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maigesPack 1.2.0
Gustavo H. Esteves
Last Changed Date: 2007-10-02 17:41:09 -0700
Last Changed Rev: 27709
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) x64  OK  OK  OK 
pitt Mac OS X (10.4.10) i386  OK [ ERROR ] OK 
Package: maigesPack
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check maigesPack_1.2.0.tar.gz
RetCode: 1
Time: 496.3 seconds
Status: ERROR
CheckDir: maigesPack.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/maigesPack.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.2.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maigesPack' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating maigesPack-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'maigesPack-Ex.R' failed.
The error most likely occurred in:

> ### * plot-methods
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: plot
> ### Title: Method plot for objects defined in this package
> ### Aliases: plot.maigesRaw plot.maiges plot.maigesANOVA plot.maigesDE
> ###   plot.maigesDEcluster plot.maigesClass plot.maigesRelNetB
> ###   plot.maigesRelNetM plot.maigesActMod plot.maigesActNet plot
> ### Keywords: array
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Example with an object of class maigesRaw, without and with backgound
> ## subtraction, also we present a plot with normexp (from limma package)
> ## subtract algorithm.
> plot(gastro.raw[,1], bkgSub="none")
> plot(gastro.raw[,1], bkgSub="subtract")
> plot(gastro.raw[,1], bkgSub="normexp")
Green channel
Corrected array 1 
Red channel
Corrected array 1 
> 
> ## Example with an object of class maigesNorm, without and with backgound
> ## subtraction, also we present a plot with normexp (from limma package)
> ## subtract algorithm.
> plot(gastro.norm[,1], bkgSub="none")
Warning in plot.window(...) : "bkgSub" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "bkgSub" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "bkgSub" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "bkgSub" is not a graphical parameter
Warning in box(...) : "bkgSub" is not a graphical parameter
Warning in title(...) : "bkgSub" is not a graphical parameter
> plot(gastro.norm[,1], bkgSub="subtract")
Warning in plot.window(...) : "bkgSub" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "bkgSub" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "bkgSub" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "bkgSub" is not a graphical parameter
Warning in box(...) : "bkgSub" is not a graphical parameter
Warning in title(...) : "bkgSub" is not a graphical parameter
> plot(gastro.summ[,1], bkgSub="normexp")
Warning in plot.window(...) : "bkgSub" is not a graphical parameter
Warning in plot.xy(xy, type, ...) :
  "bkgSub" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "bkgSub" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "bkgSub" is not a graphical parameter
Warning in box(...) : "bkgSub" is not a graphical parameter
Warning in title(...) : "bkgSub" is not a graphical parameter
> 
> 
> ## Example for objects of class maigesDE.
> 
> ## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
> ## specifies one thousand bootstraps
> gastro.ttest = deGenes2by2Ttest(gastro.summ, sLabelID="Type")
> 
> plot(gastro.ttest) ## Volcano plot
> 
> ## Example for object of class maigesClass.
> 
> ## Doing LDA classifier with 3 genes for the 6th gene group comparing
> ## the 2 categories from 'Type' sample label.
> gastro.class = classifyLDA(gastro.summ, sLabelID="Type",
+   gNameID="GeneName", nGenes=3, geneGrp=6)
> 
> plot(gastro.class) ## plot the 1st classifier
Loading required package: rgl
Error in rgl.open() : 
  X11 protocol error: BadMatch (invalid parameter attributes)
Calls: plot -> plot.maigesClass -> <Anonymous> -> rgl.open -> .C
Execution halted

maigesPack.Rcheck/00install.out:

* Installing *source* package 'maigesPack' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c Minfo.c -o Minfo.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c bootstrapT.c -o bootstrapT.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c register.c -o register.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c robustCorr.c -o robustCorr.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c stats.c -o stats.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o   -F/Library/Frameworks/R.framework/.. -framework R 
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c Minfo.c -o Minfo.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c register.c -o register.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c robustCorr.c -o robustCorr.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c stats.c -o stats.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o   -F/Library/Frameworks/R.framework/.. -framework R 
** R
** data
** inst
** preparing package for lazy loading
Loading required package: convert
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: limma
Loading required package: marray
Loading required package: graph
Loading required package: xtable
** help
 >>> Building/Updating help pages for package 'maigesPack'
     Formats: text html latex example 
  MI                                text    html    latex   example
  activeMod                         text    html    latex   example
  activeModScoreHTML                text    html    latex   example
  activeNet                         text    html    latex   example
  activeNetScoreHTML                text    html    latex   example
  addGeneGrps                       text    html    latex   example
  addPaths                          text    html    latex   example
  bootstrapCor                      text    html    latex   example
  bootstrapMI                       text    html    latex   example
  bootstrapT                        text    html    latex   example
  boxplot-methods                   text    html    latex   example
  bracketMethods                    text    html    latex   example
  calcA                             text    html    latex   example
  calcW                             text    html    latex   example
  classifyKNN                       text    html    latex   example
  classifyKNNsc                     text    html    latex   example
  classifyLDA                       text    html    latex   example
  classifyLDAsc                     text    html    latex   example
  classifySVM                       text    html    latex   example
  classifySVMsc                     text    html    latex   example
  coerce-methods                    text    html    latex   example
  compCorr                          text    html    latex   example
  contrastsFitM                     text    html    latex
  createMaigesRaw                   text    html    latex   example
  createTDMS                        text    html    latex
  deGenes2by2BootT                  text    html    latex   example
  deGenes2by2Ttest                  text    html    latex   example
  deGenes2by2Wilcox                 text    html    latex   example
  deGenesANOVA                      text    html    latex   example
  designANOVA                       text    html    latex   example
  dim-methods                       text    html    latex   example
  gastro                            text    html    latex
  getLabels                         text    html    latex   example
  heatmapsM                         text    html    latex
  hierM                             text    html    latex   example
  hierMde                           text    html    latex   example
  image-methods                     text    html    latex   example
  kmeansM                           text    html    latex   example
  kmeansMde                         text    html    latex   example
  loadData                          text    html    latex   example
  maiges-class                      text    html    latex
  maigesANOVA-class                 text    html    latex
  maigesActMod-class                text    html    latex
  maigesActNet-class                text    html    latex
  maigesClass-class                 text    html    latex
  maigesDE-class                    text    html    latex
  maigesDEcluster-class             text    html    latex
  maigesPreRaw-class                text    html    latex
  maigesRaw-class                   text    html    latex
  maigesRelNetB-class               text    html    latex
  maigesRelNetM-class               text    html    latex
  normLoc                           text    html    latex   example
  normOLIN                          text    html    latex   example
  normRepLoess                      text    html    latex   example
  normScaleLimma                    text    html    latex   example
  normScaleMarray                   text    html    latex   example
  plot-methods                      text    html    latex   example
  plotGenePair                      text    html    latex   example
  print-methods                     text    html    latex   example
  relNet2TGF                        text    html    latex   example
  relNetworkB                       text    html    latex   example
  relNetworkM                       text    html    latex   example
  robustCorr                        text    html    latex   example
  selSpots                          text    html    latex   example
  show-methods                      text    html    latex   example
  somM                              text    html    latex   example
  somMde                            text    html    latex   example
  summarizeReplicates               text    html    latex   example
  summary-methods                   text    html    latex   example
  tableClass                        text    html    latex   example
  tablesDE                          text    html    latex   example
** building package indices ...
* DONE (maigesPack)