Package: prada

Version: 1.13.2

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check prada_1.13.2.tar.gz

RetCode: 1

Time: 40.6 seconds

Status: ERROR

CheckDir: prada.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/prada.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'prada/DESCRIPTION' ... OK
* this is package 'prada' version '1.13.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'prada' 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 ... WARNING
'library' or 'require' calls not declared from:
  tcltk
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gatePoints: no visible binding for global variable 'prev'
killProgress: no visible binding for global variable
  '.tkprogress.canceled'
killProgress: no visible binding for global variable
  '.tkprogress.window'
progress: no visible binding for global variable '.tkprogress.window'
progress: no visible binding for '<<-' assignment to
  '.tkprogress.labelText'
progress: no visible binding for global variable
  '.tkprogress.labelText'
progress: no visible binding for global variable '.tkprogress.iterator'
progress: no visible binding for global variable
  '.tkprogress.fallbackIterator'
progress : <anonymous>: no visible binding for '<<-' assignment to
  '.tkprogress.canceled'
updateProgress: no visible binding for '<<-' assignment to
  '.tkprogress.iterator'
updateProgress: no visible binding for global variable
  '.tkprogress.iterator'
updateProgress: no visible binding for '<<-' assignment to
  '.tkprogress.fallbackIterator'
updateProgress: no visible binding for global variable
  '.tkprogress.fallbackIterator'
updateProgress: no visible binding for '<<-' assignment to
  '.tkprogress.labelText'
updateProgress: no visible binding for global variable
  '.tkprogress.labelText'
* 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 prada-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'prada-Ex.R' failed.
The error most likely occurred in:

> ### * combineFrames
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: combineFrames
> ### Title: Combine the cytoFrames within a cytoSet according to some
> ###   grouping factor
> ### Aliases: combineFrames
> 
> 
> ### ** Examples
> 
> cset <- readCytoSet(path=system.file("extdata", package="prada"),
+                  pattern="[A-Z][0-9][0-9]$")
> nr1 <- csApply(cset, nrow)
> sm1 <- csApply(cset, sum)
> 
> fac <- factor(c(1,1,2,2,2,2))
> cc  <- combineFrames(cset, fac)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "pData<-", for signature "AnnotatedDataFrame", "AsIs"
Calls: combineFrames ... csApply -> is -> .class1 -> [ -> [ -> pData<- -> <Anonymous>
Execution halted

* Installing *source* package 'prada' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o prada.so inPolygon.o   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** 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()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RColorBrewer
Loading required package: grid
Scalable Robust Estimators with High Breakdown Point (version 0.3-06)
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
** help
 >>> Building/Updating help pages for package 'prada'
     Formats: text html latex example 
  analysePlate                      text    html    latex   example
  as.all                            text    html    latex   example
  barploterrbar                     text    html    latex   example
  combineFrames                     text    html    latex   example
  csApply                           text    html    latex   example
  cytoFrame-class                   text    html    latex   example
  cytoSet-class                     text    html    latex   example
  data-cytoFrame                    text    html    latex   example
  data-cytoSet                      text    html    latex   example
  devDims                           text    html    latex   example
  devRes                            text    html    latex   example
  fitNorm2                          text    html    latex   example
  gate-class                        text    html    latex   example
  gateSet-class                     text    html    latex   example
  getPradaPar                       text    html    latex   example
  new-internal                      text    html    latex
  plotNorm2                         text    html    latex   example
  plotPlate                         text    html    latex   example
  readCytoSet                       text    html    latex   example
  readFCS                           text    html    latex   example
  readFCSaux                        text    html    latex   example
  removeCensored                    text    html    latex   example
  tcltkProgress                     text    html    latex   example
  threePanelPlot                    text    html    latex   example
  thresholds                        text    html    latex   example
  touchFCS                          text    html    latex
  vpLocation                        text    html    latex   example
** building package indices ...
Loading required package: methods
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
* DONE (prada)