Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2021-06-22 12:06:03 -0400 (Tue, 22 Jun 2021).

CHECK results for MineICA on riesling1

To the developers/maintainers of the MineICA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MineICA.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 1108/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MineICA 1.33.0  (landing page)
Anne Biton
Snapshot Date: 2021-06-21 14:50:06 -0400 (Mon, 21 Jun 2021)
URL: https://git.bioconductor.org/packages/MineICA
Branch: master
Last Commit: 264a958
Last Changed Date: 2021-05-19 11:57:33 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GOstats' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MineICA
Version: 1.33.0
Command: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MineICA.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MineICA_1.33.0.tar.gz
StartedAt: 2021-06-22 01:00:53 -0400 (Tue, 22 Jun 2021)
EndedAt: 2021-06-22 01:07:33 -0400 (Tue, 22 Jun 2021)
EllapsedTime: 400.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MineICA.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MineICA.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MineICA_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/MineICA.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.33.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/Alist.Rd:26: missing link 'class-IcaSet'
  Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/Slist.Rd:28: missing link 'class-IcaSet'
  Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/class-IcaSet.Rd:321: missing link 'class-IcaSet'
  Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/getComp.Rd:33: missing link 'class-IcaSet'
See 'D:/biocbuild/bbs-3.14-bioc/meat/MineICA.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'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 'cm.colors'
annot2Color: no visible global function definition for 'rainbow_hcl'
annotFeatures: no visible global function definition for 'na.omit'
annotFeaturesComp: no visible global function definition for 'getEG'
annotFeaturesComp: no visible global function definition for
  'getSYMBOL'
annotFeaturesComp: no visible global function definition for 'llply'
annotFeaturesComp : <anonymous> : <anonymous>: no visible global
  function definition for 'median'
annotFeaturesComp : <anonymous>: no visible binding for global variable
  'median'
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'
annotReciprocal: no visible global function definition for
  'write.table'
buildIcaSet: no visible global function definition for 'new'
buildIcaSet: no visible global function definition for 'read.table'
buildMineICAParams: no visible global function definition for 'new'
clusVarAnalysis : <anonymous> : <anonymous>: no visible global function
  definition for 'chisq.test'
clusVarAnalysis : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'chisq.test'
clusVarAnalysis: no visible binding for global variable 'p.adjust'
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'
clusVarAnalysis: no visible global function definition for
  'write.table'
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 'cor'
clusterFastICARuns: no visible global function definition for 'hclust'
clusterFastICARuns: no visible global function definition for 'as.dist'
clusterFastICARuns: no visible global function definition for 'cutree'
clusterFastICARuns: no visible global function definition for 'agnes'
clusterFastICARuns: no visible global function definition for
  'as.hclust'
clusterFastICARuns: no visible global function definition for 'pam'
clusterFastICARuns: no visible global function definition for 'kmeans'
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
  'kmeans'
clusterSamplesByComp: no visible global function definition for 'pam'
clusterSamplesByComp: no visible global function definition for 'dist'
clusterSamplesByComp: no visible global function definition for
  'hclust'
clusterSamplesByComp: no visible global function definition for
  'cutree'
clusterSamplesByComp: no visible global function definition for 'agnes'
clusterSamplesByComp: no visible global function definition for
  'as.hclust'
clusterSamplesByComp: no visible binding for global variable 'cluster'
clusterSamplesByComp: no visible global function definition for
  'write.table'
clusterSamplesByComp_multiple: no visible global function definition
  for '%do%'
clusterSamplesByComp_multiple: no visible global function definition
  for 'foreach'
clusterSamplesByComp_multiple: no visible global function definition
  for 'aggregate'
clusterSamplesByComp_multiple: no visible global function definition
  for 'write.table'
compareAn: no visible global function definition for 'combn'
compareAn2graphfile : <anonymous>: no visible binding for global
  variable 'cor'
compareAn2graphfile: no visible global function definition for
