[Biopython] problem building biopython 1.53 on ubuntu 9.10 possibly involving cpairwise...

[Björn Johansson]

Hi, I recently made a fresh install on ubuntu 9.10 on a laptop. I got the
following error trying to install biopython 1.53. It seems to deal with GCC
and cpairwise2....
does anyone have a clue? could it be some header files for gcc missing?
/bjorn

bjorn at bjorn-laptop:~/Desktop/biopython-1.53$ sudo python setup.py build
running build
running build_py
running build_ext
building 'Bio.cpairwise2' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -fPIC -IBio -I/usr/include/python2.6 -c
Bio/cpairwise2module.c -o build/temp.linux-i686-2.6/Bio/cpairwise2module.o
Bio/cpairwise2module.c:12:20: error: Python.h: No such file or directory
In file included from Bio/cpairwise2module.c:13:
Bio/csupport.h:2: error: expected ‘)’ before ‘*’ token
Bio/cpairwise2module.c: In function ‘IndexList_init’:
Bio/cpairwise2module.c:45: warning: implicit declaration of function
‘memset’
Bio/cpairwise2module.c:45: warning: incompatible implicit declaration of
built-in function ‘memset’
Bio/cpairwise2module.c: In function ‘IndexList_free’:
Bio/cpairwise2module.c:51: warning: implicit declaration of function ‘free’
Bio/cpairwise2module.c:51: warning: incompatible implicit declaration of
built-in function ‘free’
Bio/cpairwise2module.c: In function ‘IndexList__verify_free_index’:
Bio/cpairwise2module.c:91: warning: implicit declaration of function
‘realloc’
Bio/cpairwise2module.c:91: warning: incompatible implicit declaration of
built-in function ‘realloc’
Bio/cpairwise2module.c:92: warning: implicit declaration of function
‘PyErr_SetString’
Bio/cpairwise2module.c:92: error: ‘PyExc_MemoryError’ undeclared (first use
in this function)
Bio/cpairwise2module.c:92: error: (Each undeclared identifier is reported
only once
Bio/cpairwise2module.c:92: error: for each function it appears in.)
Bio/cpairwise2module.c: At top level:
Bio/cpairwise2module.c:143: error: expected ‘)’ before ‘*’ token
Bio/cpairwise2module.c:191: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘*’ token
Bio/cpairwise2module.c:525: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘*’ token
Bio/cpairwise2module.c:543: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or
‘__attribute__’ before ‘cpairwise2Methods’
Bio/cpairwise2module.c: In function ‘initcpairwise2’:
Bio/cpairwise2module.c:557: warning: implicit declaration of function
‘Py_InitModule3’
Bio/cpairwise2module.c:557: error: ‘cpairwise2Methods’ undeclared (first use
in this function)
error: command 'gcc' failed with exit status 1
bjorn at bjorn-laptop:~/Desktop/biopython-1.53$