[BioRuby] Subversion (Fwd: [Root-l] [Open-bio Board] OBF services)

Toshiaki Katayama ktym at hgc.jp
Tue Apr 3 20:30:39 UTC 2007


Just for notice, I'm not sure when it will happen but Trevor and O|B|F staffs are now working on migration of the BioRuby code base to subversion.

I failed to install svn on my MacBook with DarwinPorts. Does anyone know how to solve this?

% sudo port install subversion
--->  Staging zlib into destroot
--->  Configuring libz.a
Error: Target com.apple.destroot returned: invalid command name "command_exec"
Error: The following dependencies failed to build: neon openssl zlib
Error: Status 1 encountered during processing.


Begin forwarded message:

> From: Chris Dagdigian <dag at sonsorol.org>
> Date: 2007年4月3日 4:35:57:JST
> To: Jason Stajich <jason at bioperl.org>
> Cc: Trevor Wennblom <trevor at umn.edu>, Pjotr Prins <pjotr2007 at thebird.nl>, Root-l Admins <root-l at open-bio.org>, Katayama Toshiaki <k at bioruby.org>, OBF Board Board <board at open-bio.org>
> Subject: Re: [Root-l] [Open-bio Board] OBF services
> Hi folks,
> Another update
> I've been working via Trevor on this separately -- we've got a helpdesk ticket pending on the switchover for BioRuby.
> -Chris
> On Apr 2, 2007, at 2:32 PM, Jason Stajich wrote:
>> Hi Trevor - this got caught in our list admin, so the lack of response was due to that, apologies.
>> SVN is available - we've done that for a few projects on a test basis and biopython is getting ready to migrate to SVN.  BioJava has talked about it for a while but it has not actually happened yet.  We would be more than happy to see this happen and can help as much as we can- although CVS to SVN migration may require some babysitting on your part.
>> In terms of setting up Trac - I think it is possible in principle, one thing is we protect our main code repository server (dev) where there are users which have r/w access by mirroring the code repository to a separate machine which is running web services (code.open-bio.org). I am not sure how Trac will interact with this, but it should be possible.  Let's see if Chris Dagdigian (hopefully) can look into it a little and report back on what the challenges will be.
>> -jason
>> On Mar 15, 2007, at 10:03 AM, Trevor Wennblom wrote:
>>> Hi guys,
>>> I'm a regular contributor to the BioRuby project and we're looking to
>>> improve some of our services and interaction with the community.  My
>>> first question is if Subversion access is available?  It would be
>>> nice to transition from CVS to SVN sometime in the future.  Also, if
>>> it is available, would it be possible to run a Trac instance from an
>>> open-bio server?
>>> Thanks for your help,
>>> Trevor
>>> ===
>>> Trevor Wennblom <trevor at umn.edu>
>>> Software Development
>>> Center for Biomedical Research Informatics
>>> University of Minnesota
>>> _______________________________________________
>>> Board mailing list
>>> Board at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/board
>> --
>> Jason Stajich
>> Miller Research Fellow
>> University of California, Berkeley
>> lab: 510.642.8441
>> http://pmb.berkeley.edu/~taylor/people/js.html
>> http://fungalgenomes.org/
>> _______________________________________________
>> Root-l mailing list
>> Root-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/root-l

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