  'write.table'
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'
compareGenes: no visible binding for global variable 'median'
cor2An: no visible global function definition for 'rcorr'
cor2An : <anonymous>: no visible global function definition for
  'cor.test'
cor2An: no visible global function definition for 'cor.test'
correl2Comp: no visible global function definition for 'cor.test'
correl2Comp: no visible global function definition for 'cor'
doEnrichment: no visible global function definition for 'na.omit'
doEnrichment: no visible global function definition for 'new'
doEnrichment: no visible global function definition for 'hyperGTest'
heatmap.plus: no visible binding for global variable 'dist'
heatmap.plus: no visible binding for global variable 'agnes'
heatmap.plus : <anonymous>: no visible global function definition for
  'reorder'
heatmap.plus: no visible global function definition for 'as.dendrogram'
heatmap.plus: no visible global function definition for 'as.hclust'
heatmap.plus: no visible global function definition for
  'order.dendrogram'
heatmap.plus: no visible global function definition for 'par'
heatmap.plus: no visible global function definition for 'layout'
heatmap.plus: no visible global function definition for 'axis'
heatmap.plus: no visible global function definition for 'quantile'
heatmap.plus: no visible global function definition for 'heat.colors'
heatmap.plus: no visible global function definition for 'mtext'
heatmap.plus: no visible global function definition for 'frame'
heatmap.plus: no visible global function definition for 'title'
hypergeoAn: no visible global function definition for 'na.omit'
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 'capture.output'
mergeGostatsResults : <anonymous>: no visible global function
  definition for '%do%'
mergeGostatsResults: no visible global function definition for 'xtable'
mergeGostatsResults: no visible global function definition for
  'capture.output'
nbOccInComp: no visible global function definition for 'read.table'
nbOccInComp: no visible global function definition for 'aggregate'
nbOccInComp: no visible global function definition for 'pdf'
nbOccInComp: no visible global function definition for 'dev.off'
nbOccInComp: no visible global function definition for '%dopar%'
nbOccInComp: no visible global function definition for 'foreach'
nbOccInComp: no visible global function definition for 'xtable'
nbOccInComp: no visible global function definition for 'capture.output'
nodeAttrs: no visible global function definition for '%do%'
nodeAttrs: no visible global function definition for 'foreach'
nodeAttrs: no visible global function definition for 'write.table'
plotAllMix: no visible binding for global variable 'Mclust'
plotAllMix: no visible global function definition for 'par'
plotAllMix: no visible global function definition for 'dev.off'
plotCorGraph: no visible global function definition for 'brewer.pal'
plotCorGraph: no visible global function definition for 'llply'
plotCorGraph: no visible global function definition for 'new'
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'
plotMclust: no visible global function definition for 'points'
plotMix: no visible global function definition for 'shapiro.test'
plotMix: no visible global function definition for 'cdens'
plotMix: no visible global function definition for 'hist'
plotMix: no visible global function definition for 'points'
plotMix : <anonymous>: no visible global function definition for
  'points'
plotMix: no visible global function definition for 'lm'
plotMix: no visible global function definition for 'axis'
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 binding for global variable 'lm'
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'
plotPos2classInComp: no visible global function definition for 'pdf'
plotPos2classInComp: no visible global function definition for 'par'
plotPos2classInComp: no visible global function definition for 'hist'
plotPos2classInComp: no visible global function definition for 'lm'
plotPos2classInComp: no visible global function definition for 'axis'
plotPos2classInComp: no visible global function definition for 'abline'
plotPos2classInComp: no visible global function definition for 'legend'
plotPos2classInComp: no visible global function definition for
  'dev.off'
plotPosAnnotInComp : <anonymous>: no visible global function definition
  for 'graphics.off'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'pdf'
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'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  'dev.off'
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: no visible global function definition for 'pdf'
