Back to the "Multiple platform build/check report"
| Package 124/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
| 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 |
* 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)