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 <dicknetherla...@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_moel...@gmx.de>
Hi Richard,
Anthony Boureux <anthony.bour...@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.
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