Numeric + Lapack/Blas/ATLAS [Re: [BioPython] Installation help]

[Catherine Letondal]

On Dec 20, 2004, at 5:30 PM, Catherine Letondal wrote:

>
> On Apr 7, 2004, at 12:39 AM, Brad Chapman wrote:
>
>> Hi Jim;
>> [Condensing both answers into a single mail]
>>
>>> I'm pulling together the dependencies for biopython
>>> and need to know whether I should download "numeric"
>>> or "numarray".
>>
>> Numeric. Although Numarray is supposed to be API compatible to some
>> extent with Numeric, I don't believe that anyone has fully tested
>> that out. Numeric should work for now -- at some point in the future
>> someone will likely go through and ensure everything works and we'll
>> move on to Numarray.
>>
>
> Hi,
>
> Has someone succesfully installed Numeric on MacOSX/PPC/G4? I have 
> some problems while installing this package, because it needs another 
> package (Lapack):
>
> % python setup.py install
> [...]
> building 'lapack_lite' extension
> gcc -fno-strict-aliasing -Wno-long-double -no-cpp-precomp 
> -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 -Wall 
> -Wstrict-prototypes -I/usr/include/atlas -IInclude 
> -IPackages/FFT/Include -IPackages/RNG/Include 
> -I/Library/Frameworks/Python.framework/Versions/2.4/include/python2.4 
> -c Src/lapack_litemodule.c -o 
> build/temp.darwin-7.6.0-Power_Macintosh-2.4/Src/lapack_litemodule.o
> ld: warning -L: directory name (/usr/lib/atlas) does not exist
> ld: can't locate file for: -llapack
> error: command 'gcc' failed with exit status 1
>
> So, I have tried to install Lapack+Blas 
> (http://www.netlib.org/lapack/), and also ATLAS (an alternative to 
> install Lapack+Blas)  but I got many errors. Has someone already 
> installed it on MacOSX, for:
> 	- either Atlas does not compile
> 	- Lapack needs BLAS (http://www.netlib.org/blas/), which is provided 
> without any Makefile!


Hi,

I would like to first thank a lot Michael Maibaum for his help with 
installing a darwinport version of biopython.

However, we still need to be able to compile and install Numeric (and 
thus biopython) in a Python path that we choose. Indeed, we install 
software for a 4 monthes course on aserver that we share with other 
users, and we have to mount a dedicated part of its filesystem on a set 
of 16 G4 clients for this purpose, so mounting a separate /opt 
directory does not really suit the system administrator of this server. 
Besides, we would be happier of course to be able to compile the 
Numeric package ourselves.

So, could someone help? Has someone succedeed in the installation of 
Numeric/Lapack/Atlas/Blas on MacOSX 10.3?  (The python version that is 
used for the course is 2.3. )
Another question/request is: would it be possible to use biopython 
without Numeric?

Thanks a lot in advance, we really need biopython for our course (and 
enjoy using it),

--
Catherine Letondal -- Institut Pasteur -- Cours d'Informatique en 
Biologie
www.pasteur.fr/formation/infobio