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BioC 3.3: CHECK report for MineICA on windows2.bioconductor.org

This page was generated on 2015-10-27 12:15:12 -0400 (Tue, 27 Oct 2015).

Package 644/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MineICA 1.11.0
Anne Biton
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MineICA
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MineICA
Version: 1.11.0
Command: rm -rf MineICA.buildbin-libdir MineICA.Rcheck && mkdir MineICA.buildbin-libdir MineICA.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MineICA.buildbin-libdir MineICA_1.11.0.tar.gz >MineICA.Rcheck\00install.out 2>&1 && cp MineICA.Rcheck\00install.out MineICA-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MineICA.buildbin-libdir --install="check:MineICA-install.out" --force-multiarch --no-vignettes --timings MineICA_1.11.0.tar.gz
StartedAt: 2015-10-27 04:10:01 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:14:14 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 253.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MineICA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MineICA.buildbin-libdir MineICA.Rcheck && mkdir MineICA.buildbin-libdir MineICA.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MineICA.buildbin-libdir MineICA_1.11.0.tar.gz >MineICA.Rcheck\00install.out 2>&1 && cp MineICA.Rcheck\00install.out MineICA-install.out  && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=MineICA.buildbin-libdir --install="check:MineICA-install.out" --force-multiarch --no-vignettes --timings MineICA_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/MineICA.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MineICA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MineICA' version '1.11.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'

