Re: ccplot 1.5-rc7 build error

[Peter K. <pet...@wa...>]

Hi Ryan,

I think this could be a similar problem as with the include path. The
solution depends on where the libmfhdf.so library is, I assume it is
/opt/local/lib. Please try adding the path to hdf_library_dirs in setup.py:

-    hdf_library_dirs = []
+    hdf_library_dirs = ['/opt/local/lib']

(line 25)

Or, if it does not work, please try locate libmfhdf.so.

The current master incorporates both fixes for the include path and
MAX_VAR_DIMS.

Regards,

Peter

On 11/22/2013 01:38 AM, Ryan Scott wrote:
> Hello Peter,
> 
> I have attempted to build both ccplot-master as well as ccplot-1.5-rc7,
> ensuring that hdf.c everywhere reads H4_MAX_VAR_DIMS where necessary.
> However, still no luck on the build.
> 
> Here is the output from my latest try:
> 
> bash-3.2$ python setup.py build
> running build
> running build_py
> running build_ext
> skipping 'ccplot/hdf.c' Cython extension (up-to-date)
> building 'ccplot.hdf' extension
> clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common
> -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX
> -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os
> -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64
> -I/Users/ryan/Desktop/src/boost_1_53_0 -pipe -I/usr/include/hdf
> -I/usr/local/include/hdf -I/opt/local/include
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -c ccplot/hdf.c -o build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o
> clang: warning: argument unused during compilation: '-mno-fused-madd'
> In file included from ccplot/hdf.c:314:
> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:14:
> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:26:
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1532:1:
> warning: 
>       unused function '_import_array' [-Wunused-function]
> _import_array(void)
> ^
> In file included from ccplot/hdf.c:315:
> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h:152:
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h:226:1:
> warning: 
>       unused function '_import_umath' [-Wunused-function]
> _import_umath(void)
> ^
> 2 warnings generated.
> In file included from ccplot/hdf.c:314:
> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:14:
> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:26:
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1532:1:
> warning: 
>       unused function '_import_array' [-Wunused-function]
> _import_array(void)
> ^
> In file included from ccplot/hdf.c:315:
> In file included from
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h:152:
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h:226:1:
> warning: 
>       unused function '_import_umath' [-Wunused-function]
> _import_umath(void)
> ^
> 2 warnings generated.
> clang -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 -arch x86_64
> -L/Users/ryan/Desktop/src/hdf5-1.8.10/hdf5/lib
> -I/Users/ryan/Desktop/src/boost_1_53_0
> build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o -lmfhdf -ldf -ljpeg -lz -o
> build/lib.macosx-10.8-intel-2.7/ccplot/hdf.so
> ld: library not found for -lmfhdf
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> error: command 'clang' failed with exit status 1
> 
> Hopefully this is also an easy fix. Best,
> 
> Ryan
> 
> 
> On Thu, Nov 21, 2013 at 2:10 PM, Peter Kuma <pet...@wa...
> <mailto:pet...@wa...>> wrote:
> 
>     Hi Ryan,
> 
>     Thanks for the follow-up. It is nice to hear you find ccplot useful.
> 
>     I was afraid there may be more problems. I'm sure other mac users will
>     be happy to see this sorted out.
> 
>     The reason is that MAX_VAR_DIMS is only available when HDF4 was compiled
>     with netcdf-3 compatibility. It should be easy to fix by replacing all
>     occurrences of MAX_VAR_DIMS with H4_MAX_VAR_DIMS.
> 
>     Please try an updated version from github:
> 
>     https://github.com/peterkuma/ccplot/archive/master.zip
> 
>     Regards,
> 
>     Peter
> 
>     On 11/21/2013 09:37 PM, Ryan Scott wrote:
>     > Hello Peter,
>     >
>     > I very much appreciate the timely response and your willingness to
>     help.
>     > I was happy to see that a new version of ccplot was available without
