Package: maigesPack

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch maigesPack_1.15.0.tar.gz

StartedAt: 2011-03-17 16:46:22 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:53:28 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 425.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: maigesPack.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.15.0'
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... ERROR
Running examples in 'maigesPack-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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")
Array 1 corrected
Array 1 corrected
> 
> ## Example with an object of class maigesNorm.
> plot(gastro.norm[,1])
> 
> 
> 
> ## 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
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
Error in rgl.open() : rgl.open failed
Calls: plot -> plot.maigesClass -> <Anonymous> -> rgl.open
Execution halted

* installing *source* package 'maigesPack' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Minfo.c -o Minfo.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c bootstrapT.c -o bootstrapT.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c register.c -o register.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c robustCorr.c -o robustCorr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c stats.c -o stats.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck/maigesPack/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: limma
Loading required package: marray
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (maigesPack)

name	user	system	elapsed
MI	0.005	0.001	0.004
activeMod	3.933	0.012	3.945
activeModScoreHTML	1.913	0.019	1.932
activeNet	5.841	0.004	5.846
activeNetScoreHTML	5.893	0.011	5.904
addGeneGrps	0	0	0
addPaths	0	0	0
bootstrapCor	0.072	0.001	0.074
bootstrapMI	0.296	0.001	0.297
bootstrapT	0.005	0.001	0.005
boxplot-methods	112.238	2.477	114.719
bracketMethods	0.307	0.011	0.318
calcA	0.272	0.140	0.412
calcW	0.268	0.136	0.405
classifyKNN	0.356	0.006	0.363
classifyKNNsc	0.500	0.003	0.503
classifyLDA	1.741	0.008	1.749
classifyLDAsc	2.964	0.004	2.968
classifySVM	0.802	0.005	0.808
classifySVMsc	1.352	0.003	1.355
coerce-methods	0.212	0.025	0.236
compCorr	0	0	0
createMaigesRaw	0.478	0.005	0.483
deGenes2by2BootT	0.941	0.006	0.947
deGenes2by2Ttest	0.436	0.003	0.437
deGenes2by2Wilcox	0.394	0.003	0.396
deGenesANOVA	0.417	0.005	0.422
designANOVA	0.171	0.004	0.175
dim-methods	0.107	0.001	0.108
getLabels	0.114	0.007	0.120
hierM	2.611	0.078	2.635
hierMde	0.631	0.011	0.641
image-methods	4.445	0.339	4.784
kmeansM	2.408	0.062	2.454
kmeansMde	0.612	0.009	0.632
loadData	0	0	0
normLoc	2.778	0.086	2.864
normOLIN	0.113	0.002	0.115
normRepLoess	0.114	0.002	0.116
normScaleLimma	103.658	1.741	105.613
normScaleMarray	71.832	0.223	72.057