Depends: includes the non-default packages:
  'BiocGenerics' 'Biobase' 'plyr' 'ggplot2' 'scales' 'foreach' 'xtable'
  'biomaRt' 'gtools' 'GOstats' 'cluster' 'marray' 'mclust'
  'RColorBrewer' 'colorspace' 'igraph' 'Rgraphviz' 'graph' 'annotate'
  'Hmisc' 'fastICA' 'JADE'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'MineICA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'biomaRt' 'GOstats' 'cluster' 'mclust' 'igraph'
A package should be listed in only one of these fields.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GOstats' which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'lumiHumanAll.db'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GOstats' 'Hmisc' 'JADE' 'RColorBrewer' 'Rgraphviz' 'annotate'
  'biomaRt' 'cluster' 'colorspace' 'fastICA' 'foreach' 'ggplot2'
  'graph' 'gtools' 'igraph' 'marray' 'mclust' 'methods' 'plyr' 'scales'
  'xtable'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'Biobase:::annotation' 'Biobase:::validMsg' 'fpc:::pamk'
  'lumi:::getChipInfo' 'mclust:::adjustedRandIndex'
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: 'Biobase:::isValidVersion'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGenesToGoReport: no visible global function definition for
  'geneIdsByCategory'
addGenesToGoReport: no visible global function definition for
  'geneIdUniverse'
addGenesToGoReport: no visible global function definition for
  'conditional'
addGenesToGoReport: no visible global function definition for
  'sigCategories'
annot2Color: no visible global function definition for 'brewer.pal'
annot2Color: no visible global function definition for 'heat_hcl'
annot2Color: no visible global function definition for 'terrain_hcl'
annot2Color: no visible global function definition for 'rainbow_hcl'
annotFeaturesComp: no visible global function definition for 'getEG'
annotFeaturesComp: no visible global function definition for
  'getSYMBOL'
annotFeaturesComp: no visible global function definition for 'llply'
annotFeaturesWithBiomaRt: no visible global function definition for
  'useMart'
annotFeaturesWithBiomaRt: no visible global function definition for
  'listFilters'
annotFeaturesWithBiomaRt: no visible global function definition for
  'listAttributes'
annotFeaturesWithBiomaRt: no visible global function definition for
  'getBM'
clusVarAnalysis: no visible global function definition for '%do%'
clusVarAnalysis: no visible global function definition for 'foreach'
clusVarAnalysis: no visible global function definition for 'ggplot'
clusVarAnalysis: no visible global function definition for 'geom_bar'
clusVarAnalysis: no visible global function definition for 'aes'
clusVarAnalysis: no visible binding for global variable 'cluster'
clusVarAnalysis: no visible global function definition for 'xlab'
clusVarAnalysis: no visible global function definition for 'ggtitle'
clusVarAnalysis: no visible global function definition for
  'scale_fill_manual'
clusVarAnalysis: no visible global function definition for 'ggsave'
clusterFastICARuns: no visible global function definition for 'fastICA'
clusterFastICARuns: no visible global function definition for '%dopar%'
clusterFastICARuns: no visible global function definition for 'foreach'
clusterFastICARuns: no visible global function definition for 'agnes'
clusterFastICARuns: no visible global function definition for 'pam'
clusterSamplesByComp: no visible global function definition for '%do%'
clusterSamplesByComp: no visible global function definition for
  'foreach'
clusterSamplesByComp: no visible global function definition for
  'Mclust'
clusterSamplesByComp: no visible global function definition for 'pam'
clusterSamplesByComp: no visible global function definition for 'agnes'
clusterSamplesByComp: no visible binding for global variable 'cluster'
clusterSamplesByComp_multiple: no visible global function definition
  for '%do%'
clusterSamplesByComp_multiple: no visible global function definition
  for 'foreach'
compareGenes: no visible global function definition for 'useMart'
compareGenes: no visible global function definition for '%dopar%'
compareGenes: no visible global function definition for 'foreach'
compareGenes: no visible global function definition for 'llply'
cor2An: no visible global function definition for 'rcorr'
doEnrichment: no visible global function definition for 'hyperGTest'
heatmap.plus: no visible binding for global variable 'agnes'
hypergeoAn: no visible global function definition for 'llply'
mergeGostatsResults: no visible global function definition for
  '%dopar%'
mergeGostatsResults: no visible global function definition for
  'foreach'
mergeGostatsResults : <anonymous>: no visible global function
  definition for '%dopar%'
mergeGostatsResults : <anonymous>: no visible global function
  definition for 'foreach'
mergeGostatsResults : <anonymous>: no visible global function
  definition for 'xtable'
mergeGostatsResults : <anonymous>: no visible global function
  definition for '%do%'
mergeGostatsResults: no visible global function definition for 'xtable'
nbOccInComp: no visible global function definition for '%dopar%'
nbOccInComp: no visible global function definition for 'foreach'
nbOccInComp: no visible global function definition for 'xtable'
nodeAttrs: no visible global function definition for '%do%'
nodeAttrs: no visible global function definition for 'foreach'
plotAllMix: no visible binding for global variable 'Mclust'
plotCorGraph: no visible global function definition for 'brewer.pal'
plotCorGraph: no visible global function definition for 'llply'
plotCorGraph: no visible global function definition for
  'igraph.from.graphNEL'
plotCorGraph: no visible global function definition for 'V'
plotCorGraph: no visible global function definition for 'V<-'
plotCorGraph: no visible global function definition for 'E'
plotCorGraph: no visible global function definition for 'E<-'
plotCorGraph: no visible global function definition for
  'layout.fruchterman.reingold'
plotCorGraph: no visible global function definition for 'vcount'
plotCorGraph: no visible global function definition for
  'tkplot.fit.to.screen'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'ggplot'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'geom_density'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'aes'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'geom_point'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'scale_colour_gradientn'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'maPalette'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'scale_x_discrete'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'geom_hline'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'annotate'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'geom_histogram'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'scale_y_continuous'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'scale_x_continuous'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'geom_boxplot'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'theme_bw'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'geom_jitter'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'position_jitter'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'theme'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'element_text'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'unit'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'scale_linetype_manual'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'scale_fill_manual'
plotDens2classInComp_plotOnly: no visible global function definition
  for 'ggtitle'
plotDensAllAnnotInAllComp: no visible global function definition for
  '%dopar%'
plotDensAllAnnotInAllComp: no visible global function definition for
  'foreach'
plotDensOneAnnotInAllComp : vplayout: no visible global function
  definition for 'viewport'
plotDensOneAnnotInAllComp: no visible global function definition for
  'ggsave'