>     > the PyNIO dependency, which has prevented me from using it in the
>     past.
>     > ccplot appears to be far superior than what is possible using
>     Matlab and
>     > NCAR Command Language!
>     >
>     > I have modified line 24 of setup.py to reflect '/opt/local/include' as
>     > well, and I no longer receive the error regarding hntdefs.h.
>     >
>     > Unfortunately, though I'm presented with a new error. To give you as
>     > much detail as possible, here's the new issue:
>     >
>     > "bash-3.2$ python setup.py build
>     > running build
>     > running build_py
>     > running build_ext
>     > skipping 'ccplot/hdf.c' Cython extension (up-to-date)
>     > building 'ccplot.hdf' extension
>     > clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe
>     -fno-common
>     > -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX
>     > -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -Os
>     > -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64
>     > -I/Users/ryan/Desktop/src/boost_1_53_0 -pipe -I/usr/include/hdf
>     > -I/usr/local/include/hdf -I/opt/local/include
>     >
>     -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include
>     >
>     -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
>     > -c ccplot/hdf.c -o build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o
>     > clang: warning: argument unused during compilation: '-mno-fused-madd'
>     > ccplot/hdf.c:5266:30: error: use of undeclared identifier
>     'MAX_VAR_DIMS'
>     >   __pyx_t_1 = PyInt_FromLong(MAX_VAR_DIMS); if (unlikely(!__pyx_t_1))
>     > {__pyx_filename =...
>     >                              ^
>     > ccplot/hdf.c:7066:30: error: use of undeclared identifier
>     'MAX_VAR_DIMS'
>     >   __pyx_t_1 = PyInt_FromLong(MAX_VAR_DIMS); if (unlikely(!__pyx_t_1))
>     > {__pyx_filename =...
>     >                              ^
>     > 2 errors generated.
>     > error: command 'clang' failed with exit status 1"
>     >
>     > Perhaps there is an easy fix?
>     >
>     > Best,
>     >
>     > -Ryan
>     >
>     >
>     >
>     >
>     >
>     >
>     > On Thu, Nov 21, 2013 at 12:11 AM, Peter Kuma
>     <pet...@wa... <mailto:pet...@wa...>
>     > <mailto:pet...@wa... <mailto:pet...@wa...>>>
>     wrote:
>     >
>     >     On 11/21/2013 02:07 AM, ryan scott wrote:
>     >     > I have installed all dependencies for ccplot. However, when
>     >     attempting to build ccplot before installation, I receive the
>     >     following error message:
>     >     >
>     >     > "ccplot/hdf.c:317:10: fatal error: 'hntdefs.h' file not found
>     >     > #include "hntdefs.h"
>     >     >          ^
>     >     > 1 error generated.
>     >     > error: command 'clang' failed with exit status 1"
>     >     >
>     >     > I do, however, have the hdf4 library installed (via
>     MacPorts), the
>     >     following
>     >     >
>     >     > bash-3.2$ locate hntdefs.h
>     >     > /opt/local/include/hntdefs.h
>     >     >
>     >     > shows that I do have this file. Could anyone please point me in
>     >     the right direction?
>     >     >
>     >     > Any help is very much appreciated. Thanks,
>     >     >
>     >     > Ryan
>     >
>     >     Dear Ryan,
>     >
>     >     Sorry - I think this is a problem with ccplot rather than your
>     >     configuration. It assumes that hdf is available under either
>     >     /usr/include/hdf or /usr/local/include/hdf, which is a valid
>     assumption
>     >     on linux, but not on mac. For now, could you please just add
>     the path to
>     >     hdf_include_dirs in setup.py?
>     >
>     >     -   hdf_include_dirs = ['/usr/include/hdf',
>     '/usr/local/include/hdf']
>     >     +   hdf_include_dirs = ['/usr/include/hdf',
>     '/usr/local/include/hdf',
>     >     '/opt/local/include']
>     >
>     >     (line 24)
>     >
>     >     Unfortunately, I don't have access to a mac system for testing
>     now, so I
>     >     would not find out. Hopefully, darwin will be good enough for
>     this. I'll
>     >     try to fix these issues soon.
>     >
>     >     Thank you very much for reporting the problem.
>     >
>     >     Regards,
>     >
>     >     Peter
>     >
>     >
> 
>