Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:09 -0400 (Fri, 15 Oct 2021).

CHECK results for IsoformSwitchAnalyzeR on tokay2

To the developers/maintainers of the IsoformSwitchAnalyzeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IsoformSwitchAnalyzeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 951/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IsoformSwitchAnalyzeR 1.14.1  (landing page)
Kristoffer Vitting-Seerup
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/IsoformSwitchAnalyzeR
git_branch: RELEASE_3_13
git_last_commit: 215dc6f
git_last_commit_date: 2021-10-01 07:42:43 -0400 (Fri, 01 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IsoformSwitchAnalyzeR
Version: 1.14.1
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.14.1.tar.gz
StartedAt: 2021-10-15 00:56:55 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 01:17:22 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 1226.7 seconds
RetCode: 0
Status:   OK  
CheckDir: IsoformSwitchAnalyzeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings IsoformSwitchAnalyzeR_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/IsoformSwitchAnalyzeR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.14.1'
* 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  6.9Mb
  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'
analyzeNovelIsoformORF: no visible binding for global variable
  'orf_origin'
analyzeNovelIsoformORF: no visible binding for global variable
  'orfStartGenomic'
analyzeNovelIsoformORF: no visible binding for global variable
  'isoform_id'
analyzeNovelIsoformORF: no visible binding for global variable
  'orfEndGenomic'
compareAnnotationOfTwoIsoforms: no visible global function definition
  for 'queryHits'
compareAnnotationOfTwoIsoforms: no visible global function definition
  for 'subjectHits'
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 'ref_gene_id'
importRdata: no visible binding for global variable 'n_ref_gene_ids'
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_ref_gene_id'
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_ref_gene_id'
importRdata: no visible binding for global variable 'has_novel_iso'
importRdata: no visible binding for global variable 'gene_name'
importRdata: no visible binding for global variable 'n_ref'
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'
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_novel_iso has_ref_gene_id idNr isoFraction
  isoform_feature isoform_id known_ref_gene_id log2_overlap_ratio
  metadata nTot n_iso_na n_ref n_ref_gene_ids novel_iso
  nrGenesWithConsequences nrIsoWithConsequences nt_overlap
  orfEndGenomic orfStartGenomic orf_origin propCiHi propCiLo
  propOfRelevantEvents propUp propUpCiHi propUpCiLo queryHits
  ref_gene_id 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 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IsoformSwitchAnalyzeR/libs/i386/IsoformSwitchAnalyzeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.13-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
IsoformSwitchTestDEXSeq       56.59   1.52   63.38
importSalmonData              44.97   1.25   62.34
isoformSwitchAnalysisCombined 42.66   1.26   43.93
extractSequence               18.68   0.06   18.76
IsoformSwitchTestDRIMSeq      18.34   0.03   23.62
extractTopSwitches            16.50   0.05   16.55
analyzeORF                    16.29   0.04   16.35
extractSwitchSummary          16.10   0.03   16.12
isoformSwitchAnalysisPart1    15.98   0.04   16.01
prepareSalmonFilesDataFrame   15.39   0.25   23.59
analyzeAlternativSplicing      7.10   0.02    7.13
isoformToGeneExp               2.82   0.07   10.78
switchAnalyzeRlist             2.38   0.02    7.64
importRdata                    2.30   0.00    8.33
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
IsoformSwitchTestDEXSeq       63.16   0.20   68.59
isoformSwitchAnalysisCombined 43.40   0.80   44.21
importSalmonData              40.51   1.45   57.16
IsoformSwitchTestDRIMSeq      24.62   0.05   29.95
analyzeORF                    19.89   0.03   19.92
extractSequence               19.25   0.01   19.27
extractSwitchSummary          19.02   0.00   19.02
extractTopSwitches            18.29   0.04   18.33
isoformSwitchAnalysisPart1    15.36   0.03   15.39
prepareSalmonFilesDataFrame   14.08   0.33   21.28
analyzeAlternativSplicing      7.73   0.00    7.74
isoformToGeneExp               2.93   0.03   10.85
importRdata                    2.24   0.03    7.48
switchAnalyzeRlist             1.98   0.00    7.25
* 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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log'
for details.

Installation output

IsoformSwitchAnalyzeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/IsoformSwitchAnalyzeR_1.14.1.tar.gz && rm -rf IsoformSwitchAnalyzeR.buildbin-libdir && mkdir IsoformSwitchAnalyzeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL IsoformSwitchAnalyzeR_1.14.1.zip && rm IsoformSwitchAnalyzeR_1.14.1.tar.gz IsoformSwitchAnalyzeR_1.14.1.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
  0 2918k    0 16225    0     0   132k      0  0:00:22 --:--:--  0:00:22  133k
100 2918k  100 2918k    0     0  3046k      0 --:--:-- --:--:-- --:--:-- 3046k

install for i386

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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

    addORFfromGTF                           html  
    analyzeAlternativSplicing               html  
    analyzeCPAT                             html  
    analyzeCPC2                             html  
    analyzeIUPred2A                         html  
    analyzeNetSurf2                         html  
    analyzeNovelIsoformORF                  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"C:/Users/BIOCBU~1/BBS-3~1.13-/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 -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/IsoformSwitchAnalyzeR.buildbin-libdir/IsoformSwitchAnalyzeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IsoformSwitchAnalyzeR' as IsoformSwitchAnalyzeR_1.14.1.zip
* DONE (IsoformSwitchAnalyzeR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'IsoformSwitchAnalyzeR' successfully unpacked and MD5 sums checked

