[Biocorba-l] Re: cvs.bioperl.org running ensembl perl corba

[Jason Stajich]

Brad - I updated server code and ensembl cvs code.  Obj -> DBAdaptor msgs
should be going away (had to update the server perl script as well).

I am piping output to cvs.bioperl.org/~jason/enscorba.out.txt

So you should be able to see the errorlog online.

srv restarted.


On Sun, 15 Apr 2001, Brad Chapman wrote:

> Hey Jason;
>
> > I've fixed where necessary - might take a while
> > for code to show up on sanger anonymous CVS so I'll update the
> > cvs.bioperl.org code later on when I .
>
> Thanks for the fixes! As of this morning, the server is complaining
> about your DBAdaptor vs. Obj change, so it doesn't seem to be
> happy... not sure what to do about this. No big deal, just wanted to
> let you know.
>
> > Will you be checking in your code to a biopython repository? I'd like to
> > plug in to a test suite at some point so I can re-verify things myself.
> > I'll probably need to spend the time an create a complete perl test
> > suite
>
> Yeah, everything I have is in the biopython-corba module in CVS. I
> keep it updated all the time, so if you stay current with that, you'll
> have what I have.
>
> I'm also hoping to make a new release today. I just fixed my memory
> leaking bugs this weekend (I can now run through the entire
> Arabidopsis genome and not have any appreciable gain in memory for the
> server. Yee-ha!) and have started trying to add support for the python
> ORBit bindings. There are a lot of problems with the python bindings
> (which seem to be due to bugs in either the bindings or ORBit itself)
> but I'm going to put it out there and maybe people'll be able to help
> me fix it up.
>
> BTW, I was daring and started playing around with different versions
> of ORBit this weekend. It seems like there are interoperability
> problems with more recent versions of ORBit. For me, with CORBA::ORBit
> 0.4.3 and any version of ORBit greater than 0.5.2, both omniORB and
> Fnorb will complain that ORBit is generating improper IIOP
> messages.
>
> So anyways, I read back on one of your old messages and added the
> identical orbitrc that you have on cvs.bioperl.org, and now things
> work snazzily. Can you explain to me what the difference is between
> ORBIIOPIPv4 and ORBIIOPIPv6? Just curious.
>
You know it would really bite if our troubles stemmed from an improper
orbitrc file, but I'll try and rule that out.  We are running ORBit 0.5.7 with no
problems on opensbsd wrt ORBit.

IPv4 versus IPv6 - I suspect that if you tell it to expect IPv6 traffic
and there is no IPv6 interface defined things get mucky - perhaps with the
faith interface IPv4/IPv6 translation daemon on freebsd it make ORBit
confused?  Older versions perhaps didn't support it?  I know you're not a
former CS student so this protocol mess might be better explained here:
http://www.cs-ipv6.lancs.ac.uk/

> Well, that's all the news to report from the CORBA front. Talk to you
> soon!
>
> Brad
>
>

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/