[Biojava-dev] Biojava3 structure

[Andreas Prlic]

Hi Trevor,

I can confirm the same behaviour from our anonymous SVN. Developer SVN
seems to be ok and I also ran an svnadmin verify without problems. I
suppose we are having issues with the anonymous SVN server again...
I'll ask the OBF helpdesk to take a another look ...

Can you try and let us know if checkout from svn/git  from github
works for you in the meanwhile ? e.g.

svn co http://svn.github.com/biojava/biojava.git ./biojava

Thanks,

Andreas



On Tue, Apr 13, 2010 at 4:41 AM, trevor paterson (RI)
<trevor.paterson at roslin.ed.ac.uk> wrote:
> Andreas
>
> I am trying to do an anoymous checkout of the whole bio-java 3 trunk  and it is failing on the structure module
>
> I cant even do a copy command
>
> the src/main tree seems corrupted - throwing an error
> Error: Decompression of svndiff data failed
>
> Trevor Paterson PhD
> new email trevor.paterson at roslin.ed.ac.uk
>
> Bioinformatics
> The Roslin Institute
> The Royal (Dick) School of Veterinary Studies
> University of Edinburgh
> Scotland EH25 9PS
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>
>> -----Original Message-----
>> From: biojava-dev-bounces at lists.open-bio.org
>> [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of
>> Andreas Prlic
>> Sent: 29 March 2010 03:03
>> To: Scooter Willis
>> Cc: biojava-dev
>> Subject: Re: [Biojava-dev] Biojava3 structure
>>
>> Hi Scooter,
>>
>> at the present the structure modules depend on the alignment
>> module and on the (old) core module.  This is for aligning
>> ATOM and SEQRES residues in the PDB files, and for the Smith
>> Waterman alignment based 3D structure superposition. If we
>> target a release of biojava 3 in about a month, I don't think
>> it will be possible to break this out, mainly because the
>> alignment module is still based on the biojava 1 code base.
>> Overall I think that the core module probably should still be
>> part of the BioJava 3 release. Any opinions on that?
>>
>> Andreas
>>
>> On Sun, Mar 28, 2010 at 3:06 PM, Scooter Willis
>> <HWillis at scripps.edu> wrote:
>>
>> > Andreas
>> >
>> > I needed to do some work with a PDB file so started to use the
>> > structure library. It looks like it depends on all the old biojava
>> > code. Mainly the structure exceptions that extend
>> bioexception is the
>> > first thing tripping me up. Should the biojava3-structure
>> module have
>> > any external dependencies or am I working with the wrong package?
>> >
>> > Thanks
>> >
>> > Scooter
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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