[Biopython-dev] need help with Genbank - additional error

[Jeffrey Chang]

On Thu, Jul 18, 2002 at 12:30:40PM -0500, Dinakar Desai wrote:
> > Thanks for your email. I downloaded cvs version of biopython. I install 
> > numarray0.3.5. I get the following error message when I tried to install 
> >  biopython with following command:
> > python setup.py install
> > 
> > <error_msg>
> >  building 'Bio.Tools.KDTree._KDTreecmodule' extension
> >   skipping Bio/Tools/KDTree/_KDTree.C (build/temp.linux-i686-2.2/_KDTree.o
> >  g -O3 -Wall -Wstrict-prototypes -fPIC -I/home/desas2/inclu
> > de/python2.2 -c Bio/Tools/KDTree/_KDTree.swig.C -o 
> > build/temp.linux-i686-2.2/_KD
> > Tree.swig.o
> > </error_msg>
> > 
> > Please let me know what else I need to install to fix this problem of 
> > install of cvs version of biopython.

You can safely ignore this error message.  It is code in development
for the next release of biopython and will not affect the GenBank
package.  In the setup.py file, comment out the lines at the end of
the file that contain "KDTree":
                     #Extension('Bio.Tools.KDTree._KDTreecmodule',
                     #          ["Bio/Tools/KDTree/_KDTree.C", 
                     #           "Bio/Tools/KDTree/_KDTree.swig.C"],
                     #          libraries=["stdc++"]
                     #          )

Jeff