[Bioperl-l] BioPerl 1.6 RC1

Sendu Bala bix at sendu.me.uk
Sun Dec 28 08:37:04 EST 2008

Alex Lancaster wrote:
>>>>>> "SB" == Sendu Bala  writes:
> SB> Alex Lancaster wrote:
>>> I'm the Fedora packager for bioperl.  I note on the release notes
>>> page that Bio::Graphics has been split off into it's own CPAN
>>> module.  Since in most Linux distributions a single tarball = a
>>> single RPM = a single package. How many .tar.gz files (and
>>> therefore packages) are now required to install bioperl?
> SB> BioPerl has started to move toward a number of smaller packages
> SB> that will let people install only what they actually need. There
> SB> will be a core' package of essential modules, and a bunch of these
> SB> new smaller packages that rely on core.
> OK, so this will happen sometime post-1.6?  It seems that currently
> for 1.5.9 there is still just one tarball/CPAN module.  
> How many separate modules are we talking about?  If it's core + 4-5
> separate CPAN modules that doesn't seem too bad

It'll be a small number. Note that currently it is a large core + 
Bio::Graphics + Bio::ASN1::EntrezGene + BioPerl-run + BioPerl-db + 
BioPerl-network + BioPerl-ext. So already it's at least 7 different 
tarballs if you wanted 'everything' BioPerl related.

> SB> From a certain point of view it could be that 'to install bioperl'
> SB> == to install bioperl core', in which case the answer to your
> SB> question is 1' .tar.gz to install.
> SB> As a convenience to the user who wants to install all BioPerl
> SB> packages, there will be a CPAN Bundle (at the least). Fedora
> SB> package-wise, I guess you'd do whatever you currently do to
> SB> emulate CPAN bundles.
> Would these CPAN bundles be updated to include the latest CPAN modules
> as they are individually updated?

There would most likely be a single CPAN bundle specifying all the 
different BioPerl packages but without any version number 
specifications. When a user installs the bundle it would install the 
latest version of each package.

Each individual sub-package, on the other hand, would specify the 
version of any other sub-packages or core that it depends on.

>>> If Bio::Graphics is now not included inside the bioperl tarball and
>>> is required for bioperl
> SB> It isn't. Bio::Graphics depends on BioPerl, but BioPerl does not
> SB> depend on Bio::Graphics.
> OK, thanks for the clarification, although I'm still puzzled as to why
> the package still generates:
> "Requires: perl(Bio::Graphics)"
> see bottom of:
> http://koji.fedoraproject.org/koji/getfile?taskID=1022559&name=build.log

I don't understand that output. Can you state what caused that 
particular require? Nothing should: it's a bug that must be fixed.


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