[Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
Sebastian Bassi
sbassi at gmail.com
Tue Apr 10 15:11:04 UTC 2007
Hello,
I tried to build biopython 1.43 in Ubuntu 6.10 (Edgy Eft). First I met
all dependencies and then I did:
python setup.py build and it failed. So the second try was with N in
the question about compiling Bio.KDTree and I got the same:
sbassi at inet2BALC:~/bioinfo/biopython-1.43$ python setup.py build
running build
running build_py
*** Bio.KDTree *** NOT built by default
The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
which in turn, depends on C++ code that does not compile cleanly on
all platforms. Hence, Bio.KDTree is not built by default.
Would you like to build Bio.KDTree ? (y/N)
running build_ext
building 'Bio.clistfns' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c
Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o
In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
from /usr/include/python2.4/Python.h:18,
from Bio/clistfnsmodule.c:10:
/usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
limits.h: No such file or directory
In file included from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/Python.h:32:19: error: stdio.h: No such file or directory
/usr/include/python2.4/Python.h:34:5: error: #error "Python.h requires
that stdio.h define NULL."
/usr/include/python2.4/Python.h:37:20: error: string.h: No such file
or directory
/usr/include/python2.4/Python.h:38:19: error: errno.h: No such file or directory
/usr/include/python2.4/Python.h:39:20: error: stdlib.h: No such file
or directory
/usr/include/python2.4/Python.h:41:20: error: unistd.h: No such file
or directory
/usr/include/python2.4/Python.h:53:20: error: assert.h: No such file
or directory
In file included from /usr/include/python2.4/Python.h:55,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyport.h:7:20: error: stdint.h: No such file or directory
In file included from /usr/include/python2.4/Python.h:55,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyport.h:73: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_uintptr_t'
/usr/include/python2.4/pyport.h:74: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_intptr_t'
/usr/include/python2.4/pyport.h:94:76: error: math.h: No such file or directory
/usr/include/python2.4/pyport.h:101:22: error: sys/time.h: No such
file or directory
/usr/include/python2.4/pyport.h:102:18: error: time.h: No such file or directory
/usr/include/python2.4/pyport.h:120:24: error: sys/select.h: No such
file or directory
/usr/include/python2.4/pyport.h:159:22: error: sys/stat.h: No such
file or directory
In file included from /usr/include/python2.4/Python.h:74,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pymem.h:50: warning: parameter names (without
types) in function declaration
/usr/include/python2.4/pymem.h:51: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:76,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/object.h:227: error: expected declaration
specifiers or '...' before 'FILE'
/usr/include/python2.4/object.h:371: error: expected declaration
specifiers or '...' before 'FILE'
In file included from /usr/include/python2.4/Python.h:77,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/objimpl.h:97: warning: parameter names (without
types) in function declaration
/usr/include/python2.4/objimpl.h:98: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/objimpl.h:292: warning: parameter names
(without types) in function declaration
In file included from /usr/include/python2.4/Python.h:81,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/unicodeobject.h:55:19: error: ctype.h: No such
file or directory
/usr/include/python2.4/unicodeobject.h:118:21: error: wchar.h: No such
file or directory
In file included from /usr/include/python2.4/Python.h:81,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/unicodeobject.h:131: error: expected '=', ',',
';', 'asm' or '__attribute__' before 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:376: error: expected
specifier-qualifier-list before 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:422: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:422: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:429: error: expected '=', ',',
';', 'asm' or '__attribute__' before '*' token
/usr/include/python2.4/unicodeobject.h:440: error: expected '=', ',',
';', 'asm' or '__attribute__' before 'PyUnicodeUCS4_GetMax'
/usr/include/python2.4/unicodeobject.h:511: warning: type defaults to
'int' in declaration of 'wchar_t'
/usr/include/python2.4/unicodeobject.h:511: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:529: warning: type defaults to
'int' in declaration of 'wchar_t'
/usr/include/python2.4/unicodeobject.h:529: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:621: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:621: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:654: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:654: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:683: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:683: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:760: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:760: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:779: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:779: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:796: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:796: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:827: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:827: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:849: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:849: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:891: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:891: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:912: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:912: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:965: error: expected ')' before '*' token