plotPosSamplesInComp: no visible global function definition for 'par'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'chisq.test'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'par'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'hist'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'lm'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'axis'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'legend'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'abline'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'points'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'quantile'
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 : <anonymous>: no visible global function
  definition for 'mtext'
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for 'title'
plotPosSamplesInComp: no visible global function definition for
  'dev.off'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'pdf'
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'
plotPosSamplesInComp_ggplot: no visible global function definition for
  'dev.off'
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 'pdf'
plot_heatmapsOnSel: no visible global function definition for
  'plot.new'
plot_heatmapsOnSel: no visible global function definition for 'legend'
plot_heatmapsOnSel: no visible global function definition for 'dev.off'
plot_heatmapsOnSel: no visible global function definition for '%dopar%'
plot_heatmapsOnSel: no visible global function definition for 'par'
plot_heatmapsOnSel: no visible global function definition for
  'maColorBar'
plot_heatmapsOnSel: no visible global function definition for 'odd'
qualVarAnalysis : <anonymous> : <anonymous>: no visible global function
  definition for 'wilcox.test'
qualVarAnalysis : <anonymous> : <anonymous>: no visible global function
  definition for 'kruskal.test'
qualVarAnalysis: no visible binding for global variable 'p.adjust'
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 : <anonymous> : <anonymous>: no visible global
  function definition for 'cor.test'
quantVarAnalysis: no visible binding for global variable 'p.adjust'
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'
readA: no visible global function definition for 'read.table'
readS: no visible global function definition for 'read.table'
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 : <anonymous>: no visible global function definition for
  'na.omit'
runEnrich: no visible global function definition for 'na.omit'
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'
subIcaSet: no visible global function definition for 'validObject'
wilcoxOrKruskalOnA: no visible global function definition for '%dopar%'
wilcoxOrKruskalOnA: no visible global function definition for 'foreach'
wilcoxOrKruskalOnA: no visible global function definition for
  'wilcox.test'
wilcoxOrKruskalOnA: no visible global function definition for
  'kruskal.test'
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'
writeGenes: no visible global function definition for 'capture.output'
writeGostatsHtmltable: no visible global function definition for
  'xtable'
writeGostatsHtmltable: no visible global function definition for
  'capture.output'
writeHtmlResTestsByAnnot: no visible global function definition for
  'llply'
writeHtmlResTestsByAnnot: no visible global function definition for
  'xtable'
writeHtmlResTestsByAnnot: no visible global function definition for
  'capture.output'
writeProjByComp: no visible global function definition for 'useMart'
writeProjByComp: no visible global function definition for '%do%'
writeProjByComp: no visible global function definition for 'foreach'
writeRnkFiles : <anonymous>: no visible global function definition for
  'write.table'
A<-,IcaSet: no visible global function definition for 'validObject'
Afile<-,MineICAParams: no visible global function definition for
  'validObject'
S<-,IcaSet: no visible global function definition for 'validObject'
SByGene<-,IcaSet: no visible global function definition for
  'validObject'
Sfile<-,MineICAParams: no visible global function definition for
  'validObject'
[<-,IcaSet-ANY-ANY-ANY: no visible global function definition for
  'validObject'
[<-,MineICAParams-ANY-ANY-ANY: no visible global function definition
  for 'validObject'
annot2col<-,MineICAParams: no visible global function definition for
  'validObject'
annotfile<-,MineICAParams: no visible global function definition for
  'validObject'
chipManu<-,IcaSet: no visible global function definition for
  'validObject'
chipVersion<-,IcaSet: no visible global function definition for
  'validObject'
compNames<-,IcaSet: no visible global function definition for
  'validObject'
dat<-,IcaSet: no visible global function definition for 'validObject'
datByGene<-,IcaSet: no visible global function definition for
  'validObject'
datfile<-,MineICAParams: no visible global function definition for
  'validObject'
genesPath<-,ANY: no visible global function definition for
  'validObject'
indComp<-,IcaSet: no visible global function definition for
  'validObject'
