[Bioperl-l] Packaging BioPerl for mandrake linux
rousse at ccr.jussieu.fr
Fri Jan 9 17:47:00 EST 2004
On Friday 09 January 2004 16:49, Aaron J. Mackey wrote:
> On Jan 9, 2004, at 7:35 AM, Guillaume Rousse wrote:
> > First, the compilation doesn't support parallel build on multiple-cpu
> > build
> > host, as readm.pm get installed after it is needed:
> I'm not sure how to fix this ...
Me neither :-)
> > Second, correct optimisation flags (-O2 -fomit-frame-pointer -pipe
> > -march=i586
> > -mcpu=pentiumpro) are not passed to all gcc invocations:
> But this I did fix in CVS, thanks for pointing it out ...
> > Third, I can't find any installed binary files at the end of the
> > compilation
> > process, only source C files and headers
> When you run "make install" what do you see? I get (on Mac OS X 10.3):
Seems the source dir is installed instead of build dir.
perl Makefile.PL INSTALLDIRS=vendor
for generating the makefile, and a rpm macro evaluating to
make DESTDIR=/home/guillomovitch/rpm/tmp/perl-Bioperl-Ext-root install
> That .bundle file is the dynamically loaded binary.
I thought native files had to get installed only
> > I don't have previous experience of using Inline::C, however
> The Bio/Ext/Align/ stuff doesn't use Inline::C, that's only the
> Bio::SeqIO::staden stuff. You might consider packaging the two
> separately ...
Just because one use Inline::C and not the other? I would like to split
bioperl core first, there are tons of dependencies there :-)
> > Fourth, invocating make test as part of the build process fails for
> > some
> > uninstalled module:
> This is an Inline::C problem; Inline::C-based modules are a little
> tricky to get right for testing before installation. Generally I see
> this error when I've had a failed compilation (because of the .h errors
> you found) and don't have a completely "clean" build environment.
> You're right that the error message is misleading.
> > BTW, some modules in main bioperl package have references to some
> > modules in
> > bioperl-run package:
> > Bio::Root::Version
> This is in bioperl-live, or at least it should be ... there is no
> Bio::Root::* in bioperl-run.
My fault, something wrong in a quick diff between bioperl requires and
> > This make both packages to requires each other. Maybe those modules
> > should be
> > moved to bioperl-run, to make bioperl self-sufficient ?
> bioperl-run requires bioperl, period. bioperl makes use of many
> "external" packages, but they are mostly optional (required only for a
> very small subset of bioperl functionality). In general, we'd like
> people to be able to install the core BioPerl without a ton of other
> packages (and certainly without requiring bioperl-run). All bioperl
> tests should pass (i.e. be skipped, if necessary) without bioperl-run
> installed (is that not true?)
Those dependencies are generated by rpm automatic dependencies computing,
because they are some files in bioperl triggering them. A quick grep shows
the included scripts are responsable:
I'll silent them manually.
> > Does a fish get cramps after eating?
> > -- Why Why Why n°2
> I think so, but only when eating raw humans
A bad dinner with your wife is worth more than a good one in the company of
-- A law for married men
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