR-Ex.timings

nameusersystemelapsed
IsoformSwitchTestDEXSeq36.61 0.3642.27
IsoformSwitchTestDRIMSeq20.86 0.0526.20
analyzeAlternativSplicing6.530.026.55
analyzeCPAT0.070.010.07
analyzeCPC20.060.000.06
analyzeIUPred2A2.290.002.28
analyzeORF7.400.027.42
analyzePFAM0.470.020.48
analyzeSignalP0.060.010.08
analyzeSwitchConsequences0.740.020.75
expressionAnalysisPlots0.590.010.62
extractConsequenceEnrichment0.330.020.36
extractConsequenceEnrichmentComparison0.480.030.53
extractConsequenceSummary0.750.020.77
extractGeneExpression0.050.000.04
extractGenomeWideAnalysis1.670.011.69
extractGenomeWideSplicingAnalysis1.880.021.89
extractSequence9.680.059.74
extractSplicingEnrichment0.80.00.8
extractSplicingEnrichmentComparison0.990.000.99
extractSplicingSummary0.810.000.83
extractSwitchOverlap0.390.010.42
extractSwitchSummary8.750.008.80
extractTopSwitches9.360.009.36
getCDS000
importCufflinksGalaxyData25.30 0.1125.41
importGTF0.780.003.42
importIsoformExpression0.590.003.33
importRdata1.500.066.85
importSalmonData36.64 1.1748.08
isoformSwitchAnalysisCombined11.22 0.1011.31
isoformSwitchAnalysisPart18.060.068.12
isoformSwitchAnalysisPart24.140.054.18
isoformToGeneExp2.070.039.97
isoformToIsoformFraction0.360.010.42
preFilter0.010.020.03
prepareSalmonFilesDataFrame15.25 0.3420.75
subsetSwitchAnalyzeRlist0.020.020.03
switchAnalyzeRlist1.330.026.67
switchPlot2.570.012.61
switchPlotTranscript1.800.031.84
testData0.020.000.01