initialize,IcaSet: no visible global function definition for 'new'
initialize,IcaSet: no visible global function definition for 'useMart'
initialize,IcaSet: no visible global function definition for
  'callNextMethod'
mart<-,IcaSet: no visible global function definition for 'validObject'
organism<-,IcaSet: no visible global function definition for
  'validObject'
package<-,IcaSet: no visible global function definition for
  'validObject'
pvalCutoff<-,MineICAParams: no visible global function definition for
  'validObject'
refSamples<-,IcaSet: no visible global function definition for
  'validObject'
resPath<-,ANY: no visible global function definition for 'validObject'
sampleNames<-,IcaSet: no visible global function definition for
  'callNextMethod'
selCutoff<-,MineICAParams: no visible global function definition for
  'validObject'
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'
setA<-,IcaSet: no visible global function definition for 'validObject'
setAfile<-,MineICAParams: no visible global function definition for
  'validObject'
setAnnot2col<-,MineICAParams: no visible global function definition for
  'validObject'
setAnnotation<-,IcaSet: no visible global function definition for
  'validObject'
setAnnotfile<-,MineICAParams: no visible global function definition for
  'validObject'
setChipManu<-,IcaSet: no visible global function definition for
  'validObject'
setChipVersion<-,IcaSet: no visible global function definition for
  'validObject'
setDatfile<-,MineICAParams: no visible global function definition for
  'validObject'
setGenesPath<-,ANY: no visible global function definition for
  'validObject'
setIndComp<-,IcaSet: no visible global function definition for
  'validObject'
setLabelsComp<-,IcaSet: no visible global function definition for
  'validObject'
setMart<-,IcaSet: no visible global function definition for
  'validObject'
setPackage<-,IcaSet: no visible global function definition for
  'validObject'
setPvalCutoff<-,MineICAParams: no visible global function definition
  for 'validObject'
setRefSamples<-,IcaSet: no visible global function definition for
  'validObject'
setResPath<-,ANY: no visible global function definition for
  'validObject'
setSByGene<-,IcaSet: no visible global function definition for
  'validObject'
setSelCutoff<-,MineICAParams: no visible global function definition for
  'validObject'
setSfile<-,MineICAParams: no visible global function definition for
  'validObject'
setTypeID<-,IcaSet: no visible global function definition for
  'validObject'
setWitGenes<-,IcaSet: no visible global function definition for
  'validObject'
show,IcaSet: no visible global function definition for 'callNextMethod'
typeID<-,IcaSet: no visible global function definition for
  'validObject'
witGenes<-,IcaSet: no visible global function definition for
  'validObject'
Undefined global functions or variables:
  %do% %dopar% ..count.. E E<- JADE Mclust V V<- abline aes aggregate
  agnes annotate as.dendrogram as.dist as.hclust axis brewer.pal
  callNextMethod capture.output cdens chisq.test cluster cm.colors
  combn comp.proj conditional cor cor.test cutree cutt dev.off dist
  element_text fastICA foreach frame geneIdUniverse geneIdsByCategory
  geom_bar geom_boxplot geom_density geom_histogram geom_hline
  geom_jitter geom_point geom_smooth getBM getEG getSYMBOL ggplot
  ggsave ggtitle graphics.off grid.layout grid.newpage hclust
  heat.colors heat_hcl hist hyperGTest igraph.from.graphNEL kmeans
  kruskal.test layout layout.fruchterman.reingold legend listAttributes
  listFilters llply lm maColorBar maPalette median mtext na.omit new
  odd order.dendrogram p.adjust pam par pdf plot.new points
  position_jitter pushViewport quantile rainbow_hcl rcorr read.table
  reorder scale_colour_gradientn scale_colour_manual scale_fill_manual
  scale_linetype_manual scale_shape_manual scale_x_continuous
  scale_x_discrete scale_y_continuous shapiro.test sigCategories
  terrain_hcl theme theme_bw title tkplot.fit.to.screen unit useMart
  validObject vcount viewport wilcox.test write.table xlab xtable
Consider adding
  importFrom("grDevices", "cm.colors", "dev.off", "graphics.off",
             "heat.colors", "pdf")
  importFrom("graphics", "abline", "axis", "frame", "hist", "layout",
             "legend", "mtext", "par", "plot.new", "points", "title")
  importFrom("methods", "callNextMethod", "new", "validObject")
  importFrom("stats", "aggregate", "as.dendrogram", "as.dist",
             "as.hclust", "chisq.test", "cor", "cor.test", "cutree",
             "dist", "hclust", "kmeans", "kruskal.test", "lm", "median",
             "na.omit", "order.dendrogram", "p.adjust", "quantile",
             "reorder", "shapiro.test", "wilcox.test")
  importFrom("utils", "capture.output", "combn", "read.table",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Alist.Rd':
  'class-IcaSet'

