[Bioperl-l] bioperl-db install doing more than burping

[Jason Stajich]

The map, marker, ePCR stuff was all from my - now rotting - code.

bioperl-db-0.1 was built for bioperl 0.7, we've improved the object
structure since that release so the Annotation objects and the RootI
inheritance has changed, hence lots of the msgs and errors (confusing eh?)

Do this
% cvs -d:pserver:cvs@cvs.bioperl.org:/home/repository/bioperl login
password:
(enter cvs)
% cvs -d:pserver:cvs@cvs.bioperl.org:/home/repository/bioperl co bioperl-db

The bioperl-db distro that works with bioperl 1.0 will be packaged up
after 1.0 goes out and we are confident that the bugs are shaken out.  The
CVS version is the best option we have at this point.  I can generate a
tarball for you if aren't able to get the CVS past a firewall.

-j

On Wed, 13 Mar 2002, Keith Allen wrote:

> Hey Guys,
>
> Filled with a glowing sense of optimism, I tried to build the
> bioperl-db package (latest distro, 0.1), on Redhat 7.2, perl 5.6.0,
> and gcc 3.0.2.  The patient did more than burp, I'm afraid, in
> fact, I'm going to spray the output from make test (make
> proceeded with nary a whimper).  The summary from make
> test looks like:
>
> Failed Test  Status Wstat Total Fail  Failed  List of failed
> -------------------------------------------------------------------------------
>
> t/ePCRdb.t      255 65280     3    2  66.67%  2-3
> t/ensembl.t     255 65280    14    1   7.14%  14
> t/map.t         255 65280     6    5  83.33%  2-6
> t/marker.t      255 65280    19   18  94.74%  2-19
> Failed 4/14 test scripts, 71.43% okay. 26/152 subtests failed, 82.89% okay.
> make: *** [test_dynamic] Error 29
>
> Though it may well be that some of the errors are just in the
> test scripts (there is a lot of carrying on about Bio::Root::RootI being
> deprecated).
>
> Being a programmer of very little brain, I went ahead and did
> the make install, and then tried to run load_seqdatabase.pl (after
> using the supplied SQL code to build the basicseqdb).  I ended up
> hitting a number of snags, but I'm guessing that these are not
> informative before I know how bad the state of my build is based on
> the failed tests.
>
> Any thoughts?
>
> -Keith Allen
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu