[Bioc-sig-seq] Trouble loading development version of ShortRead on OS X

[Michael Muratet]

On Oct 1, 2009, at 8:08 PM, Martin Morgan wrote:

> Hi Mike --
>
> Probably the problem is that your version of ShortRead and of the  
> other
> Bioconductor packages are not in sync. Probably what you want to do is
> use the 'svn' version control system, and 'check out' the relevant
> packages from the bioconductor code repository, and use the checked  
> out
> copies for installation instead of biocLite(). Then copy your changed
> files into the repository and go from there. Very roughly
>
>  cd some/directory
>  svn co -N https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks
>  cd Rpacks
>  svn up IRanges Biostrings BSgenome ShortRead
>  R CMD INSTALL --clean IRanges Biostrings BSgenome
>  cp my/modified/ShortRead/R/AllClasses.R ShortRead/R/AllClasses
>  R CMD INSTALL --clean ShortRead


Martin

That does the job, thanks.

Mike