Missing link or links in documentation object 'Slist.Rd':
  'class-IcaSet'

Missing link or links in documentation object 'class-IcaSet.Rd':
  'class-IcaSet'

Missing link or links in documentation object 'getComp.Rd':
  'class-IcaSet'

Missing link or links in documentation object 'runAn.Rd':
  '[Category:class-GOHyperGParams]{GOHyperGParams}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'MineICAParams'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
clusterFastICARuns 0.63   0.08   20.76
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
clusterFastICARuns 0.74   0.04   22.64
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  'D:/biocbuild/bbs-3.14-bioc/meat/MineICA.Rcheck/00check.log'
for details.



Installation output

MineICA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MineICA_1.33.0.tar.gz && rm -rf MineICA.buildbin-libdir && mkdir MineICA.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MineICA.buildbin-libdir MineICA_1.33.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MineICA_1.33.0.zip && rm MineICA_1.33.0.tar.gz MineICA_1.33.0.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  721k  100  721k    0     0  3796k      0 --:--:-- --:--:-- --:--:-- 3796k

install for i386

* installing *source* package 'MineICA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'sampleNames<-' in package 'MineICA'
** help
*** installing help indices
  converting help for package 'MineICA'
    finding HTML links ... done
    A                                       html  
REDIRECT:topic	 A<- -> A.html [ FAIL ]
REDIRECT:topic	 S<- -> A.html [ FAIL ]
REDIRECT:topic	 SByGene<- -> A.html [ FAIL ]
REDIRECT:topic	 setA<- -> A.html [ FAIL ]
REDIRECT:topic	 setS<- -> A.html [ FAIL ]
REDIRECT:topic	 setSByGene<- -> A.html [ FAIL ]
REDIRECT:topic	 A<-,IcaSet,data.frame-method -> A.html [ FAIL ]
REDIRECT:topic	 A<-,IcaSet-method -> A.html [ FAIL ]
REDIRECT:topic	 S<-,IcaSet,data.frame-method -> A.html [ FAIL ]
REDIRECT:topic	 S<-,IcaSet-method -> A.html [ FAIL ]
REDIRECT:topic	 SByGene<-,IcaSet,data.frame-method -> A.html [ FAIL ]
REDIRECT:topic	 SByGene<-,IcaSet-method -> A.html [ FAIL ]
    Alist                                   html  
    finding level-2 HTML links ... done

Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/Alist.Rd:26: missing link 'class-IcaSet'
    Slist                                   html  
Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/Slist.Rd:28: missing link 'class-IcaSet'
    addGenesToGoReport                      html  
    annot2Color                             html  
    annotCarbayo                            html  
    annotFeatures                           html  
    annotFeaturesComp                       html  
    annotFeaturesWithBiomaRt                html  
    annotInGene                             html  
    annotReciprocal                         html  
    buildIcaSet                             html  
    buildMineICAParams                      html  
    build_sortHeatmap                       html  
    class-IcaSet                            html  
REDIRECT:topic	 class:IcaSet -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 [<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 [<-,IcaSet,ANY,ANY,ANY,ANY-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 [<-,IcaSet,ANY,ANY,ANY-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 [<-,IcaSet,ANY,ANY-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 organism<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 organism<-,IcaSet-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 mart<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 mart<-,IcaSet-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 mart<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 chipVersion<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 chipVersion<-,IcaSet-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 chipVersion<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 indComp<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 compNames<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 witGenes<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 refSamples<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 refSamples<-,IcaSet-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 refSamples<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 typeID<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 typeID<-,IcaSet-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 typeID<-,IcaSet,list-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 chipManu<- -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 chipManu<-,IcaSet-method -> class-IcaSet.html [ FAIL ]
REDIRECT:topic	 chipManu<-,IcaSet,character-method -> class-IcaSet.html [ FAIL ]
Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/class-IcaSet.Rd:321: missing link 'class-IcaSet'
    class-MineICAParams                     html  
REDIRECT:topic	 class:MineICAParams -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 Sfile<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 Sfile<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 datfile<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 annotfile<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 genesPath<-,ANY-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 resPath<-,ANY-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 selCutoff<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 pvalCutoff<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 Afile<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 Sfile<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 annot2col<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 datfile<-,MineICAParams-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 datfile<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 Afile<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 Afile<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 annotfile<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 annotfile<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 resPath<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 resPath<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 genesPath<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 genesPath<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 annot2col<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 annot2col<-,MineICAParams,character-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 pvalCutoff<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 pvalCutoff<-,MineICAParams,numeric-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 selCutoff<- -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 selCutoff<-,MineICAParams,numeric-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 [<-,MineICAParams,ANY,ANY,ANY,ANY-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 [<-,MineICAParams,ANY,ANY,ANY-method -> class-MineICAParams.html [ FAIL ]
REDIRECT:topic	 [<-,MineICAParams,ANY,ANY-method -> class-MineICAParams.html [ FAIL ]
    clusVarAnalysis                         html  
    clusterFastICARuns                      html  
    clusterSamplesByComp                    html  
    clusterSamplesByComp_multiple           html  
    compareAn                               html  
    compareAn2graphfile                     html  
    compareGenes                            html  
    cor2An                                  html  
    correl2Comp                             html  
    dat                                     html  
REDIRECT:topic	 dat<- -> dat.html [ FAIL ]
REDIRECT:topic	 dat<-,IcaSet-method -> dat.html [ FAIL ]
REDIRECT:topic	 dat<-,IcaSet,matrix-method -> dat.html [ FAIL ]
REDIRECT:topic	 datByGene<- -> dat.html [ FAIL ]
REDIRECT:topic	 datByGene<-,IcaSet-method -> dat.html [ FAIL ]
REDIRECT:topic	 datByGene<-,IcaSet,matrix-method -> dat.html [ FAIL ]
    dataCarbayo                             html  
    doEnrichment                            html  
    getComp                                 html  
Rd warning: D:/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4CVfbn/R.INSTALL2e04512b4664/MineICA/man/getComp.Rd:33: missing link 'class-IcaSet'
    getProj                                 html  
    getSdExpr                               html  
    hgOver                                  html  
    hypergeoAn                              html  
    icaSetCarbayo                           html  
    icaSetKim                               html  
    icaSetRiester                           html  
    icaSetStransky                          html  
    indComp                                 html  
REDIRECT:topic	 indComp<- -> indComp.html [ FAIL ]
REDIRECT:topic	 indComp<-,IcaSet-method -> indComp.html [ FAIL ]
REDIRECT:topic	 compNames<- -> indComp.html [ FAIL ]
REDIRECT:topic	 compNames<-,IcaSet-method -> indComp.html [ FAIL ]
REDIRECT:topic	 witGenes<- -> indComp.html [ FAIL ]
REDIRECT:topic	 witGenes<-,IcaSet-method -> indComp.html [ FAIL ]
    mergeGostatsResults                     html  
    nbOccByGeneInComp                       html  
    nbOccInComp                             html  
    nbOccInComp_simple                      html  
    nodeAttrs                               html  
    plotAllMix                              html  
    plotCorGraph                            html  
    plotDens2classInComp_plotOnly           html  
    plotDensAllAnnotInAllComp               html  
    plotDensOneAnnotInAllComp               html  
    plotMclust                              html  
    plotMix                                 html  
    plotPosAnnotInComp                      html  
    plotPosOneAnnotInComp_ggplot            html  
    plotPosOneAnnotLevInComp_ggplot         html  
    plotPosSamplesInComp                    html  
    plot_heatmapsOnSel                      html  
    qualVarAnalysis                         html  
    quantVarAnalysis                        html  
    readA                                   html  
    readS                                   html  
    relativePath                            html  
    runAn                                   html  
    runCompareIcaSets                       html  
    runEnrich                               html  
    runICA                                  html  
    selectContrib                           html  
    selectFeatures_IQR                      html  
    selectWitnessGenes                      html  
    wilcoxOrKruskalOnA                      html  
    writeGenes                              html  
    writeGostatsHtmltable                   html  
    writeHtmlResTestsByAnnot                html  
    writeProjByComp                         html  
    writeRnkFiles                           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 'MineICA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MineICA' as MineICA_1.33.0.zip
* DONE (MineICA)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'MineICA' successfully unpacked and MD5 sums checked