plotMclust: no visible global function definition for 'cdens'
plotMix: no visible global function definition for 'cdens'
plotNumVarComp: no visible global function definition for 'ggplot'
plotNumVarComp: no visible global function definition for 'geom_point'
plotNumVarComp: no visible global function definition for 'aes'
plotNumVarComp: no visible global function definition for 'geom_smooth'
plotNumVarComp: no visible global function definition for
  'scale_colour_manual'
plotNumVarComp: no visible global function definition for
  'scale_shape_manual'
plotNumVarComp: no visible global function definition for 'ggtitle'
plotNumVarComp: no visible global function definition for
  'scale_colour_gradientn'
plotNumVarComp: no visible global function definition for 'maPalette'
plotPosOneAnnotInComp_ggplot : vplayout: no visible global function
  definition for 'viewport'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  '%dopar%'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'foreach'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'grid.newpage'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'pushViewport'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'viewport'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'grid.layout'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'ggplot'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'geom_histogram'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'aes'
plotPosOneAnnotLevInComp_ggplot: no visible binding for global variable
  '..count..'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'scale_fill_manual'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'theme'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'element_text'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'unit'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'xlab'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'geom_point'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'scale_colour_gradientn'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'maPalette'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'geom_hline'
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for 'annotate'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'maPalette'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'maColorBar'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'odd'
plotPosSamplesInComp_ggplot : vplayout: no visible global function
  definition for 'viewport'
plotPosSamplesInComp_ggplot: no visible global function definition for
  '%dopar%'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'foreach'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'ggplot'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'geom_histogram'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'aes'
plotPosSamplesInComp_ggplot: no visible binding for global variable
  '..count..'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'theme'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'element_text'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'unit'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'xlab'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'ggtitle'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'geom_point'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'scale_colour_gradientn'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'maPalette'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'geom_hline'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'annotate'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'grid.newpage'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'pushViewport'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'viewport'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'grid.layout'
plot_heatmapsOnSel: no visible global function definition for
  'maPalette'
plot_heatmapsOnSel: no visible global function definition for '%do%'
plot_heatmapsOnSel: no visible global function definition for 'foreach'
plot_heatmapsOnSel: no visible global function definition for '%dopar%'
plot_heatmapsOnSel: no visible global function definition for
  'maColorBar'
plot_heatmapsOnSel: no visible global function definition for 'odd'
qualVarAnalysis: no visible global function definition for '%dopar%'
qualVarAnalysis: no visible global function definition for 'foreach'
qualVarAnalysis : <anonymous>: no visible global function definition
  for 'ggsave'
quantVarAnalysis: no visible global function definition for '%dopar%'
quantVarAnalysis: no visible global function definition for 'foreach'
quantVarAnalysis : <anonymous>: no visible global function definition
  for 'ggsave'
runAn: no visible global function definition for 'useMart'
runAn: no visible global function definition for '%do%'
runAn: no visible global function definition for 'foreach'
runAn: no visible global function definition for 'maPalette'
runCompareIcaSets: no visible global function definition for '%do%'
runCompareIcaSets: no visible global function definition for 'foreach'
runEnrich: no visible global function definition for 'llply'
runEnrich: no visible global function definition for 'listFilters'
runEnrich: no visible global function definition for 'getBM'
runICA: no visible global function definition for 'JADE'
runICA: no visible global function definition for 'fastICA'
wilcoxOrKruskalOnA: no visible global function definition for '%dopar%'
wilcoxOrKruskalOnA: no visible global function definition for 'foreach'
writeGenes: no visible global function definition for 'useMart'
writeGenes: no visible global function definition for 'listFilters'
writeGenes: no visible global function definition for 'listAttributes'
writeGenes: no visible global function definition for 'getBM'
writeGenes: no visible global function definition for 'xtable'
writeGostatsHtmltable: no visible global function definition for
  'xtable'
writeHtmlResTestsByAnnot: no visible global function definition for
  'llply'
writeHtmlResTestsByAnnot: no visible global function definition for
  'xtable'
writeProjByComp: no visible global function definition for 'useMart'
writeProjByComp: no visible global function definition for '%do%'
writeProjByComp: no visible global function definition for 'foreach'
initialize,IcaSet: no visible global function definition for 'useMart'
selectContrib,IcaSet-numeric-character: no visible global function
  definition for '%do%'
selectContrib,IcaSet-numeric-character: no visible global function
  definition for 'foreach'
selectContrib,IcaSet-numeric-character: no visible binding for global
  variable 'comp.proj'
selectContrib,IcaSet-numeric-character: no visible binding for global
  variable 'cutt'
selectContrib,list-numeric-ANY: no visible global function definition
  for '%do%'
selectContrib,list-numeric-ANY: no visible global function definition
  for 'foreach'
Undefined global functions or variables:
  %do% %dopar% ..count.. E E<- JADE Mclust V V<- aes agnes annotate
  brewer.pal cdens cluster comp.proj conditional cutt element_text
  fastICA foreach geneIdUniverse geneIdsByCategory geom_bar
  geom_boxplot geom_density geom_histogram geom_hline geom_jitter
  geom_point geom_smooth getBM getEG getSYMBOL ggplot ggsave ggtitle
  grid.layout grid.newpage heat_hcl hyperGTest igraph.from.graphNEL
  layout.fruchterman.reingold listAttributes listFilters llply
  maColorBar maPalette odd pam position_jitter pushViewport rainbow_hcl
  rcorr scale_colour_gradientn scale_colour_manual scale_fill_manual
  scale_linetype_manual scale_shape_manual scale_x_continuous
  scale_x_discrete scale_y_continuous sigCategories terrain_hcl theme
  theme_bw tkplot.fit.to.screen unit useMart vcount viewport xlab
  xtable
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [20s] OK
** running examples for arch 'x64' ... [22s] 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: 4 NOTEs
See
  'c:/biocbld/bbs-3.3-bioc/meat/MineICA.Rcheck/00check.log'
for details.

