Re: [Fwd: bio-das.* (was Re: New upstream release of GBrowse)]
Hi Anthony,
On 28 Aug 2009, at 16:41, Anthony Boureux wrote:
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).
I just meant that it would be nice to be able to configure the build
of ProServer, which you could use to produce a package without the
offending proxy plugin. But understanding better the way things are
packaged, I think it makes sense to subpackage the plugins separately,
as you describe. I think those subpackages you list are appropriate,
it is up to you which of the other optional dependencies are included
in the core proserver package (e.g. Net::IP and LWP which are also
optional).
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.
Indeed, I reported the bug on CPAN. I believe I have figured out what
needs to be done to fix the problem and have forwarded my findings to
the author of Bio::Das::Lite, but I think he still plans to remove
Parallel entirely. But there is no timeline for this.
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.
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