Hi, I'm not sure how that space got in there but it shouldn't be there. I'm now going from the file 'docs/Mac_framework_build_3way' that comes with relax:
"Install the appropriate GNU fortran version to add to Xcode (for example gfortran-42-5664.pkg from http://r.research.att.com/tools/). Xcode does not come with a Fortran compiler and the fink version will not be able to create Universal 3-way binaries." I find it a bit crazy that Xcode does not bundle gfortran when it has all the other gcc compilation tools. The link should provide the best Fortan compiler for a Mac. I hope this one finally solves the Scipy problems! Regards, Edward On 11 August 2013 17:08, Paul Schanda <[email protected]> wrote: > By the way, I guess in the command you suggested there should not be a space > in between include/ and suitesparse. > That's at least how I understood it. > > paul > > > On 11.08.13 15:35, Edward d'Auvergne wrote: >> >> That is a stranger error. It looks like it cannot find swig on the >> $PATH environmental variable! Weird. For that problem, try adding >> the directory with swig to the PATH variable with: >> >> bash gre:scipy-0.12.0 $ PATH=/opt/local/bin/:/usr/local/bin/:$PATH >> C_INCLUDE_PATH=/sw/include/ suitesparse/ ~/bin/python2.7 setup.py >> install >> >> Let's see if that helps the scipy setup along a little ;) >> >> Regards, >> >> Edward >> >> >> >> On 11 August 2013 07:20, Paul Schanda <[email protected]> wrote: >>> >>> Well, there is possibly some progress. I have to admit that I have no >>> clue >>> what fat3 commands and swig exactly do, though. >>> >>> The following seemed to work (or at least not produce any error message): >>> >>> bash-3.2$ pwd >>> /Users/paul/Downloads/scipy-0.12.0 >>> bash-3.2$ /opt/local/bin/swig -I/sw/include/suitesparse/ >>> -I/opt/local/include -python -o >>> >>> build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir >>> build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> bash-3.2$ >>> >>> However, this does not really solve the swig problem when installing >>> scipy. >>> I guess there is still some problem with the path. >>> (Note that I slightly modified your command, that you suggested: >>> >>> [gre:~/Downloads/scipy-0.12.0] % bash >>> gre:scipy-0.12.0 $ PATH=/usr/local/bin/:$PATH >>> C_INCLUDE_PATH=/sw/include/ >>> suitesparse/ ~/bin/python2.7 setup.py >>> install >>> >>> as my pythone2.7 is somewhere else) >>> >>> Here is what I get. >>> >>> >>> bash-3.2$ PATH=/usr/local/bin/:$PATH >>> C_INCLUDE_PATH=/sw/include/suitesparse >>> /usr/bin/python2.7 setup.py install >>> >>> Running from scipy source directory. >>> >>> blas_opt_info: >>> >>> FOUND: >>> >>> extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] >>> >>> define_macros = [('NO_ATLAS_INFO', 3)] >>> >>> extra_compile_args = ['-msse3', >>> '-I/System/Library/Frameworks/vecLib.framework/Headers'] >>> >>> lapack_opt_info: >>> >>> FOUND: >>> >>> extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] >>> >>> define_macros = [('NO_ATLAS_INFO', 3)] >>> >>> extra_compile_args = ['-msse3'] >>> >>> umfpack_info: >>> >>> libraries umfpack not found in >>> /System/Library/Frameworks/Python.framework/Versions/2.7/lib >>> >>> libraries umfpack not found in /usr/local/lib >>> >>> libraries umfpack not found in /usr/lib >>> >>> amd_info: >>> >>> libraries amd not found in >>> /System/Library/Frameworks/Python.framework/Versions/2.7/lib >>> >>> libraries amd not found in /usr/local/lib >>> >>> libraries amd not found in /usr/lib >>> >>> FOUND: >>> >>> libraries = ['amd'] >>> >>> library_dirs = ['/opt/local/lib'] >>> >>> swig_opts = ['-I/opt/local/include'] >>> >>> define_macros = [('SCIPY_AMD_H', None)] >>> >>> include_dirs = ['/opt/local/include'] >>> >>> FOUND: >>> >>> libraries = ['umfpack', 'amd'] >>> >>> library_dirs = ['/opt/local/lib'] >>> >>> swig_opts = ['-I/opt/local/include', '-I/opt/local/include'] >>> >>> define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)] >>> >>> include_dirs = ['/opt/local/include'] >>> >>> running install >>> >>> running build >>> >>> running config_cc >>> >>> unifing config_cc, config, build_clib, build_ext, build commands >>> --compiler >>> options >>> >>> running config_fc >>> >>> unifing config_fc, config, build_clib, build_ext, build commands >>> --fcompiler >>> options >>> >>> running build_src >>> >>> build_src >>> >>> building py_modules sources >>> >>> building library "dfftpack" sources >>> >>> building library "fftpack" sources >>> >>> building library "linpack_lite" sources >>> >>> building library "mach" sources >>> >>> building library "quadpack" sources >>> >>> building library "odepack" sources >>> >>> building library "dop" sources >>> >>> building library "fitpack" sources >>> >>> building library "odrpack" sources >>> >>> building library "minpack" sources >>> >>> building library "rootfind" sources >>> >>> building library "superlu_src" sources >>> >>> building library "arpack_scipy" sources >>> >>> building library "sc_c_misc" sources >>> >>> building library "sc_cephes" sources >>> >>> building library "sc_mach" sources >>> >>> building library "sc_amos" sources >>> >>> building library "sc_cdf" sources >>> >>> building library "sc_specfun" sources >>> >>> building library "statlib" sources >>> >>> building extension "scipy.cluster._vq" sources >>> >>> building extension "scipy.cluster._hierarchy_wrap" sources >>> >>> building extension "scipy.fftpack._fftpack" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.fftpack.convolve" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.integrate._quadpack" sources >>> >>> building extension "scipy.integrate._odepack" sources >>> >>> building extension "scipy.integrate.vode" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.integrate.lsoda" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.integrate._dop" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.interpolate.interpnd" sources >>> >>> building extension "scipy.interpolate._fitpack" sources >>> >>> building extension "scipy.interpolate.dfitpack" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> adding >>> >>> 'build/src.macosx-10.8-intel-2.7/scipy/interpolate/src/dfitpack-f2pywrappers.f' >>> to sources. >>> >>> building extension "scipy.interpolate._interpolate" sources >>> >>> building extension "scipy.io.matlab.streams" sources >>> >>> building extension "scipy.io.matlab.mio_utils" sources >>> >>> building extension "scipy.io.matlab.mio5_utils" sources >>> >>> building extension "scipy.lib.blas.fblas" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> adding >>> >>> 'build/src.macosx-10.8-intel-2.7/build/src.macosx-10.8-intel-2.7/scipy/lib/blas/fblas-f2pywrappers.f' >>> to sources. >>> >>> building extension "scipy.lib.blas.cblas" sources >>> >>> adding 'build/src.macosx-10.8-intel-2.7/scipy/lib/blas/cblas.pyf' to >>> sources. >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.lib.lapack.flapack" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.lib.lapack.clapack" sources >>> >>> adding 'build/src.macosx-10.8-intel-2.7/scipy/lib/lapack/clapack.pyf' >>> to >>> sources. >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.lib.lapack.calc_lwork" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.linalg._fblas" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> adding >>> >>> 'build/src.macosx-10.8-intel-2.7/build/src.macosx-10.8-intel-2.7/scipy/linalg/_fblas-f2pywrappers.f' >>> to sources. >>> >>> building extension "scipy.linalg._flapack" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> adding >>> >>> 'build/src.macosx-10.8-intel-2.7/build/src.macosx-10.8-intel-2.7/scipy/linalg/_flapack-f2pywrappers.f' >>> to sources. >>> >>> building extension "scipy.linalg._flinalg" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.linalg.calc_lwork" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.odr.