[BioC] snapCGH fails in runBioHMM

Ramon Diaz-Uriarte rdiaz at cnio.es
Tue May 12 13:17:42 CEST 2009

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?




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 

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

File: /Part-ramon/sources.programs/R-patched/library/snapCGH/Meta/package.rds 

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


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