Re: ccplot 1.5-rc7 build error

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

Ryan,

Yes it helped! The library_dirs option is apparently not even applied.
Could you please send me your current setup.py - in case anything was
wrongly applied?

Attached is one that should have all modifications needed.

Peter

On 11/22/2013 08:11 PM, Ryan Scott wrote:
> Hi Peter,
> 
> Here's the build output after having applied the .diff file in the
> ccplot-master directory:
> 
> bash-3.2$ cd ~/Desktop/ccplot-master/
> bash-3.2$ ls
> LICENSEccplot
> MANIFEST.inccplot-verbose-link.diff
> NEWScmap
> README.mdman
> binsetup.py
> buildtest
> bash-3.2$ patch < ccplot-verbose-link.diff
> (Stripping trailing CRs from patch.)
> patching file setup.py
> 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 -v
> Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
> Target: x86_64-apple-darwin12.4.0
> Thread model: posix
>  "/usr/bin/ld" -demangle -dynamic -arch i386 -bundle -macosx_version_min
> 10.8.0 -undefined dynamic_lookup -undefined dynamic_lookup -o
> /var/folders/fx/t186xjbj1wl66fscp60wm0yw0000gp/T//i8J7H3.out
> -L/Users/ryan/Desktop/src/hdf5-1.8.10/hdf5/lib -F.
> build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o -lmfhdf -ldf -ljpeg -lz
> -arch_multiple -final_output
> build/lib.macosx-10.8-intel-2.7/ccplot/hdf.so -lSystem
> /usr/bin/../lib/clang/4.2/lib/darwin/libclang_rt.eprintf.a
> /usr/bin/../lib/clang/4.2/lib/darwin/libclang_rt.osx.a
> 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 helps!
> 
> -Ryan
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Fri, Nov 22, 2013 at 10:58 AM, Peter Kuma <pet...@wa...
> <mailto:pet...@wa...>> wrote:
> 
>     Hi Ryan,
> 
>     dylib is the equivalent of so files on other unix systems. The linker
>     should find the library just fine if it is indeed located under
>     /opt/local/lib/libmfhdf.dylib. I don't know why it does not.
> 
>     The best I can think of is to add a verbose flag to the linker to get a
>     more detailed error report. A patch is attached. It can be applied with:
> 
>     patch < ccplot-verbose-link.diff
> 
>     in the ccplot directory. If you can send me the build output that would
>     be great.
> 
>     Regards,
> 
>     Peter
> 
>     On 11/22/2013 06:47 PM, Ryan Scott wrote:
>     > Hi Peter,
>     >
>     > After receiving the same error with the up-to-date ccplot-master, I
>     > checked /opt/local/lib and I have the following libmfhdf* files
>     >
>     > libmfhdf.0.dylib
>     > libmfhdf.a
>     > libmfhdf.dylib
>     > libmfhdf.la <http://libmfhdf.la> <http://libmfhdf.la>
>     >
>     > The lack of the libmfhdf.so file is presumably then the root of the
>     > error. Do you know where this can be obtained?
>     >
>     > Best, Ryan
>     >
>     >
>     >
>     > On Thu, Nov 21, 2013 at 11:53 PM, Peter Kuma
>     <pet...@wa... <mailto:pet...@wa...>
>     > <mailto:pet...@wa... <mailto:pet...@wa...>>>
>     wrote:
>     >
>     >     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...>
>     <mailto:pet...@wa... <mailto:pet...@wa...>>
>     >     > <mailto:pet...@wa...
>     <mailto:pet...@wa...> <mailto: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...>>
>     >     <mailto:pet...@wa... <mailto:pet...@wa...>
>     <mailto:pet...@wa... <mailto:pet...@wa...>>>
>     >     >     > <mailto:pet...@wa...
>     <mailto:pet...@wa...>
>     >     <mailto:pet...@wa...
>     <mailto:pet...@wa...>> <mailto: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
>     >     >     >
>     >     >     >
>     >     >
>     >     >
>     >
>     >
> 
>