Tests output

Example timings

IsoformSwitchAnalyzeR.Rcheck/examples_i386/IsoformSwitchAnalyzeR-Ex.timings

nameusersystemelapsed
IsoformSwitchTestDEXSeq56.59 1.5263.38
IsoformSwitchTestDRIMSeq18.34 0.0323.62
addORFfromGTF1.270.033.92
analyzeAlternativSplicing7.100.027.13
analyzeCPAT0.060.000.36
analyzeCPC20.130.000.14
analyzeIUPred2A2.870.012.89
analyzeNovelIsoformORF0.740.020.75
analyzeORF16.29 0.0416.35
analyzePFAM0.470.020.51
analyzeSignalP0.100.000.11
analyzeSwitchConsequences0.970.020.98
expressionAnalysisPlots0.760.000.77
extractConsequenceEnrichment0.420.010.43
extractConsequenceEnrichmentComparison0.670.030.71
extractConsequenceSummary0.690.000.68
extractGeneExpression0.040.000.05
extractGenomeWideAnalysis2.380.142.52
extractGenomeWideSplicingAnalysis3.190.073.25
extractSequence18.68 0.0618.76
extractSplicingEnrichment1.140.031.17
extractSplicingEnrichmentComparison1.200.051.25
extractSplicingSummary0.970.010.98
extractSwitchOverlap0.500.020.52
extractSwitchSummary16.10 0.0316.12
extractTopSwitches16.50 0.0516.55
getCDS000
importCufflinksGalaxyData000
importGTF1.270.003.89
importIsoformExpression1.290.063.98
importRdata2.300.008.33
importSalmonData44.97 1.2562.34
isoformSwitchAnalysisCombined42.66 1.2643.93
isoformSwitchAnalysisPart115.98 0.0416.01
isoformSwitchAnalysisPart23.560.033.60
isoformToGeneExp 2.82 0.0710.78
isoformToIsoformFraction0.510.020.54
preFilter0.050.000.05
prepareSalmonFilesDataFrame15.39 0.2523.59
subsetSwitchAnalyzeRlist0.030.000.04
switchAnalyzeRlist2.380.027.64
switchPlot3.680.013.70
switchPlotTranscript2.460.022.47
testData0.010.010.03

IsoformSwitchAnalyzeR.Rcheck/examples_x64/IsoformSwitchAnalyzeR-Ex.timings

nameusersystemelapsed
IsoformSwitchTestDEXSeq63.16 0.2068.59
IsoformSwitchTestDRIMSeq24.62 0.0529.95
addORFfromGTF1.270.003.90
analyzeAlternativSplicing7.730.007.74
analyzeCPAT0.050.010.06
analyzeCPC20.050.020.06
analyzeIUPred2A3.000.013.02
analyzeNovelIsoformORF0.840.020.86
analyzeORF19.89 0.0319.92
analyzePFAM0.420.000.42
analyzeSignalP0.10.00.1
analyzeSwitchConsequences0.930.020.95
expressionAnalysisPlots0.830.010.84
extractConsequenceEnrichment0.470.000.47
extractConsequenceEnrichmentComparison0.70.00.7
extractConsequenceSummary0.690.000.69
extractGeneExpression0.040.000.05
extractGenomeWideAnalysis2.190.022.20
extractGenomeWideSplicingAnalysis2.380.002.37
extractSequence19.25 0.0119.27
extractSplicingEnrichment1.130.001.13
extractSplicingEnrichmentComparison1.270.001.26
extractSplicingSummary0.940.020.95
extractSwitchOverlap0.480.010.50
extractSwitchSummary19.02 0.0019.02
extractTopSwitches18.29 0.0418.33
getCDS000
importCufflinksGalaxyData000
importGTF1.280.003.91
importIsoformExpression1.200.063.91
importRdata2.240.037.48
importSalmonData40.51 1.4557.16
isoformSwitchAnalysisCombined43.40 0.8044.21
isoformSwitchAnalysisPart115.36 0.0315.39
isoformSwitchAnalysisPart23.890.023.90
isoformToGeneExp 2.93 0.0310.85
isoformToIsoformFraction0.290.010.29
preFilter0.050.000.05
prepareSalmonFilesDataFrame14.08 0.3321.28
subsetSwitchAnalyzeRlist0.030.000.03
switchAnalyzeRlist1.980.007.25
switchPlot3.740.003.74
switchPlotTranscript2.230.022.25
testData0.020.000.01