Re: [Fwd: bio-das.* (was Re: New upstream release of GBrowse)]

[Anthony Boureux <Anthony.Boureux@gmail.com>]

Hello,

Thank you very much for your answer and your reactivity to all of you.
I answered to Andy (inside the mail) and I have some questions for the
debian-med team at the end of this (long) mail.


Andy Jenkinson a écrit :
> Hi all,
>
> ProServer is a DAS server library, and the dependency on 
> Bio::Das::Lite is, as you have seen, purely in the proxy 
> SourceAdaptor. It is a very niche part of the server, and by no means
>  -needs- to be included in the build. However, it is not an ideal 
> situation to silently remove it, I think.

I would not remove it silently, it will be write with the documentation
in the package.

> This and many other dependencies (e.g. the Ensembl API, BioPerl) are 
> completely optional, and so I think the best solution would be to 
> make ProServer configurable when building the Makefile and have 
> certain optional parts turned off by default. This would be a good 
> change to make anyway, since people are often confused by the 
> requirements, thinking they are all required despite the make process
>  identifying them as optional. Does this feasible, and something
> you'd be interested in contributing?

Configuration during the building process is not really simple, because
debian provide binary packages to its users. But to accommodate all
dependencies in source adaptor/transport, I can build sub-package which
will provide dependency to Bioperl, DBI, Ensembl API (this one has to be
packaged first) for each different sources (4 at this time).
ie:
libbio-das-proserver-bioperlsource-perl
libbio-das-proserver-dbisource-perl
libbio-das-proserver-ensemblsource-perl
libbio-das-proserver-proxysource-perl, this one will be not working,
because of the dependency to Parallel::UA, until Bio::Das::Lite doesn't
depend to Parallel::UA (see below).


> By the way, there are plans to remove Parallel::UA from 
> Bio::Das::Lite, but nothing concrete yet.

It will be the best solution for me.
After some research on the net, it seems that Parallel::UA will not work
easily with LWP >5.76. This bug was already reported
(http://rt.cpan.org/Public/Bug/Display.html?id=40261).
Nonetheless, I try to apply a patch (used in Bio::Das::Lite) to make
Parallel::UA working directly in Parallel::UA package : but I got the
following error :
"Deep recursion on subroutine "LWP::Parallel::UserAgent::request" at
/usr/share/perl5/LWP/Authen/Basic.pm line 40, <DAEMON> line 1.
until one of script freeze.

So, I don't think I can do more about Parallel::UA. What I saw in
Bio::Das::Lite code, it's too much work, and outside my competence in
perl, for me to use something else instead of Parallel::UA.


> Cheers, Andy
>
> On 28 Aug 2009, at 10:33, Jonathan Warren wrote:
>
> > Hi Andy
> >
> > As the DAS/perl expert - Can you give some advice on the perl 
> > libraries questions below?
> >
> > Cheers
> >
> > Jonathan.
> >
> > 2009/8/28 Richard Holland <dicknetherlands@gmail.com>:
> > > Anthony,
> > >
> > > I would recommend your third solution. If you need help tracking 
> > > down DAS people, you should talk to Jonathan Warren (copied), who
> > >  is in charge of the DAS project.
> > >
> > > cheers, Richard
> > >
> > > 2009/8/27 Steffen Moeller <steffen_moeller@gmx.de>
> > > > Hi Richard,
> > > >
> > > > Anthony Boureux <Anthony.Boureux@gmail.com> sent the attached 
> > > > email to Debian Med since he wants to package DAS-associated 
> > > > packages for Debian/Ubuntu - which sounds great to me.
> > > >
> > > > He ran into some compatibility issues that he is not completely
> > > >  comfortable to fix. Should you have some advice for him ... 
> > > > please ... I was hoping that this effort of his would save you 
> > > > time in the long run.
> > > >
> > > > TIA and best regards,
> > > >
> > > > Steffen
> > > >
> > > > Unfortunately, for my first package, I need your help: 
> > > > libbio-das-proserver is a DAS server with adaptors for 
> > > > different data sources. In one of these sources (proxy.pm) the 
> > > > library bio-das-lite is required, but this last one need the 
> > > > paralleluseragent and this one works only with libwww-perl <= 
> > > > 5.76, nut lenny is already in 5.813. The author of 
> > > > parallel-user-agent doesn't recommend to use libwww higher than
> > > >  5.76. Indeed, when I packaged parallel-user-agent : the tests 
> > > > scripts are not working. (In my server, I make the package 
> > > > without doing the tests, but it's only local and I don't use 
> > > > the proxy source for the bio-das-proserver). So I think I can't
> > > >  package parallel-user-agent, it can't be use on any debian 
> > > > distribution. I didn't ask the author, but the last release was
> > > >  in 2004 and I don't think he will do some
> > > > adjustment/correction now and so I can't package
> > > > libbio-das-lite.
> > > >
> > > > solution 1/ to package libbio-das-proserver for now, is to 
> > > > remove the dependency for libbio-das-lite and so remove the 
> > > > adaptor source proxy.pm, and put a message in the package that 
> > > > this source was removed.
> > > >
> > > > solution 2/ I don't care of errors in test scripts perl and I 
> > > > package anyway.
> > > >
> > > > solution 3/  the best solution will be the author of 
> > > > libbio-das-proserver remove the dependency for libbio-das-lite 
> > > > (same author as libbio-das-proserver) may be by using 
> > > > libbio-das or change the dependency for parallel-user-agent in 
> > > > libbio-das-lite.
> > > >
> > > > So your advices ?
> > > >
> > > > Best regards, Anthony.

So, my questions for the packaging team (I not really an expert with the
debian policy) :
Do you think I can split the package libbio-das-proserver, even if
sub-package have less than 5 files ?
and if a sub-package is broken (libbio-das-proserver-proxysource-perl)
because it can't be installed at this time without
libparallel-useragent-perl.
I can also remove this sub-package from the building process and wait 
until an upstream solution ?

Thanks everyone.

Anthony.