[Bioperl-l] [Gmod-gbrowse] quick update on bioperl nightly builds

Chris Fields cjfields at uiuc.edu
Wed Apr 2 11:03:32 EDT 2008

The changes I made were related to problems checking MySQL for  
Bio::DB::SeqFeature::Store tests when connectivity requires username/ 
password.  For some reason it tests DB connectivity up front, while  
Bio::DB::GFF assumes the DB setup is correct (no direct DB check) then  
runs tests assuming the setup is correct.

You can view the diffs for your commits here:



I'll try working on merging them together today; it shouldn't be too  
hard (the changes were fairly minor in both Build.PL and  
Module::Build).  I'll test to make sure your changes stay in as well.   
Down the road I believe we need to rethink how we want the Build  
process to run using Module::Build as it's a bit convoluted, but it  
works for now.


On Apr 2, 2008, at 7:28 AM, Scott Cain wrote:
> Hi Chris,
> (trimmed out gbrowse mailing list since this is just bioperl business)
> Speaking of the pass through stuff, Sendu mentioned that I stomped on
> some changes to Build.PL that you and he did when I committed that
> change, so it should be rolled back.  Is there a good (svn) way to do
> that?  Or should I just copy the contents of the old (good) Build.PL
> into a fresh file in my checkout and commit it?
> Thanks,
> Scott
> On Tue, 2008-04-01 at 22:59 -0500, Chris Fields wrote:
>> Nope, that isn't intended.  I fixed it and reran it manually, so it
>> should be fine now (note I didn't update the log file; the next cron
>> run will catch that).
>> I may toy around with your recent passthrough flag addition to try
>> getting automated PPM's up and running.
>> chris
>> On Apr 1, 2008, at 10:12 PM, Scott Cain wrote:
>>> Hi Chris,
>>> The tarball is currently (Apr 1) being built in a tmp directory, so
>>> that
>>> the extracted tarball is ./tmp/bioperl-live/.  Is that intended?
>>> Thanks,
>>> Scott
>>> On Tue, 2008-04-01 at 19:45 -0500, Chris Fields wrote:
>>>> I'm simplifying the nightly build archive names (removing svn
>>>> revision
>>>> # and date) in case anyone needs to update bioperl-live/run/db/
>>>> network
>>>> on a regular basis (read: GBrowse installations).  When I have time
>>>> I'll start working on automated builds, which will require some  
>>>> extra
>>>> work with Module::Build and Build.PL.
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                         cain at cshl.edu
>>> GMOD Coordinator (http://www.gmod.org/)
>>> 216-392-3087
>>> Cold Spring Harbor Laboratory
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> -------------------------------------------------------------------------
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> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   cain.cshl at gmail.com
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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