From: per f. <per...@gm...> - 2010-07-21 15:54:23
|
Hello everyone, I am having trouble compiling Pygsl on Mac OS X, using GCC 4.2. I ran the following: sudo python setup.py install And got this error: In file included from testing/src/sf/sfmodule_testing.c:49: testing/src/sf/sf__data.c:779: error: ‘gsl_sf_exprel_n_CF_e’ undeclared here (not in a function) testing/src/sf/sf__data.c:806: error: ‘gsl_sf_expint_En_e’ undeclared here (not in a function) testing/src/sf/sf__data.c:806: error: initializer element is not constant testing/src/sf/sf__data.c:806: error: (near initialization for ‘sf_expint_En_e_data[0]’) testing/src/sf/sf__data.c:806: error: initializer element is not constant testing/src/sf/sf__data.c:806: error: (near initialization for ‘sf_expint_En_e_data[1]’) testing/src/sf/sf__data.c:809: error: ‘gsl_sf_expint_En’ undeclared here (not in a function) testing/src/sf/sf__data.c:809: error: initializer element is not constant testing/src/sf/sf__data.c:809: error: (near initialization for ‘sf_expint_En_data[0]’) testing/src/sf/sf__data.c:809: error: initializer element is not constant testing/src/sf/sf__data.c:809: error: (near initialization for ‘sf_expint_En_data[1]’) testing/src/sf/sf__data.c:824: error: ‘gsl_sf_expint_En_scaled_e’ undeclared here (not in a function) testing/src/sf/sf__data.c:824: error: initializer element is not constant testing/src/sf/sf__data.c:824: error: (near initialization for ‘sf_expint_En_scaled_e_data[0]’) testing/src/sf/sf__data.c:824: error: initializer element is not constant testing/src/sf/sf__data.c:824: error: (near initialization for ‘sf_expint_En_scaled_e_data[1]’) testing/src/sf/sf__data.c:827: error: ‘gsl_sf_expint_En_scaled’ undeclared here (not in a function) testing/src/sf/sf__data.c:827: error: initializer element is not constant testing/src/sf/sf__data.c:827: error: (near initialization for ‘sf_expint_En_scaled_data[0]’) testing/src/sf/sf__data.c:827: error: initializer element is not constant testing/src/sf/sf__data.c:827: error: (near initialization for ‘sf_expint_En_scaled_data[1]’) testing/src/sf/sfmodule_testing.c:102: warning: initialization from incompatible pointer type testing/src/sf/sfmodule_testing.c:102: warning: initialization from incompatible pointer type testing/src/sf/sfmodule_testing.c:145: warning: initialization from incompatible pointer type testing/src/sf/sfmodule_testing.c:145: warning: initialization from incompatible pointer type error: Command "gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.2/include -DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=9 -UNDEBUG -I/usr/local/include -IInclude -I. -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 -c testing/src/sf/sfmodule_testing.c -o build/temp.macosx-10.5-i386-2.6/testing/src/sf/sfmodule_testing.o" failed with exit status 1 The GSL library compiled fine, it's only PyGSL that will not compile. Any idea what could be causing this? Thanks for your help. My version for GCC is: $ gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659) Copyright (C) 2007 Free Software Foundation, Inc. |
From: Pierre S. <p.s...@gs...> - 2010-07-21 15:59:16
|
I think the functions gsl_sf_exprel_n_CF_e gsl_sf_exprel_n_En_e are not defined or not included in the include files.... Can you grep through your headers and see if these functions are there? You are using a rather old version of GSL, is that intentionally? If you can not find the functions, I think you have to run the python code which generates the wrappers by hand: http://pygsl.sourceforge.net/reference/pygsl/node13.html Sincerely yours Pierre > Hello everyone, > > > I am having trouble compiling Pygsl on Mac OS X, using GCC 4.2. I ran > the following: > > sudo python setup.py install > > And got this error: > > In file included from testing/src/sf/sfmodule_testing.c:49: > testing/src/sf/sf__data.c:779: error: ‘gsl_sf_exprel_n_CF_e’ > undeclared here (not in a function) > testing/src/sf/sf__data.c:806: error: ‘gsl_sf_expint_En_e’ > undeclared here (not in a function) > testing/src/sf/sf__data.c:806: error: initializer element is not constant > testing/src/sf/sf__data.c:806: error: (near initialization for > ‘sf_expint_En_e_data[0]’) > testing/src/sf/sf__data.c:806: error: initializer element is not constant > testing/src/sf/sf__data.c:806: