Errors building PyNIO on RHEL 5.3

Hi,

I posted this once but I never saw it submitted and I don’t see it in the archives. So I’m going to post it again. Sorry if there are two copies but this is sort of important. I'm trying to build PyNIO 1.3.0b1 from source on RHEL 5.3. Here's some of the relevant information:
# uname -m
i686
# python -V
Python 2.4.3
# gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-44)

However I get the following errors trying to build the software:
# python setup.py install
====> Installing Nio to the "PyNIO" site packages directory.
running install
running build
running build_py
copying ./pynio_version.py -> build/lib.linux-i686-2.4/PyNIO
running build_ext
building 'nio' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC -DNeedFuncProto=1 -I/usr/lib/python2.4/site-packages/numpy/core/include -I/usr/local/ncl/include -Iinclude -I/usr/include/python2.4 -c niomodule.c -o build/temp.linux-i686-2.4/niomodule.o
niomodule.c:18:31: error: numpy/arrayobject.h: No such file or directory
In file included from niomodule.c:33:
niomodule.h:221: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
niomodule.c: In function ‘data_type’:
niomodule.c:381: error: ‘PyArray_SHORT’ undeclared (first use in this function)
niomodule.c:381: error: (Each undeclared identifier is reported only once
niomodule.c:381: error: for each function it appears in.)
niomodule.c:383: error: ‘PyArray_INT’ undeclared (first use in this function)
niomodule.c:385: error: ‘PyArray_LONG’ undeclared (first use in this function)
niomodule.c:387: error: ‘PyArray_FLOAT’ undeclared (first use in this function)
niomodule.c:389: error: ‘PyArray_DOUBLE’ undeclared (first use in this function)
niomodule.c:391: error: ‘PyArray_UBYTE’ undeclared (first use in this function)
niomodule.c:393: error: ‘PyArray_CHAR’ undeclared (first use in this function)
niomodule.c:395: error: ‘PyArray_BOOL’ undeclared (first use in this function)
niomodule.c:397: error: ‘PyArray_STRING’ undeclared (first use in this function)
niomodule.c:399: error: ‘PyArray_NOTYPE’ undeclared (first use in this function)
niomodule.c: In function ‘typecode’:
niomodule.c:432: error: ‘PyArray_BOOL’ undeclared (first use in this function)
niomodule.c:433: error: ‘PyArray_BOOLLTR’ undeclared (first use in this function)
niomodule.c:435: error: ‘PyArray_BYTE’ undeclared (first use in this function)
niomodule.c:436: error: ‘PyArray_BYTELTR’ undeclared (first use in this function)
niomodule.c:438: error: ‘PyArray_UBYTE’ undeclared (first use in this function)
niomodule.c:439: error: ‘PyArray_UBYTELTR’ undeclared (first use in this function)
niomodule.c:441: error: ‘PyArray_SHORT’ undeclared (first use in this function)
niomodule.c:442: error: ‘PyArray_SHORTLTR’ undeclared (first use in this function)
niomodule.c:444: error: ‘PyArray_INT’ undeclared (first use in this function)
niomodule.c:445: error: ‘PyArray_INTLTR’ undeclared (first use in this function)
niomodule.c:447: error: ‘PyArray_LONG’ undeclared (first use in this function)
niomodule.c:448: error: ‘PyArray_LONGLTR’ undeclared (first use in this function)
niomodule.c:450: error: ‘PyArray_FLOAT’ undeclared (first use in this function)
niomodule.c:451: error: ‘PyArray_FLOATLTR’ undeclared (first use in this function)
niomodule.c:453: error: ‘PyArray_DOUBLE’ undeclared (first use in this function)
niomodule.c:454: error: ‘PyArray_DOUBLELTR’ undeclared (first use in this function)
niomodule.c:456: error: ‘PyArray_STRING’ undeclared (first use in this function)
niomodule.c:457: error: ‘PyArray_STRINGLTR’ undeclared (first use in this function)
niomodule.c:459: error: ‘PyArray_CHAR’ undeclared (first use in this function)
niomodule.c: In function ‘collect_attributes’:
niomodule.c:517: error: ‘npy_intp’ undeclared (first use in this function)
niomodule.c:517: error: expected ‘;’ before ‘length’
niomodule.c:552: error: ‘length’ undeclared (first use in this function)
niomodule.c:552: error: expected ‘;’ before ‘md’
niomodule.c:554: warning: implicit declaration of function ‘PyArray_SimpleNew’
niomodule.c:554: warning: assignment makes pointer from integer without a cast
niomodule.c:556: error: ‘PyArrayObject’ undeclared (first use in this function)
niomodule.c:556: error: expected expression before ‘)’ token
niomodule.c:556: error: expected expression before ‘)’ token
niomodule.c:556: error: expected expression before ‘)’ token