Tests output


Example timings

MineICA.Rcheck/examples_i386/MineICA-Ex.timings

nameusersystemelapsed
annotFeatures0.160.030.19
annotFeaturesComp1.620.001.67
annotFeaturesWithBiomaRt000
annotInGene0.750.020.77
annotReciprocal0.010.000.02
buildIcaSet0.170.000.46
buildMineICAParams0.000.000.57
class-IcaSet0.130.001.09
class-MineICAParams000
clusVarAnalysis0.060.000.38
clusterFastICARuns 0.63 0.0820.76
clusterSamplesByComp1.230.011.52
clusterSamplesByComp_multiple0.090.020.39
compareAn0.250.060.59
compareAn2graphfile0.240.000.50
compareGenes000
cor2An0.000.020.02
getProj0.030.000.03
getSdExpr000
hypergeoAn000
nbOccByGeneInComp000
nbOccInComp0.110.000.39
nbOccInComp_simple0.020.000.35
nodeAttrs0.000.020.01
plotAllMix0.680.030.72
plotCorGraph0.460.000.74
plotDensAllAnnotInAllComp000
plotDensOneAnnotInAllComp000
plotMclust0.110.000.11
plotMix0.100.000.11
plotPosAnnotInComp000
plotPosSamplesInComp000
plot_heatmapsOnSel000
qualVarAnalysis0.040.010.36
quantVarAnalysis0.040.020.45
relativePath000
runAn000
runCompareIcaSets0.240.000.48
runEnrich000
runICA0.080.000.08
selectContrib000
selectFeatures_IQR0.040.010.06
selectWitnessGenes0.060.020.35
writeGenes000
writeGostatsHtmltable0.020.000.01
writeProjByComp000

MineICA.Rcheck/examples_x64/MineICA-Ex.timings

nameusersystemelapsed
annotFeatures0.150.020.17
annotFeaturesComp1.950.022.01
annotFeaturesWithBiomaRt000
annotInGene0.920.000.92
annotReciprocal000
buildIcaSet0.190.010.50
buildMineICAParams0.000.000.59
class-IcaSet0.140.031.07
class-MineICAParams000
clusVarAnalysis0.040.020.36
clusterFastICARuns 0.74 0.0422.64
clusterSamplesByComp1.250.001.52
clusterSamplesByComp_multiple0.160.000.42
compareAn0.410.080.78
compareAn2graphfile0.230.000.50
compareGenes000
cor2An000
getProj0.010.000.01
getSdExpr000
hypergeoAn000
nbOccByGeneInComp0.000.020.02
nbOccInComp0.130.000.40
nbOccInComp_simple0.010.000.29
nodeAttrs000
plotAllMix0.740.000.73
plotCorGraph0.510.000.80
plotDensAllAnnotInAllComp000
plotDensOneAnnotInAllComp000
plotMclust0.130.000.12
plotMix0.110.000.11
plotPosAnnotInComp000
plotPosSamplesInComp000
plot_heatmapsOnSel000
qualVarAnalysis0.060.000.36
quantVarAnalysis0.030.010.47
relativePath000
runAn000
runCompareIcaSets0.270.000.55
runEnrich000
runICA0.040.000.04
selectContrib000
selectFeatures_IQR0.060.000.07
selectWitnessGenes0.100.000.37
writeGenes000
writeGostatsHtmltable000
writeProjByComp000