Re: Errors building PyNIO on RHEL 5.3

Hi Pat,
It appears that the PyNIO build process does not account for the
possible installation of the numpy package to an ".egg" directory.
As a quick work-around you could try modifying the pynio/setup.py file
by changing the following line (~ line 220):

INC_DIRS.insert(0,os.path.join(pkgs_pth,"numpy","core","include"))

to

INC_DIRS.insert(0,os.path.join(pkgs_pth,"numpy-1.3.0-py2.4-linux-
i686.egg", "numpy","core","include"))

We will have to research this problem a little more to develop a
universal solution.
If you have further problems, please contact me directly.
  -dave

On Aug 31, 2009, at 2:21 PM, Allen, Pat wrote:

> 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'mtrying 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; (fax) 831-775-1620
>
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Received on Mon Aug 31 2009 - 16:52:37 MDT