error: (near initialization for > ‘sf_expint_En_e_data[1]’) > testing/src/sf/sf__data.c:809: error: ‘gsl_sf_expint_En’ > undeclared here (not in a function) > testing/src/sf/sf__data.c:809: error: initializer element is not constant > testing/src/sf/sf__data.c:809: error: (near initialization for > ‘sf_expint_En_data[0]’) > testing/src/sf/sf__data.c:809: error: initializer element is not constant > testing/src/sf/sf__data.c:809: error: (near initialization for > ‘sf_expint_En_data[1]’) > testing/src/sf/sf__data.c:824: error: ‘gsl_sf_expint_En_scaled_e’ > undeclared here (not in a function) > testing/src/sf/sf__data.c:824: error: initializer element is not constant > testing/src/sf/sf__data.c:824: error: (near initialization for > ‘sf_expint_En_scaled_e_data[0]’) > testing/src/sf/sf__data.c:824: error: initializer element is not constant > testing/src/sf/sf__data.c:824: error: (near initialization for > ‘sf_expint_En_scaled_e_data[1]’) > testing/src/sf/sf__data.c:827: error: ‘gsl_sf_expint_En_scaled’ > undeclared here (not in a function) > testing/src/sf/sf__data.c:827: error: initializer element is not constant > testing/src/sf/sf__data.c:827: error: (near initialization for > ‘sf_expint_En_scaled_data[0]’) > testing/src/sf/sf__data.c:827: error: initializer element is not constant > testing/src/sf/sf__data.c:827: error: (near initialization for > ‘sf_expint_En_scaled_data[1]’) > testing/src/sf/sfmodule_testing.c:102: warning: initialization > from incompatible pointer type > testing/src/sf/sfmodule_testing.c:102: warning: initialization > from incompatible pointer type > testing/src/sf/sfmodule_testing.c:145: warning: initialization > from incompatible pointer type > testing/src/sf/sfmodule_testing.c:145: warning: initialization > from incompatible pointer type > error: Command "gcc -fno-strict-aliasing -fno-common -dynamic > -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk > -I/Library/Frameworks/Python.framework/Versions/6.2/include > -DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DNUMERIC=0 > -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=9 -UNDEBUG > -I/usr/local/include -IInclude -I. > -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include > -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 > -c testing/src/sf/sfmodule_testing.c -o > build/temp.macosx-10.5-i386-2.6/testing/src/sf/sfmodule_testing.o" > failed with exit status 1 > > The GSL library compiled fine, it's only PyGSL that will not compile. > Any idea what could be causing this? Thanks for your help. > > > My version for GCC is: > > $ gcc --version > i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659) > Copyright (C) 2007 Free Software Foundation, Inc. > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > pygsl-discuss mailing list > pyg...@li... > https://lists.sourceforge.net/lists/listinfo/pygsl-discuss > -- +---------------------------------------------------------------------+ Pierre Schnizer <p.s...@gs...> Telephon : +49 6159 71 1557 Fax : +49 6159 71 2985 GSI Helmholtzzentrum für Schwerionenforschung GmbH Planckstraße 1 D-64291 Darmstadt www.gsi.de Gesellschaft mit beschränkter Haftung Sitz der Gesellschaft: Darmstadt Handelsregister: Amtsgericht Darmstadt, HRB 1528 Geschäftsführung: Professor Dr. Dr. h.c. Horst Stöcker, Christiane Neumann, Dr. Hartmut Vorsitzende des Aufsichtsrates: Dr. Beatrix Vierkorn-Rudolph Stellvertreter: Ministerialdirigent Dr. Rolf Bernhardt +---------------------------------------------------------------------+ |
From: per f. <per...@gm...> - 2010-07-21 16:37:26
|
thanks for your reply, Pierre. I upgraded the GSL version and tried again. This time I got a different error when doing "python setup.py build" (after erasing the old "build/" directory): compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DONEFILE=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=14 -UNDEBUG -I/usr/local/include -IInclude -I. -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 -c' gcc: testing/src/solvers/solvermodule.c testing/src/solvers/solvermodule.c: In function ‘_PyGSL_solver_init’: testing/src/solvers/solvermodule.c:258: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘Py_ssize_t’ gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.2/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/testing/src/solvers/solvermodule.o -L/usr/local/lib -lgsl -lgslcblas -lm -o build/lib.macosx-10.5-i386-2.6/pygsl/testing/solver.so ld: warning: in /usr/local/lib/libgsl.dylib, file was built for unsupported file format which is not the architecture being linked (i386) ld: warning: in /usr/local/lib/libgslcblas.dylib, file was built for unsupported file format which is not the architecture being linked (i386) building 'testing._ufuncs' extension C compiler: gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk -I/Library/Frameworks/Python.framework/Versions/6.2/include creating build/temp.macosx-10.5-i386-2.6/testing/src/sf compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=14 -UNDEBUG -I/usr/local/include -IInclude -I. -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 -c' gcc: testing/src/sf/sfmodule_testing.c testing/src/sf/sfmodule_testing.c:102: warning: initialization from incompatible pointer type testing/src/sf/sfmodule_testing.c:102: warning: initialization from incompatible pointer type testing/src/sf/sfmodule_testing.c:145: warning: initialization from incompatible pointer type testing/src/sf/sfmodule_testing.c:145: warning: initialization from incompatible pointer type gcc -g -L/usr/local/lib -L/Library/Frameworks/Python.framework/Versions/6.2/lib -bundle -undefined dynamic_lookup -arch i386 build/temp.macosx-10.5-i386-2.6/testing/src/sf/sfmodule_testing.o -L/usr/local/lib -lgsl -lgslcblas -lm -o build/lib.macosx-10.5-i386-2.6/pygsl/testing/_ufuncs.so ld: warning: in /usr/local/lib/libgsl.dylib, file was built for unsupported file format which is not the architecture being linked (i386) ld: warning: in /usr/local/lib/libgslcblas.dylib, file was built for unsupported file format which is not the architecture being linked (i386) I tried to do: python setup.py install nonetheless, and then when I imported pygsl, I got the following error: ==== >>> import pygsl Did you try to import pygsl in the build directory? Well, that does not work out of the box. If you want to do that, please use python setup.py build_ext -i to add the necessary extension module in the local pygsl/ directory! Please read the README first! Any further questions or missing information please post to pyg...@li...! Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/__init__.py", line 57, in <module> import pygsl.init ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so, 2): Symbol not found: _gsl_version Referenced from: /Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so Expected in: flat namespace in /Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so ==== I was not importing it from its own directory. Any idea what is wrong here? thanks. On Wed, Jul 21, 2010 at 11:58 AM, Pierre SCHNIZER <p.s...@gs...> wrote: > > I think the functions > > gsl_sf_exprel_n_CF_e > > gsl_sf_exprel_n_En_e > > are not defined or not included in the include files.... > Can you grep through your headers and see if these functions are there? > > > You are using a rather old version of GSL, is that intentionally? > > If you can not find the functions, I think you have to run the python code > which generates the wrappers by hand: > http://pygsl.sourceforge.net/reference/pygsl/node13.html > > Sincerely yours > Pierre >> >> Hello everyone, >> >> >> I am having trouble compiling Pygsl on Mac OS X, using GCC 4.2. I ran >> the following: >> >> sudo python setup.py install >> >> And got this error: >> >> In file included from testing/src/sf/sfmodule_testing.c:49: >> testing/src/sf/sf__data.c:779: error: ‘gsl_sf_exprel_n_CF_e’ >> undeclared here (not in a function) >> testing/src/sf/sf__data.c:806: error: ‘gsl_sf_expint_En_e’ >> undeclared here (not in a function) >> testing/src/sf/sf__data.c:806: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:806: error: (near initialization for >> ‘sf_expint_En_e_data[0]’) >> testing/src/sf/sf__data.c:806: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:806: error: (near initialization for >> ‘sf_expint_En_e_data[1]’) >> testing/src/sf/sf__data.c:809: error: ‘gsl_sf_expint_En’ >> undeclared here (not in a function) >> testing/src/sf/sf__data.c:809: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:809: error: (near initialization for >> ‘sf_expint_En_data[0]’) >> testing/src/sf/sf__data.c:809: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:809: error: (near initialization for >> ‘sf_expint_En_data[1]’) >> testing/src/sf/sf__data.c:824: error: ‘gsl_sf_expint_En_scaled_e’ >> undeclared here (not in a function) >> testing/src/sf/sf__data.c:824: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:824: error: (near initialization for >> ‘sf_expint_En_scaled_e_data[0]’) >> testing/src/sf/sf__data.c:824: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:824: error: (near initialization for >> ‘sf_expint_En_scaled_e_data[1]’) >> testing/src/sf/sf__data.c:827: error: ‘gsl_sf_expint_En_scaled’ >> undeclared here (not in a function) >> testing/src/sf/sf__data.c:827: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:827: error: (near initialization for >> ‘sf_expint_En_scaled_data[0]’) >> testing/src/sf/sf__data.c:827: error: initializer element is not >> constant >> testing/src/sf/sf__data.c:827: error: (near initialization for >> ‘sf_expint_En_scaled_data[1]’) >> testing/src/sf/sfmodule_testing.c:102: warning: initialization >> from incompatible pointer type >> testing/src/sf/sfmodule_testing.c:102: warning: initialization >> from incompatible pointer type >> testing/src/sf/sfmodule_testing.c:145: warning: initialization >> from incompatible pointer type >> testing/src/sf/sfmodule_testing.c:145: warning: initialization >> from incompatible pointer type >> error: Command "gcc -fno-strict-aliasing -fno-common -dynamic >> -DNDEBUG -g -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk >> -I/Library/Frameworks/Python.framework/Versions/6.2/include >> -DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 -DNUMERIC=0 >> -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=9 -UNDEBUG >> -I/usr/local/include -IInclude -I. >> >> -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include >> -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 >> -c testing/src/sf/sfmodule_testing.c -o >> build/temp.macosx-10.5-i386-2.6/testing/src/sf/sfmodule_testing.o" >> failed with exit status 1 >> >> The GSL library compiled fine, it's only PyGSL that will not compile. >> Any idea what could be causing this? Thanks for your help. >> >> >> My version for GCC is: >> >> $ gcc --version >> i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5659) >> Copyright (C) 2007 Free Software Foundation, Inc. >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> pygsl-discuss mailing list >> pyg...@li... >> https://lists.sourceforge.net/lists/listinfo/pygsl-discuss >> > > > -- > +---------------------------------------------------------------------+ > Pierre Schnizer <p.s...@gs...> > Telephon : +49 6159 71 1557 > Fax : +49 6159 71 2985 > > GSI Helmholtzzentrum für Schwerionenforschung GmbH > Planckstraße 1 > D-64291 Darmstadt > www.gsi.de > > Gesellschaft mit beschränkter Haftung > Sitz der Gesellschaft: Darmstadt > Handelsregister: Amtsgericht Darmstadt, HRB 1528 > > Geschäftsführung: Professor Dr. Dr. h.c. Horst Stöcker, Christiane Neumann, > Dr. Hartmut Vorsitzende des Aufsichtsrates: Dr. Beatrix Vierkorn-Rudolph > Stellvertreter: Ministerialdirigent Dr. Rolf Bernhardt > +---------------------------------------------------------------------+ > > |
From: per f. <per...@gm...> - 2010-07-21 17:23:10
|
Hi Pierre, How can I check what architecture the file: /usr/local/lib/libgsl.dylib was for? Perhaps I need to install GSL differently than I have? Could this be a 32bit vs 64bit issue? Yes, my mac has an intel processor. On Wed, Jul 21, 2010 at 1:00 PM, Pierre SCHNIZER <p.s...@gs...> wrote: > >> thanks for your reply, Pierre. >> >> I upgraded the GSL version and tried again. This time I got a >> different error when doing "python setup.py build" (after erasing the >> old "build/" directory): >> >> > > Can you delete the whole build directory and run the compile again? > Is your MAC one with an intel processor? There is something going strange > here ... >> >> compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 >> -DONEFILE=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 >> -DPYGSL_GSL_MINOR_VERSION=14 -UNDEBUG -I/usr/local/include -IInclude >> -I. >> -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include >> -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 >> -c' >> gcc: testing/src/solvers/solvermodule.c >> testing/src/solvers/solvermodule.c: In function ‘_PyGSL_solver_init’: >> testing/src/solvers/solvermodule.c:258: warning: format ‘%d’ expects >> type ‘int’, but argument 6 has type ‘Py_ssize_t’ >> gcc -g -L/usr/local/lib >> -L/Library/Frameworks/Python.framework/Versions/6.2/lib -bundle >> -undefined dynamic_lookup -arch i386 >> build/temp.macosx-10.5-i386-2.6/testing/src/solvers/solvermodule.o >> -L/usr/local/lib -lgsl -lgslcblas -lm -o >> build/lib.macosx-10.5-i386-2.6/pygsl/testing/solver.so >> ld: warning: in /usr/local/lib/libgsl.dylib, file was built for >> unsupported file format which is not the architecture being linked >> (i386) >> ld: warning: in /usr/local/lib/libgslcblas.dylib, file was built for >> unsupported file format which is not the architecture being linked >> (i386) >> building 'testing._ufuncs' extension >> C compiler: gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g >> -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk >> -I/Library/Frameworks/Python.framework/Versions/6.2/include >> >> creating build/temp.macosx-10.5-i386-2.6/testing/src/sf >> compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 >> -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=14 >> -UNDEBUG -I/usr/local/include -IInclude -I. >> >> -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include >> -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 >> -c' >> gcc: testing/src/sf/sfmodule_testing.c >> testing/src/sf/sfmodule_testing.c:102: warning: initialization from >> incompatible pointer type >> testing/src/sf/sfmodule_testing.c:102: warning: initialization from >> incompatible pointer type >> testing/src/sf/sfmodule_testing.c:145: warning: initialization from >> incompatible pointer type >> testing/src/sf/sfmodule_testing.c:145: warning: initialization from >> incompatible pointer type >> gcc -g -L/usr/local/lib >> -L/Library/Frameworks/Python.framework/Versions/6.2/lib -bundle >> -undefined dynamic_lookup -arch i386 >> build/temp.macosx-10.5-i386-2.6/testing/src/sf/sfmodule_testing.o >> -L/usr/local/lib -lgsl -lgslcblas -lm -o >> build/lib.macosx-10.5-i386-2.6/pygsl/testing/_ufuncs.so >> ld: warning: in /usr/local/lib/libgsl.dylib, file was built for >> unsupported file format which is not the architecture being linked >> (i386) >> ld: warning: in /usr/local/lib/libgslcblas.dylib, file was built for >> unsupported file format which is not the architecture being linked >> (i386) >> >> > > The error below is a result that the init was not built properly. >> >> I tried to do: python setup.py install nonetheless, and then when I >> imported pygsl, I got the following error: >> >> ==== >> >>>>> >>>>> import pygsl >>>>> >> >> Did you try to import pygsl in the build directory? >> >> Well, that does not work out of the box. If you want to do that, please >> use >> python setup.py build_ext -i >> to add the necessary extension module in the local pygsl/ directory! >> >> Please read the README first! Any further questions or missing information >> please post to pyg...@li...! >> >> Traceback (most recent call last): >> File "<stdin>", line 1, in <module> >> File >> "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/__init__.py", >> line 57, in <module> >> import pygsl.init >> ImportError: >> dlopen(/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so, >> 2): Symbol not found: _gsl_version >> Referenced from: >> >> /Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so >> Expected in: flat namespace >> in >> /Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so >> ==== >> >> I > > Your whole build has a problem. Delete the build directory and try over > again. > Sometimes one is simply lucky ... > > Pierre > > -- > +---------------------------------------------------------------------+ > Pierre Schnizer <p.s...@gs...> > Telephon : +49 6159 71 1557 > Fax : +49 6159 71 2985 > > GSI Helmholtzzentrum für Schwerionenforschung GmbH > Planckstraße 1 > D-64291 Darmstadt > www.gsi.de > > Gesellschaft mit beschränkter Haftung > Sitz der Gesellschaft: Darmstadt > Handelsregister: Amtsgericht Darmstadt, HRB 1528 > > Geschäftsführung: Professor Dr. Dr. h.c. Horst Stöcker, Christiane Neumann, > Dr. Hartmut Vorsitzende des Aufsichtsrates: Dr. Beatrix Vierkorn-Rudolph > Stellvertreter: Ministerialdirigent Dr. Rolf Bernhardt > +---------------------------------------------------------------------+ > > |
