maigesPack 1.3.3
Gustavo H. Esteves
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/maigesPack | | Last Changed Rev: 28882 / Revision: 29143 | | Last Changed Date: 2007-11-21 10:01:47 -0800 (Wed, 21 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ ERROR ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | ERROR | OK |
* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/maigesPack.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-18 r43497)
* checking for file 'maigesPack/DESCRIPTION' ... OK
* this is package 'maigesPack' version '1.3.3'
* 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:
> ### * normScaleLimma
>
> flush(stderr()); flush(stdout())
>
> ### Name: normScaleLimma
> ### Title: Scale adjust a cDNA Microarray Object
> ### Aliases: normScaleLimma
> ### Keywords: classes
>
> ### ** Examples
>
> ## Loading the dataset
> data(gastro)
>
> ## Doing the scale adjustment from median-absolute-value method (from
> ## limma)
> gastro.norm = normScaleLimma(gastro.norm, method="scale")
> boxplot(gastro.norm) ## To see the efect of adjustment
>
> ## To do VSN scale adjustment (from vsn package) use the command. Be
> ## carefull that this method adjust the variance along A values and not
> ## between chips!!
> gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
Loading required package: vsn
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Warning: The function 'vsn' is deprecated.
It will stay around for some time, for backward compatibility.
For new projects, please use 'vsn2'.
Error in ncol(y@exprs) :
no slot of name "exprs" for this object of class "ExpressionSet"
Calls: normScaleLimma -> normalizeBetweenArrays -> ncol
Execution halted
* Installing *source* package 'maigesPack' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c bootstrapT.c -o bootstrapT.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c Minfo.c -o Minfo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c register.c -o register.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c robustCorr.c -o robustCorr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c stats.c -o stats.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o maigesPack.so bootstrapT.o Minfo.o register.o robustCorr.o stats.o -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** 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
** 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)