Package: MiPP

Version: 1.7.0

Command: /loc/biocbuild/2.0d/R/bin/R CMD check MiPP_1.7.0.tar.gz

RetCode: 1

Time: 271.3 seconds

Status: ERROR

CheckDir: MiPP.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/MiPP.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'MiPP/DESCRIPTION' ... OK
* this is package 'MiPP' version '1.7.0'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  MASS
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'MiPP' 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 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 ... 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
* creating MiPP-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'MiPP-Ex.R' failed.
The error most likely occurred in:

> ### * mipp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: mipp
> ### Title: MiPP-based Classification
> ### Aliases: mipp
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> ##########
> #Example 1: When an independent test set is available
> 
> data(leukemia)
> 
> #Normalize combined data
> leukemia <- cbind(leuk1, leuk2)
> leukemia <- mipp.preproc(leukemia, data.type="MAS4")
> 
> #Train set
> x.train <- leukemia[,1:38]
> y.train <- factor(c(rep("ALL",27),rep("AML",11)))
> 
> #Test set
> x.test <- leukemia[,39:72]
> y.test <- factor(c(rep("ALL",20),rep("AML",14)))
> 
> #Compute MiPP
> out <- mipp(x=x.train, y=y.train, x.test=x.test, y.test=y.test, probe.ID = 1:nrow(x.train), n.fold=5, percent.cut=0.05, rule="lda")
Loading required package: MASS
Please wait. Done. 
> 
> #Print candidate models
> out$model
   Order Gene  Tr.ER Tr.MiPP Tr.sMiPP  Te.ER Te.MiPP Te.sMiPP Select
1      1  571 0.0526   30.86   0.8122 0.1176   23.92   0.7035       
2      2  436 0.0000   36.89   0.9707 0.0294   30.41   0.8945       
3      3  366 0.0000   37.95   0.9988 0.0294   31.35   0.9222       
4      4  457 0.0000   38.00   0.9999 0.0294   32.14   0.9453       
5      5  413 0.0000   38.00   1.0000 0.0294   32.18   0.9464       
6      6  635 0.0000   38.00   1.0000 0.0000   33.75   0.9927     **
7      7  648 0.0000   38.00   1.0000 0.0000   33.60   0.9883       
8      8  181 0.0000   38.00   1.0000 0.0294   31.95   0.9397       
9      9  309 0.0000   38.00   1.0000 0.0000   33.37   0.9816       
10    10   99 0.0000   38.00   1.0000 0.0588   29.82   0.8772       
> 
> 
> ##########
> #Example 2: When an independent test set is not available
> 
> data(colon)
> 
> #Normalize data
> x <- mipp.preproc(colon)
> y <- factor(c("T", "N", "T", "N", "T", "N", "T", "N", "T", "N", 
+        "T", "N", "T", "N", "T", "N", "T", "N", "T", "N",
+        "T", "N", "T", "N", "T", "T", "T", "T", "T", "T", 
+        "T", "T", "T", "T", "T", "T", "T", "T", "N", "T", 
+        "T", "N", "N", "T", "T", "T", "T", "N", "T", "N", 
+        "N", "T", "T", "N", "N", "T", "T", "T", "T", "N", 
+        "T", "N"))
> 
> #Deleting comtaminated chips
> x <- x[,-c(51,55,45,49,56)]
> y <- y[ -c(51,55,45,49,56)]
> 
> #Compute MiPP
> out <- mipp(x=x, y=y, probe.ID = 1:nrow(x), n.fold=5, p.test=1/3, n.split=5, n.split.eval=100, 
+ percent.cut= 0.1, rule="lda")
Please wait.....Error in as.double.default(gene.list[jj, 1:k]) : 
	(list) object cannot be coerced to 'double'
Execution halted

* Installing *source* package 'MiPP' ...
** R
** data
** inst
** preparing package for lazy loading
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: e1071
Loading required package: class
** help
 >>> Building/Updating help pages for package 'MiPP'
     Formats: text html latex example 
  colon                             text    html    latex
  cv.mipp.rule                      text    html    latex
  get.mipp                          text    html    latex
  get.mipp.lda                      text    html    latex
  get.mipp.logistic                 text    html    latex
  get.mipp.qda                      text    html    latex
  get.mipp.svm.linear               text    html    latex
  get.mipp.svm.rbf                  text    html    latex
  leuk1                             text    html    latex
  leuk2                             text    html    latex
  leukemia                          text    html    latex
  linearkernel.decision.function    text    html    latex
  mipp                              text    html    latex   example
  mipp.preproc                      text    html    latex   example
  mipp.rule                         text    html    latex
  mipp.seq                          text    html    latex   example
  pre.select                        text    html    latex
  quant.normal                      text    html    latex
  quant.normal2                     text    html    latex
  rbfkernel.decision.function       text    html    latex
** building package indices ...
* DONE (MiPP)