[Bioperl-l] Re: RPMs for Bioperl and GMOD

[Allen Day]

> Do you mean your RPM or bioperl-db on Oracle? I'm running the latter 
> all the time.

i mean the RPM.  it is the same as bioperl-db cvs head as of last night.

> > I'd also like someone with Oracle to help me make a DBD::Oracle rpm.
> > Having a DBD::Oracle RPM will allow me to leave the Oracle code in
> > Bioperl-DB.
> 
> If installing the supposed DBD::Oracle is then a prerequisite for being 
> able to install the rest, then you are taking the wrong path. 
> DBD::Oracle itself will depend on the Oracle client libraries being 
> installed which aren't even available on all platforms, aside from the 
> fact that installing those is beyond your control and involves 
> downloading about 350MB from OTN.
>
> Frankly, I can't believe that there is no way to specify dependencies
> that are optional. Why would you require all of DBD::mysql, DBD::Pg, and
> DBD::Oracle if all a persons wants is mysql?? All of these will link to
> compiled runtime libraries and why should a failure to install DBD::Pg
> be of any concern to someone who wants to use mysql?

the problem is something internal to the rpm installer -- it determines 
perl library dependencies at install-time rather than requiring you to 
explicitly specify perl packages in the rpm metafiles (aka specfile).

so, for instance, if i i tried to install perl-Generic-Genome-Browser, i 
might get an error like:

  requires perl(Bio::Root::Root)

which could be removed by one of:

  (1) installing the perl-bioperl package
  (2) installing bioperl from cvs
  (3) installing bioperl from cpan

there may be a way to code into the metafile to ignore missing perl
dependencies detected in the installation process -- i need to look into
this.

> BTW DBD::Oracle is on CPAN. I thought that would make it easy to 
> construct an RPM? (There's few if any binaries though - for a reason. 
> Compiling DBD::Oracle may be a charm on some but involve some major 
> tweaking on other platforms. I've been there multiple times, I know 
> what I'm talking about.)

given what i've said above, if i had a DBD::Oracle perl module installed,
it would prevent rpm from throwing errors about missing dependency
"perl(DBD::Oracle)".  however, i can't build DBD::Oracle into an rpm
because the make process links to the oracle headers and .so files.  the 
DBD::Oracle can be made w/o having explicit dependencies on the oracle 
binary install, so it would install on a machine that didn't have oracle 
installed (but wouldn't work).  so as far as a bioperl-db rpm goes, here 
are the options i'm looking into:

  (1) get a binary perl-DBD-Oracle rpm built by someone with Oracle,
      leaving out the binary Oracle file dependency.  distribute 
      bioperl-db from cvs as-is
  (2) patch Oracle classes out of bioperl-db as part of the rpm build
      process.  distribute modified bioperl-db.
  (3) modify rpm "detection of installed perl modules" functionality
      to have rpm explicitly ignore missing DBD::Oracle dependency.

(1) and (2) will definitely work.  i don't yet know the feasibility of
(3).

-allen