[Bioperl-l] Packaging BioPerl for mandrake linux

[Aaron J. Mackey]

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 ...

> 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):

Installing  
/usr/local/lib/perl5/site_perl/5.8.1/darwin-2level/auto/Bio/Ext/Align/ 
Align.bs
Installing  
/usr/local/lib/perl5/site_perl/5.8.1/darwin-2level/auto/Bio/Ext/Align/ 
Align.bundle

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  
separately ...

> 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.

> 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

-Aaron