maigesPack 1.16.0
Gustavo H. Esteves
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/maigesPack | | Last Changed Rev: 54800 / Revision: 59457 | | Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ ERROR ] | OK |
* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/maigesPack.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.16.0'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 sizes of PDF files under inst/doc ... NOTE
'qpdf' made some significant size reductions:
compacted 'maigesPack_tutorial.pdf' from 386Kb to 189Kb
consider running tools::compactPDF() on these files
* 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-4.2 -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-4.2 -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-4.2 -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-4.2 -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-4.2 -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-4.2 -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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (maigesPack)