[BioC] snapCGH fails in runBioHMM

[Wolfgang Raffelsberger]

Hi Ramon,

just to say that I posted another message concerning an error with 
snapCGH package on this list on may 4th, but got no reply.
I my case it was one particular array that for some reason caused 
runBioHMM() to stall.  I found a workaround, by just inverting R & G 
channel for the array causing the trouble and runBioHMM() ran fine (of 
course after segmentation I had to re-flip R&G for the array in question). 
Besides, I had and "fixed" another problem with runGLAD() that wasn't 
expecting snapCGH objects ...

But I haven't tried the snapCGH v.1.12  yet ...

cheers,
Wolfgang



Ramon Diaz-Uriarte a écrit :
> Dear All,
>
> snapCGH (v. 1.12 in BioC 2.4 for sure; most likely v. 1.13 in BioC 2.5 too) 
> fails with the error  
>
> C symbol name "runNelderMead" not in DLL for package "snapCGH"
>
> The problem is that the NAMESPACE file is not loading the required code. Sure 
> enough, if one loads the .so file manually (e.g., 
> via "dyn.load('path-to-library/snapCGH.so')") things work. 
>
>
> So, while the package gets fixed, what would be the orthodox way to get 
> packages that depend on snapCGH to work?
>
>
> Best,
>
> R
>
> ************************
>
> Two reproducible examples:
>
> a) Using function fit.model (which is docummented but not exported in the 
> NAMESPACE, which is available since v. 1.12):
>
> ydat <- matrix(rnorm(100), ncol = 1)
> datainfo <- data.frame(Name = 1:100, Chrom = rep(1, 100), Position = 1:100)
>
> snapCGH:::fit.model(sample = 1, chrom = 1, dat = ydat,
>                     datainfo = datainfo)
>
>
>
> b) Using the code in the vignette (the vignette does not fail, as the crucial 
> chunck has "eval=FALSE", and the help for runBioHMM has no runnable 
> examples):
>
> datadir <- system.file("testdata", package="snapCGH")
> targets <- readTargets("targets.txt", path=datadir)
> RG1 <- read.maimages(targets$FileName, path=datadir, source = "genepix")
> RG1 <- read.clonesinfo("cloneinfo.txt", RG1, path=datadir)
> RG1$printer <- getLayout(RG1$genes)
> types <- readSpotTypes("SpotTypes.txt", path=datadir)
> RG1$genes$Status <- controlStatus(types, RG1)
> RG1$design <- c(-1,-1)
> RG2 <- backgroundCorrect(RG1, method="minimum")
> MA <- normalizeWithinArrays(RG2, method="median")
> MA2 <- processCGH(MA,method.of.averaging=mean, ID = "ID")
> SegInfo.Bio <- runBioHMM(MA2)
>
>
>
>   
>> version
>>     
>                _                                          
> platform       x86_64-unknown-linux-gnu                   
> arch           x86_64                                     
> os             linux-gnu                                  
> system         x86_64, linux-gnu                          
> status         Patched                                    
> major          2                                          
> minor          9.0                                        
> year           2009                                       
> month          05                                         
> day            11                                         
> svn rev        48528                                      
> language       R                                          
> version.string R version 2.9.0 Patched (2009-05-11 r48528)
>
>   
>> packageDescription("snapCGH")
>>     
> Package: snapCGH
> Title: Segmentation, normalisation and processing of aCGH data.
> Version: 1.12.0
> Date: 2000-04-07
> Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas
>         Hardcastle, Natalie P. Thorne
> Description: Methods for segmenting, normalising and processing aCGH
>         data; including plotting functions for visualising raw and
>         segmented data for individual and multiple arrays.
> biocViews: Microarray, DNACopyNumber, TwoChannel, Preprocessing
> Maintainer: John Marioni <marioni at uchicago.edu>
> Depends: limma,tilingArray,DNAcopy,GLAD,cluster,methods,aCGH
> License: GPL
> Packaged: 2009-04-21 09:40:04 UTC; biocbuild
> Built: R 2.9.0; x86_64-unknown-linux-gnu; 2009-05-12 10:31:17 UTC; unix
>
>   


. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
CNRS UMR7104, IGBMC,  
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr