[BioPython] LAPACK error

Michiel Jan Laurens de Hoon mdehoon at ims.u-tokyo.ac.jp
Mon Sep 27 22:09:28 EDT 2004

 > And just BTW, any idea of when Biopython might move from Numeric to
 > Numarray?

I am not sure to what degree numarray has been accepted by the user community as 
a replacement for Numeric. For example, SciPy expects this transition to take 
years. The transition will not be that straightforward either, as some of the C 
extension modules will have to be modified. So my personal expectation is that 
it may take some time. What do other users/developers think?

Paul-Michael Agapow wrote:
> gcc -pthread -shared build/temp.linux-i686-2.3/Src/lapack_litemodule.o  
> -L/usr/lib/atlas -llapack -lcblas -lf77blas -latlas -lg2c -o  
> build/lib.linux-i686-2.3/lapack_lite.so  
> /usr/lib/gcc-lib/i586-suse-linux/3.3.3/../../../../i586-suse-linux/bin/ 
> ld: cannot find -llapack
> collect2: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1

I have seen this error before, but only with the latest version of Numeric 
(23.3). With to the earlier version (23.1) of Numeric, I had no such problems. 
So that might be your easiest solution.


Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639

More information about the BioPython mailing list