[Bioperl-l] BioPerl 1.6 RC1

Alex Lancaster alexl at users.sourceforge.net
Sat Dec 27 22:03:01 EST 2008

>>>>> "SB" == Sendu Bala  writes:

SB> Alex Lancaster wrote:


>> Is this the expected behaviour upon missing optional dependencies?

SB> Yes, though I can see how it's broken from your point of view. It
SB> is set up to install everything, but simply not everything will
SB> work without the optionals. I hadn't considered not installing the
SB> modules that won't work.

Yes, not installing modules for which optional deps are missing would
be the most sensible and would conform with the principle of least
surprise.  C programs built using autoconf/automake with the usual
"./configure", "make", "make install" series steps, if an optional dep
(say a shared library) is missing, the configure script notices that
and program is compiled without that feature and any relevant files
aren't installed.  Even though Perl programs don't link at
compile-time, conceptually it should be no different to the way a C
program handles missing shared libraries or other deps.

SB> Something to think about, but it's probably not going to happen
SB> for 1.6?

Sure, so for the moment (while I'm packaging the deps) I can simply
remove the relevant .pm files from before final packaging of the RPM
so that the automatic Perl dependency generator won't find them, but
in the long term it would be better to not install the files for which
deps are missing.  Would it be best to open up a bug for this? (don't
have a bugzilla account myself just now).

On a related note, it would also be good if command-line options could
be passed to the Build.PL script to provide answers to the questions
that the Build.PL asks.  Running interactive prompts during the build
means that the Fedora .spec file has to simulate the interactive
answering of questions (as shown at the top of the build.log, below)
and makes the process of generating the RPM very fragile:



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