[BioPython] biopython 1.47 installation fails - and modified how to install instructions on wiki

Giovanni Marco Dall'Olio dalloliogm at gmail.com
Fri Jul 18 13:20:48 UTC 2008


Hi,
I have two things to say.

First, I have added instructions on how to install biopython with
easy_install to the biopython wiki:
- http://biopython.org/wiki/Download#Easy_Install

for those of you who don't know what easy_install is, it's a nice way to
install python packages on the fly, something similar to perl -MCPAN.
Can you please check whether the easy_install installation works fine for
you too?


Second, I was trying to install biopython 1.47 using the tar/zip archives on
http://biopython.org/DIST/biopython-1.47.tar.gz

There it seems to be a problem with the installation; after running sudo
python setup.py install, I receive the following error:

Would you like to build Bio.KDTree ? (y/N)
running build
running build_py
running build_ext
building 'Bio.clistfns' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.5 -c Bio/clistfnsmodule.c
-o build/temp.linux-i686-2.5/Bio/clistfnsmodule.o
Bio/clistfnsmodule.c:10:20: error: Python.h: No such file or directory
Bio/clistfnsmodule.c:25: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
Bio/clistfnsmodule.c:80: error: expected '=', ',', ';', 'asm' or
'__attribute__' before '*' token
Bio/clistfnsmodule.c:146: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'clistfnsMethods'
Bio/clistfnsmodule.c: In function 'initclistfns':
Bio/clistfnsmodule.c:160: warning: implicit declaration of function
'Py_InitModule3'
Bio/clistfnsmodule.c:160: error: 'clistfnsMethods' undeclared (first use in
this function)
Bio/clistfnsmodule.c:160: error: (Each undeclared identifier is reported
only once
Bio/clistfnsmodule.c:160: error: for each function it appears in.)
error: command 'gcc' failed with exit status 1


It seems a file Python.h is missing or mispelled.
Con you confirm that?

Cheers


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