[BioC] unable to load shared library

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Hi ? ??,


? ?? wrote:
> hi,all
>    
>   I run R & Bioconductor on SUSE LINUX Enterprise Server 9(x86_64)
>   The R is complied from the source file R-2.4.1.tar.gz, and the used packages are all installed from the source file with the command: 
>    
>    >install.packages("/bwdata/bdb/pengchy/R/library/package.tar.gz",repos=NULL)

This is bad idea. I'm not surprised that you get a lot of dependency problems. The correct
and recommended way to install Bioconductor packages is to use biocLite():

  http://bioconductor.org/docs/install-howto.html

Any given Bioconductor package can have dependencies that live in other repositories
than the Bioconductor software repo itself (including CRAN) so, unless you've downloaded
the content of all those repositories to your local disk too, you will end up with
many many missing dependencies...

Cheers,
H.

>    
>   What confused me is several packages can't be installed because the depend package can't be loaded. Take 'siggenes' package for example:
>    
>   > install.packages("/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.tar.gz",repos=NULL)
>   
> * Installing *source* package 'siggenes' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Loading required package: multtest
> Loading required package: Biobase
> Loading required package: tools
>   Welcome to Bioconductor
>       Vignettes contain introductory material. To view, type
>     'openVignette()' or start with 'help(Biobase)'. For details
>     on reading vignettes, see the openVignette help page.
>   Loading required package: survival
> Loading required package: splines
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library '/bwdata/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so':
>   /bwdata/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so: cannot open shared object file: No such file or directory
> Error: package 'multtest' could not be loaded
> Execution halted
> ERROR: lazy loading failed for package 'siggenes'
> ** Removing '/bwdata/bdb/pengchy/R-2.4.1/library/siggenes'
> Warning message:
> installation of package '/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.tar.gz' had non-zero exit status in: install.packages("/bwdata/bdb/pengchy/R/library/siggenes_1.8.0.tar.gz",
>    
>   when I load 'multtest'  following is the returned message:
>    
>   >library(multtest)
>   Loading required package: survival
> Loading required package: splines
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library '/home/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so':
>   /home/bdb/pengchy/R-2.4.1/library/multtest/libs/multtest.so: cannot open shared object file: No such file or directory
> Error: package/namespace load failed for 'multtest'
> 
>   The same problem happen to some other packages, such as: 'vsn', 'akima',etc.
>    
>   Some one meet the same problem on Mac OX, and "created a symlink (from libs/multtest.so to libs/ppc/multtest.so)", but it doesn't work on SUSE. 
>    
>   Anyone can help me will be appreciated!
> 
> 
> Best wishes!
>    
>                                                               Sincerely, pengcheng
> 
>        
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