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
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