[BioC] snapCGH fails in runBioHMM

[Ramon Diaz-Uriarte]

Dear Wolfgang,

On Tuesday 12 May 2009 16:52:30 Wolfgang Raffelsberger wrote:
> 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.

Yes, I am expecting something similar. For my own particualr problem (with 
package ADaCGH) I've just surrounded all calls to snapCGH functions with 
a "try", so the help examples at least can run, and I return to the user the 
error message that results from snapCGH.


> 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 ...

As far as I can tell, there are no differences whatsoever in the code itself 
between versions 1.11 and 1.12 (or between 1.12 and 1.13). 1.12 and 1.13 seem 
identical except for their version number.  1.12 and 1.11 differ in a few 
changes in the documentation (formatting changes and fixes of types) and in 
the addition of the (buggy) NAMESPACE in 1.12.

Best,


R.



>
> 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



-- 
Ramón Díaz-Uriarte
Biocomputing Programm
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz




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