[BioC] unexpected behaviour of pairwiseAlignment() in Biostrings

Coghlan, Avril A.Coghlan at ucc.ie
Wed Jul 21 16:44:19 CEST 2010


Dear Patrick and Steve,

Thank you for your helpful replies. 

I think that perhaps the problem was that I was using an old version of
R (R 2.10).
I had tried to update the Biostrings library by typing:
>source("http://bioconductor.org/biocLite.R"
>biocLite("Biostrings")
>library("Biostrings")
However, the pairwiseAlignment() function still seemed to give the wrong
result.

I updated my version of R (to R 2.11.1), and found that I could update
the Biostrings library by typing the commands above.
The pairwiseAlignment() function then seemed to work fine for me, and
gave the correct result.

I hadn't realised that using an old version of R (R 2.10) could be the
problem, but it seemed to be.

Thanks again for your help, and for fixing the function so quickly.

Kind Regards,
Avril

Avril Coghlan
Dept. Microbiology
University College Cork
Ireland


-----Original Message-----
From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org] 
Sent: 12 July 2010 17:07
To: Coghlan, Avril
Cc: Steve Lianoglou; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] unexpected behaviour of pairwiseAlignment() in
Biostrings

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/Rpac
ks/
>
> 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/Rpac
ks/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,
>
>    



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