/usr/include/python2.4/unicodeobject.h:1143: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1147: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1151: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1155: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1159: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1162: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToLowercase'
/usr/include/python2.4/unicodeobject.h:1166: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToUppercase'
/usr/include/python2.4/unicodeobject.h:1170: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToTitlecase'
/usr/include/python2.4/unicodeobject.h:1175: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1179: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1183: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1187: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1191: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1195: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1199: error: expected ')' before 'ch'
In file included from /usr/include/python2.4/Python.h:82,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/intobject.h:35: error: expected ')' before '*' token
In file included from /usr/include/python2.4/Python.h:84,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/longobject.h:46: error: expected ')' before '*' token
/usr/include/python2.4/longobject.h:63: error: expected '=', ',', ';',
'asm' or '__attribute__' before '_PyLong_NumBits'
/usr/include/python2.4/longobject.h:79: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/longobject.h:102: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:101,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/fileobject.h:12: error: expected
specifier-qualifier-list before 'FILE'
/usr/include/python2.4/fileobject.h:38: error: expected ')' before '*' token
/usr/include/python2.4/fileobject.h:40: error: expected '=', ',', ';',
'asm' or '__attribute__' before '*' token
/usr/include/python2.4/fileobject.h:57: error: expected declaration
specifiers or '...' before 'FILE'
/usr/include/python2.4/fileobject.h:58: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_UniversalNewlineFread'
In file included from /usr/include/python2.4/Python.h:112,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyerrors.h:156: warning: type defaults to 'int'
in declaration of 'Py_UNICODE'
/usr/include/python2.4/pyerrors.h:156: error: expected ';', ',' or ')'
before '*' token
/usr/include/python2.4/pyerrors.h:160: warning: type defaults to 'int'
in declaration of 'Py_UNICODE'
/usr/include/python2.4/pyerrors.h:160: error: expected ';', ',' or ')'
before '*' token
/usr/include/python2.4/pyerrors.h:226: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/pyerrors.h:227: error: format string argument
not a string type
/usr/include/python2.4/pyerrors.h:228: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:117,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pythonrun.h:32: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:33: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:35: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:36: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:40: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:41: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:42: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:43: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:44: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:45: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:46: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:49: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:55: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:59: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:60: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:64: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:66: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:82: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:123: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:125: error: expected ')' before '*' token
In file included from /usr/include/python2.4/Python.h:119,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/sysmodule.h:12: error: expected '=', ',', ';',
'asm' or '__attribute__' before '*' token
In file included from /usr/include/python2.4/Python.h:121,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/import.h:25: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/import.h:25: error: expected declaration
specifiers or '...' before 'FILE'
In file included from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/Python.h:131: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:149,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyfpe.h:129:20: error: signal.h: No such file
or directory
/usr/include/python2.4/pyfpe.h:130:20: error: setjmp.h: No such file
or directory
In file included from /usr/include/python2.4/Python.h:149,
from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyfpe.h:132: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'PyFPE_jbuf'
Bio/clistfnsmodule.c: In function 'clistfns_count':
Bio/clistfnsmodule.c:33: error: 'NULL' undeclared (first use in this function)
Bio/clistfnsmodule.c:33: error: (Each undeclared identifier is
reported only once
Bio/clistfnsmodule.c:33: error: for each function it appears in.)
Bio/clistfnsmodule.c: In function 'clistfns_contents':
Bio/clistfnsmodule.c:90: error: 'NULL' undeclared (first use in this function)
Bio/clistfnsmodule.c: At top level:
Bio/clistfnsmodule.c:149: error: 'NULL' undeclared here (not in a function)
error: command 'gcc' failed with exit status 1
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