[BioC] snapCGH doesn't work: unable to load shared library ...

[Martin Morgan]

On 02/24/2011 04:38 PM, Gregory Gentlemen wrote:
> Could someone please help me out with getting snapCGH to work? Installation of snapCGH and its dependencies didn't suggest any problems but when I try to load snapCGH I get the error below. I would email the authors of this package but I haven't been able to find their email addresses.
> 
> Thanks for any help!
> 
> Windows vista:
> 
>> library(snapCGH)
> Error in inDL(x, as.logical(local), as.logical(now), ...) : 
>   unable to load shared library 'c:/PROGRA~1/R/R-2.11.1/library/GLAD/libs/GLAD.dll':
>   LoadLibrary failure:  The specified module could not be found.

Hi Greg -- The problem is likely with the GLAD package. The GLAD package
DESCRIPTION file (not that this is easy to find!) has

SystemRequirements: gsl. Note: users should have GSL installed. Windows
users: 'consult the README file available in the inst directory of the
source distribution for necessary configuration instructions'.

The mentioned file is available in the 'tar.gz' file mentioned on page

http://bioconductor.org/help/bioc-views/release/bioc/html/GLAD.html

which says

You need the GNU Scientific Library (GSL) for the GLAD package. Make
sure it is installed on your machine if you want to use GLAD. GSL is
free and can be downloaded at http://www.gnu.org/software/gsl/ for unix
distributions and at http://gnuwin32.sourceforge.net/packages/gsl.htm
for Windows.

Windows users
=============

To install a pre-built binary of GLAD and to load the package
successfully you need to tell R where to link GSL. You can do that by
adding /path/to/libgsl.dll to the Path environment variable. To add this
you may right click on "My Computer", choose "Properties", select the
"Advanced" tab, and click the button "Environment Variables". In the
dialog box that opens, click "Path" in the variable list, and then click
"Edit". Add /path/to/libgsl.dll to the Variable value field. It is
important that the file path does not contain any space characters; to
avoid this you may simply use the short forms (8.3 DOS file names) found
by typing "dir /x" at the Windows command line. For example, I added the
following on my Windows machine:
C:/PROGRA~1/GNUWIN32/bin
and used ";" to separate it from existing paths.

The file goes on to discuss building from source, but that is not
relevant to you.

Hope that helps.

Martin

> Error: package/namespace load failed for 'snapCGH'
>> sessionInfo()
> R version 2.11.1 (2010-05-31) 
> i386-pc-mingw32 
> 
> locale:
> [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252   
> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
> [5] LC_TIME=English_Canada.1252    
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] DNAcopy_1.22.1     limma_3.4.5        MASS_7.3-6         lme4_0.999375-35  
> [5] Matrix_0.999375-39 lattice_0.18-8     xtable_1.5-6      
> 
> loaded via a namespace (and not attached):
>  [1] aCGH_1.26.0     Biobase_2.8.0   cluster_1.12.3  grid_2.11.1    
>  [5] multtest_2.7.1  nlme_3.1-96     splines_2.11.1  stats4_2.11.1  
>  [9] survival_2.35-8 tools_2.11.1   
>>
> 
> 
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