Package: a4Classif

Version: 1.1.1

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings a4Classif_1.1.1.tar.gz

StartedAt: 2011-05-09 12:02:16 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:04:39 -0700 (Mon, 09 May 2011)

EllapsedTime: 142.9 seconds

RetCode: 1

Status:  ERROR

CheckDir: a4Classif.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/a4Classif.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'a4Classif/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Classif' version '1.1.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'a4Classif' can be installed ... OK
* checking installed package size ... 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 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 examples ... ERROR
Running examples in 'a4Classif-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lassoClass
> ### Title: Classify using the Lasso
> ### Aliases: lassoClass
> ### Keywords: models
> 
> ### ** Examples
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   ALL <- addGeneInfo(ALL)
+   ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+ 
+   resultLasso <- lassoClass(object = ALL, groups = "BTtype")
+   plot(resultLasso, label = TRUE,
+     main = "Lasso coefficients in relation to degree of penalization.")
+   featResultLasso <- topTable(resultLasso, n = 15)
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "topTable", for signature "lognet"
Calls: topTable -> <Anonymous>
Execution halted

* installing *source* package 'a4Classif' ...
** R
** 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: glmnet
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loaded glmnet 1.6 
Loading required package: AnnotationDbi
Loading required package: MASS
Loading required package: genefilter

Attaching package: 'genefilter'

The following object(s) are masked from 'package:MASS':

    area

Loading required package: rpart
Loading required package: rda
Loading required package: annotate
Loading required package: cluster
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object(s) are masked from 'package:Biobase':

    combine

The following object(s) are masked from 'package:stats':

    nobs

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: caTools
Loading required package: bitops
Loading required package: grid

Attaching package: 'gplots'

The following object(s) are masked from 'package:stats':

    lowess

Loading required package: survival
Loading required package: splines
Loading required package: randomForest
randomForest 4.6-2
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

The following object(s) are masked from 'package:gdata':

    combine

The following object(s) are masked from 'package:Biobase':

    combine

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Loaded glmnet 1.6 

* DONE (a4Classif)

name	user	system	elapsed
ROCcurve	5.00	0.09	5.19