[Bioperl-l] Packaging BioPerl for mandrake linux
Aaron J. Mackey
amackey at pcbi.upenn.edu
Fri Jan 9 10:49:25 EST 2004
On Jan 9, 2004, at 7:35 AM, Guillaume Rousse wrote:
> First, the compilation doesn't support parallel build on multiple-cpu
> host, as readm.pm get installed after it is needed:
I'm not sure how to fix this ...
> Second, correct optimisation flags (-O2 -fomit-frame-pointer -pipe
> -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
> process, only source C files and headers
When you run "make install" what do you see? I get (on Mac OS X 10.3):
That .bundle file is the dynamically loaded binary.
> 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
> Fourth, invocating make test as part of the build process fails for
> 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:
This is in bioperl-live, or at least it should be ... there is no
Bio::Root::* in bioperl-run.
> 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?)
> Does a fish get cramps after eating?
> -- Why Why Why n°2
I think so, but only when eating raw humans
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