[BioC] unexpected behaviour of pairwiseAlignment() in Biostrings

[Patrick Aboyoun]

Avril,
I checked the versions of Biostrings that are available at 
bioconductor.org and they are either at or above the version number of 
the package that contains the patch. I also double-checked the packages 
in release and devel and both contain the fix. Could you please send 
session information from your R session?

As Steve noted, you can always get the latest version of any package 
directly from the Bioconductor svn.


Cheers,
Patrick



On 7/12/10 8:08 AM, Steve Lianoglou wrote:
> Hi Avril
>
> On Mon, Jul 12, 2010 at 10:53 AM, Coghlan, Avril<A.Coghlan at ucc.ie>  wrote:
>    
>> Dear Patrick,
>>
>> I've updated my copy of the Biostrings() library but the pairwiseAlignment() function doesn't seem to have been fixed yet - I wonder could you send me the patch directly please?
>>      
> You could actually grab the source changes yourself if they haven't
> propagated to the release/package servers.
>
> If you're using R 2.11 (and bioc 2.6), the subversion repository can
> be found here:
>
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/
>
> You could "check out" the Biostrings package via svn and install it from source.
>
> Assuming you're using a *unix-esque OS (linux, os x, etc.), you could
> do this from teh command line:
>
> $ svn --username readonly co
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/Biostrings
> Biostrings
> ## The password is also: readonly
>
> $ R CMD INSTALL Biostrings
>
> and voila ... you would have installed the latest package from source.
>
> Hope that helps,
>
>