[postgis-users] GDAL problems (Kyngesbury GDAL)

William Kyngesburye woklist at kyngchaos.com
Sat Dec 28 09:46:34 PST 2013 

Sorry, I didn't read to the very end, where you did recompile with the --include-dirs option.

The missing lib/ warning is no problem, just a warning.

The segfault though, doesn't say enough to figure out what's wrong.  Maybe there is something in the Console.app, like a crash report (User Diaognostic Reports section).

On Dec 28, 2013, at 11:38 AM, William Kyngesburye wrote:

> The compile flag to set the GDAL include dir is wrong for the framework.  It seems to be assuming that the framework is a 'nix lib/include structure, but really the include dir is named "Headers".  Odd that it uses supposedly gdal-config, but doesn't get the -cflags from it that have the correct include dir.
> 
> I see that Tim's instructions actually call for using --include-dirs=/Library/Frameworks/GDAL.framework/Versions/1.9/Headers/
> 
> 
> I wonder: Tim, what is it about the "virtual environment" that makes the existing GDAL python in the framework not work? (I don't know anything about python virtual env)
> 
> 
> On Dec 27, 2013, at 10:33 PM, Dheeraj Chand wrote:
> 
>> Hi, all,
>> 
>> I was working on a project, that at a high level, can be described as :
>> 
>> 1. Connect Python to PostGIS,
>> 2. Grab spatial tables' data,
>> 3. *PROCESS*,
>> 4. Spit out shapefiles.
>> 
>> In the process of doing this, I was trying to use the Python GDAL library in a new virtualenv called geo, but I got these errors.  I am using William Kyngesbury's GDAL 1.10 for OS X, and I'm running into crazy errors.  I am following the instructions from here (http://linfiniti.com/2013/02/installing-python-gdal-into-a-python-virtualenv-in-osx/), and this is what happened in my shell.
>> 
>> Can anyone help me out?
>> 
>> Best,
>> 
>> -dx
>> 
>> 
>> -----------------------------------
>> REINHEIT:~ dheerajchand$ cd ~/Python_Environments/geo/
>> REINHEIT:geo dheerajchand$ cd build/
>> REINHEIT:build dheerajchand$ ls
>> total 8
>> drwxr-xr-x   4 dheerajchand  staff   136B Dec 27 18:10 ./
>> drwxr-xr-x   7 dheerajchand  staff   238B Dec 27 18:10 ../
>> drwxr-xr-x  22 dheerajchand  staff   748B Dec 27 18:10 GDAL/
>> -rw-r--r--   1 dheerajchand  staff   185B Dec 27 18:10 pip-delete-this-directory.txt
>> /Users/dheerajchand/Python_Environments/geo/build
>> REINHEIT:build dheerajchand$ source ~/Python_Environments/geo/bin/activate
>> (geo)REINHEIT:build dheerajchand$ pip install --no-install GDAL
>> Downloading/unpacking GDAL
>>  Running setup.py egg_info for package GDAL
>> 
>> Successfully downloaded GDAL
>> (geo)REINHEIT:build dheerajchand$ pip freeze
>> numpy==1.8.0
>> psycopg2==2.5.1
>> wsgiref==0.1.2
>> (geo)REINHEIT:build dheerajchand$ sudo find / -name gdal-config
>> Password:
>> find: /dev/fd/3: Not a directory
>> find: /dev/fd/4: Not a directory
>> /Library/Frameworks/GDAL.framework/Versions/1.10/Programs/gdal-config
>> /Library/Frameworks/GDAL.framework/Versions/1.10/unix/bin/gdal-config
>> /Library/Frameworks/GDAL.framework/Versions/1.7/Programs/gdal-config
>> /Library/Frameworks/GDAL.framework/Versions/1.8/Programs/gdal-config
>> /Library/Frameworks/GDAL.framework/Versions/1.9/Programs/gdal-config
>> /Library/Frameworks/GDAL.framework/Versions/1.9/unix/bin/gdal-config
>> /opt/opengeo/pgsql/9.1/bin/gdal-config
>> (geo)REINHEIT:build dheerajchand$ cd GDAL/
>> (geo)REINHEIT:GDAL dheerajchand$ python setup.py build_ext \
>>> --gdal-config=/Library/Frameworks/GDAL.framework/Versions/1.10/Programs/gdal-config \
>>> --library-dirs=/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/
>> running build_ext
>> gcc-4.2 not found, using clang instead
>> building 'osgeo._gdal' extension
>> creating build
>> creating build/temp.macosx-10.6-intel-2.7
>> creating build/temp.macosx-10.6-intel-2.7/extensions
>> clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I../../port -I../../gcore -I../../alg -I../../ogr/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/GDAL.framework/Versions/1.10/include -c extensions/gdal_wrap.cpp -o build/temp.macosx-10.6-intel-2.7/extensions/gdal_wrap.o
>> extensions/gdal_wrap.cpp:2853:10: fatal error: 'cpl_port.h' file not found
>> #include "cpl_port.h"
>>         ^
>> 1 error generated.
>> error: command 'clang' failed with exit status 1
>> (geo)REINHEIT:GDAL dheerajchand$ python setup.py build_ext  --gdal-config=/Library/Frameworks/GDAL.framework/Versions/1.10/Programs/gdal-config  --library-dirs=/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ --include-dirs=/Library/Frameworks/GDAL.framework/Versions/1.
>> 1.10/ 1.7/  1.8/  1.9/
>> (geo)REINHEIT:GDAL dheerajchand$ python setup.py build_ext  --gdal-config=/Library/Frameworks/GDAL.framework/Versions/1.10/Programs/gdal-config  --library-dirs=/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ --include-dirs=/Library/Frameworks/GDAL.framework/Versions/1.10/Headers/
>> running build_ext
>> gcc-4.2 not found, using clang instead
>> building 'osgeo._gdal' extension
>> clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/GDAL.framework/Versions/1.10/Headers/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/GDAL.framework/Versions/1.10/include -c extensions/gdal_wrap.cpp -o build/temp.macosx-10.6-intel-2.7/extensions/gdal_wrap.o
>> extensions/gdal_wrap.cpp:7501:31: warning: conversion from string literal to
>>      'char *' is deprecated [-Wdeprecated-writable-strings]
>>        PyObject *item_list = PyMapping_Items( obj1 );
>>                              ^
>> /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/abstract.h:1354:50: note:
>>      expanded from macro 'PyMapping_Items'
>> #define PyMapping_Items(O) PyObject_CallMethod(O,"items",NULL)
>>                                                 ^
>> 1 warning generated.
>> extensions/gdal_wrap.cpp:7501:31: warning: conversion from string literal to
>>      'char *' is deprecated [-Wdeprecated-writable-strings]
>>        PyObject *item_list = PyMapping_Items( obj1 );
>>                              ^
>> /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/abstract.h:1354:50: note:
>>      expanded from macro 'PyMapping_Items'
>> #define PyMapping_Items(O) PyObject_CallMethod(O,"items",NULL)
>>                                                 ^
>> 1 warning generated.
>> creating build/lib.macosx-10.6-intel-2.7
>> creating build/lib.macosx-10.6-intel-2.7/osgeo
>> c++ -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/extensions/gdal_wrap.o -L/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ -L/Library/Frameworks/GDAL.framework/Versions/1.10/lib -lgdal -o build/lib.macosx-10.6-intel-2.7/osgeo/_gdal.so
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> building 'osgeo._gdalconst' extension
>> clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/GDAL.framework/Versions/1.10/Headers/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/GDAL.framework/Versions/1.10/include -c extensions/gdalconst_wrap.c -o build/temp.macosx-10.6-intel-2.7/extensions/gdalconst_wrap.o
>> clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/extensions/gdalconst_wrap.o -L/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ -L/Library/Frameworks/GDAL.framework/Versions/1.10/lib -lgdal -o build/lib.macosx-10.6-intel-2.7/osgeo/_gdalconst.so
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> building 'osgeo._osr' extension
>> clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/GDAL.framework/Versions/1.10/Headers/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/GDAL.framework/Versions/1.10/include -c extensions/osr_wrap.cpp -o build/temp.macosx-10.6-intel-2.7/extensions/osr_wrap.o
>> c++ -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/extensions/osr_wrap.o -L/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ -L/Library/Frameworks/GDAL.framework/Versions/1.10/lib -lgdal -o build/lib.macosx-10.6-intel-2.7/osgeo/_osr.so