niomodule.c:556: error: expected expression before ‘)’ token
niomodule.c:558: warning: implicit declaration of function ‘PyArray_Return’
niomodule.c:558: error: expected expression before ‘)’ token
niomodule.c:558: warning: assignment makes pointer from integer without a cast
niomodule.c: In function ‘set_attribute’:
niomodule.c:575: error: ‘PyArrayObject’ undeclared (first use in this function)
niomodule.c:575: error: ‘array’ undeclared (first use in this function)
niomodule.c:603: error: ‘PyArray_NOTYPE’ undeclared (first use in this function)
niomodule.c:604: error: ‘tmparray’ undeclared (first use in this function)
niomodule.c:604: error: expected expression before ‘)’ token
niomodule.c:608: error: expected expression before ‘)’ token
niomodule.c:613: error: ‘array2’ undeclared (first use in this function)
niomodule.c:613: error: expected expression before ‘)’ token
niomodule.c:626: error: ‘npy_intp’ undeclared (first use in this function)
niomodule.c: In function ‘NioFileObject_str’:
niomodule.c:1362: error: ‘PyArrayObject’ undeclared (first use in this function)
niomodule.c:1362: error: ‘att_arr_val’ undeclared (first use in this function)
niomodule.c:1362: error: expected expression before ‘)’ token
niomodule.c:1364: warning: implicit declaration of function ‘PyArray_DATA’
niomodule.c:1454: error: expected expression before ‘)’ token
niomodule.c: In function ‘NioVariableObject_value’:
niomodule.c:1633: warning: implicit declaration of function ‘NioVariable_ReadAsArray’
niomodule.c:1633: warning: return makes pointer from integer without a cast
niomodule.c: At top level:
niomodule.c:1818: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
niomodule.c: In function ‘NioVariable_ReadAsString’:
niomodule.c:2030: error: ‘PyArray_CHAR’ undeclared (first use in this function)
niomodule.c: In function ‘NioVariable_WriteArray’:
niomodule.c:2058: error: ‘PyArrayObject’ undeclared (first use in this function)
niomodule.c:2058: error: ‘array’ undeclared (first use in this function)
niomodule.c:2161: error: expected expression before ‘)’ token
niomodule.c:2163: error: ‘array2’ undeclared (first use in this function)
niomodule.c:2163: error: expected expression before ‘)’ token
niomodule.c:2168: error: expected expression before ‘)’ token
niomodule.c:2183: error: expected expression before ‘)’ token
niomodule.c:2187: error: expected expression before ‘)’ token
niomodule.c:2313: error: expected expression before ‘)’ token
niomodule.c: In function ‘NioVariable_WriteString’:
niomodule.c:2379: error: ‘PyArray_CHAR’ undeclared (first use in this function)
niomodule.c: In function ‘NioVariableObject_item’:
niomodule.c:2432: warning: return makes pointer from integer without a cast
niomodule.c: In function ‘NioVariableObject_slice’:
niomodule.c:2449: warning: return makes pointer from integer without a cast
niomodule.c: In function ‘NioVariableObject_subscript’:
niomodule.c:2476: warning: return makes pointer from integer without a cast
niomodule.c:2513: warning: return makes pointer from integer without a cast
niomodule.c: In function ‘NioVariableObject_str’:
niomodule.c:2883: error: ‘PyArrayObject’ undeclared (first use in this function)
niomodule.c:2883: error: ‘att_arr_val’ undeclared (first use in this function)
niomodule.c:2883: error: expected expression before ‘)’ token
niomodule.c: In function ‘initnio’:
niomodule.c:3349: warning: implicit declaration of function ‘import_array’
niomodule.c:3390: error: ‘NioVariable_ReadAsArray’ undeclared (first use in this function)
error: command 'gcc' failed with exit status 1

I noticed that my first error was that it couldn't find arrayobject.h:
# find / -mount -name arrayobject.h
/usr/lib/python2.4/site-packages/numpy-1.3.0-py2.4-linux-i686.egg/numpy/core/include/numpy/arrayobject.h
/usr/include/python2.4/Numeric/arrayobject.h

My arrayobject.h file doesn't appear to be in any of the paths specified on the gcc line. Has anybody had this problem before? Do I need to make any adjustments to the files before trying to do a build?

Thanks for any help!
Pat

--------------
Pat Allen (pat@mbari.org & http://www.mbari.org/staff/pat)
Monterey Bay Aquarium Research Institute (MBARI)
7700 Sandholdt Rd, Moss Landing, CA 95039
(voice) 831-775-1724 <about:blank> ; (fax) 831-775-1620 <about:blank>

 

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Received on Mon Aug 31 2009 - 14:21:25 MDT