From: per f. <per...@gm...> - 2010-07-21 17:25:17
|
another note on this: i deleted the entire pygsl-0.9.5 directory and untarred it fresh from the .tar.gz. then i tried python setup.py build and i got this: $ python setup.py build No array object was selected. Looking for a suitable array module SELECTED a NEW array module -> numpy Please make sure that all modules are built with the same setting. e.g. remove the build directory and start the build process again! numpy Building testing ufuncs! running build running build_py creating build creating build/lib.macosx-10.5-i386-2.6 creating build/lib.macosx-10.5-i386-2.6/pygsl .... that first error is strange. could it be that there are remnants of pygsl on this system? thanks. On Wed, Jul 21, 2010 at 1:22 PM, per freem <per...@gm...> wrote: > Hi Pierre, > > How can I check what architecture the file: > /usr/local/lib/libgsl.dylib was for? Perhaps I need to install GSL > differently than I have? Could this be a 32bit vs 64bit issue? > > Yes, my mac has an intel processor. > > On Wed, Jul 21, 2010 at 1:00 PM, Pierre SCHNIZER <p.s...@gs...> wrote: >> >>> thanks for your reply, Pierre. >>> >>> I upgraded the GSL version and tried again. This time I got a >>> different error when doing "python setup.py build" (after erasing the >>> old "build/" directory): >>> >>> >> >> Can you delete the whole build directory and run the compile again? >> Is your MAC one with an intel processor? There is something going strange >> here ... >>> >>> compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 >>> -DONEFILE=1 -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 >>> -DPYGSL_GSL_MINOR_VERSION=14 -UNDEBUG -I/usr/local/include -IInclude >>> -I. >>> -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include >>> -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 >>> -c' >>> gcc: testing/src/solvers/solvermodule.c >>> testing/src/solvers/solvermodule.c: In function ‘_PyGSL_solver_init’: >>> testing/src/solvers/solvermodule.c:258: warning: format ‘%d’ expects >>> type ‘int’, but argument 6 has type ‘Py_ssize_t’ >>> gcc -g -L/usr/local/lib >>> -L/Library/Frameworks/Python.framework/Versions/6.2/lib -bundle >>> -undefined dynamic_lookup -arch i386 >>> build/temp.macosx-10.5-i386-2.6/testing/src/solvers/solvermodule.o >>> -L/usr/local/lib -lgsl -lgslcblas -lm -o >>> build/lib.macosx-10.5-i386-2.6/pygsl/testing/solver.so >>> ld: warning: in /usr/local/lib/libgsl.dylib, file was built for >>> unsupported file format which is not the architecture being linked >>> (i386) >>> ld: warning: in /usr/local/lib/libgslcblas.dylib, file was built for >>> unsupported file format which is not the architecture being linked >>> (i386) >>> building 'testing._ufuncs' extension >>> C compiler: gcc -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g >>> -O3 -arch i386 -isysroot /Developer/SDKs/MacOSX10.5.sdk >>> -I/Library/Frameworks/Python.framework/Versions/6.2/include >>> >>> creating build/temp.macosx-10.5-i386-2.6/testing/src/sf >>> compile options: '-DSWIG_COBJECT_TYPES=1 -DGSL_RANGE_CHECK=1 -DDEBUG=1 >>> -DNUMERIC=0 -DPYGSL_GSL_MAJOR_VERSION=1 -DPYGSL_GSL_MINOR_VERSION=14 >>> -UNDEBUG -I/usr/local/include -IInclude -I. >>> >>> -I/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/numpy/core/include >>> -I/Library/Frameworks/Python.framework/Versions/6.2/include/python2.6 >>> -c' >>> gcc: testing/src/sf/sfmodule_testing.c >>> testing/src/sf/sfmodule_testing.c:102: warning: initialization from >>> incompatible pointer type >>> testing/src/sf/sfmodule_testing.c:102: warning: initialization from >>> incompatible pointer type >>> testing/src/sf/sfmodule_testing.c:145: warning: initialization from >>> incompatible pointer type >>> testing/src/sf/sfmodule_testing.c:145: warning: initialization from >>> incompatible pointer type >>> gcc -g -L/usr/local/lib >>> -L/Library/Frameworks/Python.framework/Versions/6.2/lib -bundle >>> -undefined dynamic_lookup -arch i386 >>> build/temp.macosx-10.5-i386-2.6/testing/src/sf/sfmodule_testing.o >>> -L/usr/local/lib -lgsl -lgslcblas -lm -o >>> build/lib.macosx-10.5-i386-2.6/pygsl/testing/_ufuncs.so >>> ld: warning: in /usr/local/lib/libgsl.dylib, file