Back to the "Multiple platform build/check report"
| Package 124/208 | OS | Arch | BUILD | CHECK | BUILD BIN |
MLInterfaces1.9.0V. Carey | Linux (SUSE 9.2) | x86_64 | OK | ERROR | |
| Linux (SUSE 10.1) | x86_64 | OK | ERROR | ||
| Linux (SUSE 9.2) | i686 | OK | ERROR | ||
| Solaris 2.9 | sparc | OK | ERROR | ||
| Windows Server 2003 | x86_64 | OK | [ ERROR ] | OK | |
| Windows Server 2003 | NA | OK | ERROR | OK | |
| Mac OS X (10.4.6) | i686 | OK | ERROR |
| Package: MLInterfaces |
| Version: 1.9.0 |
| Command: D:\biocbld\2.0d\R\bin\R.exe CMD check MLInterfaces_1.9.0.tar.gz |
| RetCode: 1 |
| Time: 84.5 seconds |
| Status: ERROR |
| CheckDir: MLInterfaces.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory 'D:/biocbld/2.0d/Rpacks/MLInterfaces.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'MLInterfaces/DESCRIPTION' ... OK
* this is package 'MLInterfaces' version '1.9.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MLInterfaces' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Error: package 'Biobase' could not be loaded
Call sequence:
3: stop(gettextf("package '%s' could not be loaded", pkg), call. = FALSE,
domain = NA)
2: .getRequiredPackages2(pkgInfo)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* 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 ... WARNING
Undocumented S4 methods:
generic 'plot' and siglist 'varImpStruct,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating MLInterfaces-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'MLInterfaces-Ex.R' failed.
The error most likely occurred in:
> ### * planarPlot-methods
>
> flush(stderr()); flush(stdout())
>
> ### Name: planarPlot-methods
> ### Title: Methods for Function planarPlot in Package `MLInterfaces'
> ### Aliases: planarPlot planarPlot-methods
> ### planarPlot,classifOutput,ExpressionSet,character-method
> ### Keywords: methods
>
> ### ** Examples
>
> library(ALL)
> data(ALL)
> #
> # restrict to BCR/ABL or NEG
> #
> bio <- which( ALL$mol.biol %in% c("BCR/ABL", "NEG"))
> #
> # restrict to B-cell
> #
> isb <- grep("^B", as.character(ALL$BT))
> kp <- intersect(bio,isb)
> all2 <- ALL[,kp]
> #
> # sample 2 genes at random
> #
> set.seed(1234)
> ng <- nrow(exprs(all2))
> pick <- sample(1:ng, size=2, replace=FALSE)
> library(hgu95av2)
> gg <- all2[pick,]
> sym <- unlist(mget(featureNames(gg), hgu95av2SYMBOL))
> featureNames(gg) <- sym
> class <- as.character(all2$mol.biol)
> gg@phenoData@data$class <- factor(class)
> gg@phenoData@varMetadata = rbind(gg@phenoData@varMetadata,class="class" )
> newpd = new("phenoData", pData=pData(gg), varLabels=varMetadata(gg)[,1])
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Error in validObject(.Object) : invalid class "phenoData" object: invalid object for slot "varLabels" in class "phenoData": got class "character", should be or extend class "list"
Execution halted
MLInterfaces.Rcheck/00install.out:
installing R.css in D:/biocbld/2.0d/Rpacks/MLInterfaces.Rcheck
---------- Making package MLInterfaces ------------
adding build stamp to DESCRIPTION
installing R files
save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
[1] "MLLabel"
[1] "predClass"
[1] "groupIndex"
[1] "MLScore"
[1] "probMat"
[1] "probArray"
[1] "membMat"
[1] "qualScore"
[1] "silhouetteVec"
[1] "MLOutput"
[1] "classifOutput"
[1] "clustOutput"
[1] "show"
[1] "show"
[1] "show"
[1] "show"
[1] "show"
[1] "RObject"
[1] "RObject"
[1] "distMat"
[1] "distMat"
[1] "show"
[1] "predLabels"
[1] "predLabels"
[1] "predLabels"
[1] "predLabels"
[1] "allClass"
[1] "allClass"
[1] "trainInds"
[1] "trainInds"
[1] "confuMat"
[1] "confuMat"
[1] "ldaB"
[1] "ldaB"
[1] "qdaB"
[1] "qdaB"
[1] "isoMDSB"
[1] "MLearn"
[1] "MLearn"
[1] "MLearn"
[1] "knnB"
[1] "knnB"
[1] "knn1B"
[1] "knn1B"
[1] "lvq1B"
[1] "lvq1B"
[1] "lvq2B"
[1] "lvq2B"
[1] "lvq3B"
[1] "lvq3B"
[1] "olvq1B"
[1] "olvq1B"
[1] "SOMB"
[1] "agnesB"
[1] "agnesB"
[1] "claraB"
[1] "claraB"
[1] "dianaB"
[1] "dianaB"
[1] "fannyB"
[1] "fannyB"
[1] "pamB"
[1] "pamB"
[1] "cvB"
[1] "cvB"
[1] "bclustB"
[1] "bclustB"
[1] "cmeansB"
[1] "cmeansB"
[1] "cshellB"
[1] "cshellB"
[1] "lcaB"
[1] "lcaB"
[1] "naiveBayesB"
[1] "naiveBayesB"
[1] "svmB"
[1] "svmB"
[1] "gbmB"
[1] "gbmB"
[1] "baggingB"
[1] "baggingB"
[1] "ipredknnB"
[1] "ipredknnB"
[1] "sldaB"
[1] "sldaB"
[1] "nnetB"
[1] "nnetB"
[1] "pamrB"
[1] "pamrB"
[1] "planarPlot"
[1] "planarPlot"
[1] "randomForestB"
[1] "randomForestB"
[1] "rpartB"
[1] "rpartB"
[1] "silhouetteB"
[1] "silhouetteB"
[1] "stat.diag.daB"
[1] "stat.diag.daB"
[1] "somout"
[1] "show"
[1] "somB"
[1] "somB"
[1] "SOMBout"
[1] "show"
[1] "SOMB"
[1] "hclustB"
[1] "hclustB"
[1] "hclustB"
[1] "hclustB"
[1] "kmeansB"
[1] "kmeansB"
[1] "varImpStruct"
[1] "getVarImp"
[1] "getVarImp"
[1] "show"
[1] "plot"
[1] "xval"
[1] "xval"
[1] "xval"
[1] "xvalLoop"
[1] "xvalLoop"
installing inst files
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'MLInterfaces'
Formats: text html latex example chm
MLIclust text html latex example chm
MLIntInternals text html latex example chm
MLearn-methods text html latex chm
SOMB text html latex example chm
classifOutput-class text html latex example chm
confuMat-methods text html latex example chm
knnB text html latex example chm
planarPlot-methods text html latex example chm
varImpStruct-class text html latex example chm
xval-methods text html latex example chm
xvalLoop-methods text html latex chm
xvalLoop text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\2.0d\Rpacks\MLInterfaces.Rcheck\00_pkg_src\MLInterfaces\chm\MLInterfaces.chm
Compile time: 0 minutes, 0 seconds
13 Topics
199 Local links
0 Internet links
1 Graphic
Created d:\biocbld\2.0d\Rpacks\MLInterfaces.Rcheck\00_pkg_src\MLInterfaces\chm\MLInterfaces.chm, 41,659 bytes
Compression decreased file by 66,280 bytes.
adding MD5 sums
* DONE (MLInterfaces)