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> building 'osgeo._ogr' extension
>> clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/GDAL.framework/Versions/1.10/Headers/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/GDAL.framework/Versions/1.10/include -c extensions/ogr_wrap.cpp -o build/temp.macosx-10.6-intel-2.7/extensions/ogr_wrap.o
>> c++ -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/extensions/ogr_wrap.o -L/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ -L/Library/Frameworks/GDAL.framework/Versions/1.10/lib -lgdal -o build/lib.macosx-10.6-intel-2.7/osgeo/_ogr.so
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> building 'osgeo._gdal_array' extension
>> clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2 -DNDEBUG -g -O3 -I/Library/Frameworks/GDAL.framework/Versions/1.10/Headers/ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include -I/Library/Frameworks/GDAL.framework/Versions/1.10/include -c extensions/gdal_array_wrap.cpp -o build/temp.macosx-10.6-intel-2.7/extensions/gdal_array_wrap.o
>> In file included from extensions/gdal_array_wrap.cpp:2899:
>> In file included from /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
>> In file included from /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
>> In file included from /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:
>> /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning:
>>      "Using deprecated NumPy API, disable it by "          "#defining
>>      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
>> #warning "Using deprecated NumPy API, disable it by " \
>> ^
>> 1 warning generated.
>> In file included from extensions/gdal_array_wrap.cpp:2899:
>> In file included from /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
>> In file included from /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
>> In file included from /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:
>> /Users/dheerajchand/Python_Environments/geo/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning:
>>      "Using deprecated NumPy API, disable it by "          "#defining
>>      NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
>> #warning "Using deprecated NumPy API, disable it by " \
>> ^
>> 1 warning generated.
>> c++ -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/extensions/gdal_array_wrap.o -L/Library/Frameworks/GDAL.framework/Versions/1.10/unix/lib/ -L/Library/Frameworks/GDAL.framework/Versions/1.10/lib -lgdal -o build/lib.macosx-10.6-intel-2.7/osgeo/_gdal_array.so
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> ld: warning: directory not found for option '-L/Library/Frameworks/GDAL.framework/Versions/1.10/lib'
>> (geo)REINHEIT:GDAL dheerajchand$ pip install --no-download GDAL
>> Installing collected packages: GDAL
>>  Running setup.py install for GDAL
>>    gcc-4.2 not found, using clang instead
>> 
>> Successfully installed GDAL
>> Cleaning up...
>> (geo)REINHEIT:GDAL dheerajchand$ python
>> Python 2.7.3 (v2.7.3:70274d53c1dd, Apr  9 2012, 20:52:43)
>> [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> from osgeo import gdal
>>>>> gdal.__version__
>> Segmentation fault: 11
>> (geo)REINHEIT:GDAL dheerajchand$
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> 
> -----
> William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
> http://www.kyngchaos.com/
> 
> "History is an illusion caused by the passage of time, and time is an illusion caused by the passage of history."
> 
> - Hitchhiker's Guide to the Galaxy
> 
> 
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-----
William Kyngesburye <kyngchaos*at*kyngchaos*dot*com>
http://www.kyngchaos.com/

"Time is an illusion - lunchtime doubly so."

- Ford Prefect

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