[Bioperl-l] BioPerl 1.6 RC1

Alex Lancaster alexl at users.sourceforge.net
Sat Dec 27 22:19:24 EST 2008

>>>>> "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, but atomising it into
40-50+ modules doesn't seem like a good idea. I raised this point in
an earlier thread on bioperl-l (and it seemed that others agreed):


The situation I want to avoid is having to push a huge number of CPAN
modules through Fedora package review, then having to individually
update them regularly just to get the same functionality as we have
right now with the single perl-bioperl package.  (Packaging
Bioconductor for R is a nightmare for this very reason).

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?  What is possible in RPM is to take
a single tarball and make subpackages from the single tarball, which
would allow the user the benefit of a more fine-grained installation
of particular bioperl modules without having the overhead of
maintaining each package separately, e.g.:

perl-bioperl (core package)
perl-bioperl-foobar (optional subpackage)
perl-bioperl-baz    ("        "         )

>> 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:


Is this a circular dependency like Bio::ASN1::EntrezGene ?


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