was built for >>> unsupported file format which is not the architecture being linked >>> (i386) >>> ld: warning: in /usr/local/lib/libgslcblas.dylib, file was built for >>> unsupported file format which is not the architecture being linked >>> (i386) >>> >>> >> >> The error below is a result that the init was not built properly. >>> >>> I tried to do: python setup.py install nonetheless, and then when I >>> imported pygsl, I got the following error: >>> >>> ==== >>> >>>>>> >>>>>> import pygsl >>>>>> >>> >>> Did you try to import pygsl in the build directory? >>> >>> Well, that does not work out of the box. If you want to do that, please >>> use >>> python setup.py build_ext -i >>> to add the necessary extension module in the local pygsl/ directory! >>> >>> Please read the README first! Any further questions or missing information >>> please post to pyg...@li...! >>> >>> Traceback (most recent call last): >>> File "<stdin>", line 1, in <module> >>> File >>> "/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/__init__.py", >>> line 57, in <module> >>> import pygsl.init >>> ImportError: >>> dlopen(/Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so, >>> 2): Symbol not found: _gsl_version >>> Referenced from: >>> >>> /Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so >>> Expected in: flat namespace >>> in >>> /Library/Frameworks/Python.framework/Versions/6.2/lib/python2.6/site-packages/pygsl/init.so >>> ==== >>> >>> I >> >> Your whole build has a problem. Delete the build directory and try over >> again. >> Sometimes one is simply lucky ... >> >> Pierre >> >> -- >> +---------------------------------------------------------------------+ >> Pierre Schnizer <p.s...@gs...> >> Telephon : +49 6159 71 1557 >> Fax : +49 6159 71 2985 >> >> GSI Helmholtzzentrum für Schwerionenforschung GmbH >> Planckstraße 1 >> D-64291 Darmstadt >> www.gsi.de >> >> Gesellschaft mit beschränkter Haftung >> Sitz der Gesellschaft: Darmstadt >> Handelsregister: Amtsgericht Darmstadt, HRB 1528 >> >> Geschäftsführung: Professor Dr. Dr. h.c. Horst Stöcker, Christiane Neumann, >> Dr. Hartmut Vorsitzende des Aufsichtsrates: Dr. Beatrix Vierkorn-Rudolph >> Stellvertreter: Ministerialdirigent Dr. Rolf Bernhardt >> +---------------------------------------------------------------------+ >> >> > |
From: Pierre S. <p.s...@gs...> - 2010-07-22 07:23:11
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per freem wrote: > another note on this: i deleted the entire pygsl-0.9.5 directory and > untarred it fresh from the .tar.gz. then i tried python setup.py build > and i got this: > > $ python setup.py build > No array object was selected. > Looking for a suitable array module > SELECTED a NEW array module -> numpy > Please make sure that all modules are built with the same setting. > e.g. remove the build directory and start the build process again! > numpy > Building testing ufuncs! > running build > running build_py > creating build > creating build/lib.macosx-10.5-i386-2.6 > creating build/lib.macosx-10.5-i386-2.6/pygsl > .... > > > that first error is strange. could it be that there are remnants of > pygsl on this system? > > thanks. > > > No thats normal for the first build. It tries to see which array module to use. (I think I should remove it as I have not been testing it for Numeric or numarray for at least 1 year). So it selected numpy thats fine. How does the build proceed then? Yes and it could be a 32 bit vs 64 bit issue. On the other hand I would expect python to set the flags correctly. Can you try to build an other python extension using "C" as an extension language? Best wishes Pierre -- +---------------------------------------------------------------------+ Pierre Schnizer <p.s...@gs...> Telephon : +49 6159 71 1557 Fax : +49 6159 71 2985 GSI Helmholtzzentrum für Schwerionenforschung GmbH Planckstraße 1 D-64291 Darmstadt www.gsi.de Gesellschaft mit beschränkter Haftung Sitz der Gesellschaft: Darmstadt Handelsregister: Amtsgericht Darmstadt, HRB 1528 Geschäftsführung: Professor Dr. Dr. h.c. Horst Stöcker, Christiane Neumann, Dr. Hartmut Vorsitzende des Aufsichtsrates: Dr. Beatrix Vierkorn-Rudolph Stellvertreter: Ministerialdirigent Dr. Rolf Bernhardt +---------------------------------------------------------------------+ |