MineICA.Rcheck/00install.out:


install for i386

* installing *source* package 'MineICA' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'sampleNames<-' in package 'MineICA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MineICA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MineICA' as MineICA_1.11.0.zip
* DONE (MineICA)

MineICA.Rcheck/examples_i386/MineICA-Ex.timings:

nameusersystemelapsed
annotFeatures0.210.010.22
annotFeaturesComp1.860.001.87
annotFeaturesWithBiomaRt000
annotInGene0.920.000.92
annotReciprocal0.010.000.02
buildIcaSet0.360.030.62
buildMineICAParams0.000.000.49
class-IcaSet0.160.020.28
class-MineICAParams000
clusVarAnalysis0.090.010.36
clusterFastICARuns0.160.000.16
clusterSamplesByComp1.810.002.04
clusterSamplesByComp_multiple0.250.020.50
compareAn0.580.000.82
compareAn2graphfile0.400.000.64
compareGenes000
cor2An0.020.000.02
getProj0.010.010.03
getSdExpr000
hypergeoAn0.000.020.01
nbOccByGeneInComp000
nbOccInComp0.300.000.54
nbOccInComp_simple0.060.000.31
nodeAttrs000
plotAllMix1.050.001.04
plotCorGraph0.940.001.19
plotDensAllAnnotInAllComp000
plotDensOneAnnotInAllComp000
plotMclust0.150.000.16
plotMix0.140.000.14
plotPosAnnotInComp000
plotPosSamplesInComp000
plot_heatmapsOnSel000
qualVarAnalysis0.100.020.34
quantVarAnalysis0.140.000.41
relativePath0.010.000.01
runAn000
runCompareIcaSets0.830.011.08
runEnrich000
runICA0.050.000.05
selectContrib000
selectFeatures_IQR0.080.020.09
selectWitnessGenes0.220.000.46
writeGenes0.000.010.01
writeGostatsHtmltable0.010.000.02
writeProjByComp000

MineICA.Rcheck/examples_x64/MineICA-Ex.timings:

nameusersystemelapsed
annotFeatures0.270.000.27
annotFeaturesComp2.110.002.13
annotFeaturesWithBiomaRt0.010.000.01
annotInGene1.140.011.16
annotReciprocal0.000.020.02
buildIcaSet0.530.080.84
buildMineICAParams0.000.000.36
class-IcaSet0.220.010.33
class-MineICAParams000
clusVarAnalysis0.080.020.36
clusterFastICARuns0.110.000.11
clusterSamplesByComp1.760.012.01
clusterSamplesByComp_multiple0.330.020.58
compareAn0.580.000.81
compareAn2graphfile0.520.000.75
compareGenes000
cor2An0.020.000.01
getProj0.030.000.03
getSdExpr000
hypergeoAn000
nbOccByGeneInComp0.010.000.02
nbOccInComp0.160.020.42
nbOccInComp_simple0.050.000.28
nodeAttrs0.010.000.02
plotAllMix1.050.001.05
plotCorGraph0.780.001.01
plotDensAllAnnotInAllComp000
plotDensOneAnnotInAllComp000
plotMclust0.140.000.14
plotMix0.450.000.45
plotPosAnnotInComp000
plotPosSamplesInComp000
plot_heatmapsOnSel000
qualVarAnalysis0.110.000.36
quantVarAnalysis0.150.000.43
relativePath000
runAn000
runCompareIcaSets0.750.001.00
runEnrich000
runICA0.060.010.08
selectContrib000
selectFeatures_IQR0.100.020.11
selectWitnessGenes0.200.010.45
writeGenes000
writeGostatsHtmltable0.000.020.01
writeProjByComp000