__odrpack" sources >>> >>> building extension "scipy.optimize._minpack" sources >>> >>> building extension "scipy.optimize._zeros" sources >>> >>> building extension "scipy.optimize._lbfgsb" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.optimize.moduleTNC" sources >>> >>> building extension "scipy.optimize._cobyla" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.optimize.minpack2" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.optimize._slsqp" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.optimize._nnls" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.signal.sigtools" sources >>> >>> building extension "scipy.signal._spectral" sources >>> >>> building extension "scipy.signal.spline" sources >>> >>> building extension "scipy.sparse.linalg.isolve._iterative" sources >>> >>> f2py options: [] >>> >>> adding 'build/src.macosx-10.8-intel-2.7/fortranobject.c' to sources. >>> >>> adding 'build/src.macosx-10.8-intel-2.7' to include_dirs. >>> >>> building extension "scipy.sparse.linalg.dsolve._superlu" sources >>> >>> building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources >>> >>> adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources. >>> >>> swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> swig -python -I/opt/local/include -I/opt/local/include >>> -I/opt/local/include >>> -o >>> >>> build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir >>> build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> unable to execute swig: No such file or directory >>> >>> error: command 'swig' failed with exit status 1 >>> >>> bash-3.2$ >>> >>> >>> paul >>> >>> >>> >>> >>> >>> >>> >>> >>> On 10.08.13 23:33, Edward d'Auvergne wrote: >>> >>> Oh, those are the fat3 commands! I.e. the universal binaries I build >>> for the relax DMG distribution archive. Try: >>> >>> bash-3.2$ swig -I/sw/include/suitesparse/ -I/opt/local/include -python >>> -o >>> >>> build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir >>> build/src.macosx-10.6-intel-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 10 August 2013 23:28, Edward d'Auvergne <[email protected]> >>> wrote: >>> >>> Hi, >>> >>> The swig command might be back to front, try: >>> >>> bash-3.2$ /opt/local/bin/swig -I/opt/local/include/ >>> -I/sw/include/suitesparse/ -python -o >>> >>> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> I'll look more into that one tomorrow. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> On 10 August 2013 22:07, Paul Schanda <[email protected]> wrote: >>> >>> Hmm, not overly successful. >>> I do have the umfpack*.h files in /opt/local/include/umfpack: >>> >>> [new-host-2:~] paul% ls /opt/local/include/umfpack*.h >>> >>> /opt/local/include/umfpack.h >>> /opt/local/include/umfpack_col_to_triplet.h >>> /opt/local/include/umfpack_defaults.h >>> /opt/local/include/umfpack_free_numeric.h >>> /opt/local/include/umfpack_free_symbolic.h >>> /opt/local/include/umfpack_get_determinant.h >>> /opt/local/include/umfpack_get_lunz.h >>> /opt/local/include/umfpack_get_numeric.h >>> /opt/local/include/umfpack_get_symbolic.h >>> /opt/local/include/umfpack_global.h >>> /opt/local/include/umfpack_load_numeric.h >>> /opt/local/include/umfpack_load_symbolic.h >>> /opt/local/include/umfpack_numeric.h >>> /opt/local/include/umfpack_qsymbolic.h >>> /opt/local/include/umfpack_report_control.h >>> /opt/local/include/umfpack_report_info.h >>> /opt/local/include/umfpack_report_matrix.h >>> /opt/local/include/umfpack_report_numeric.h >>> /opt/local/include/umfpack_report_perm.h >>> /opt/local/include/umfpack_report_status.h >>> /opt/local/include/umfpack_report_symbolic.h >>> /opt/local/include/umfpack_report_triplet.h >>> /opt/local/include/umfpack_report_vector.h >>> /opt/local/include/umfpack_save_numeric.h >>> /opt/local/include/umfpack_save_symbolic.h >>> /opt/local/include/umfpack_scale.h >>> /opt/local/include/umfpack_solve.h >>> /opt/local/include/umfpack_symbolic.h >>> /opt/local/include/umfpack_tictoc.h >>> /opt/local/include/umfpack_timer.h >>> /opt/local/include/umfpack_transpose.h >>> /opt/local/include/umfpack_triplet_to_col.h >>> /opt/local/include/umfpack_wsolve.h >>> [new-host-2:~] paul% >>> >>> >>> However, I tried using swig, and pointing to /opt/local/include as you >>> suggest (trying some variations of the command), but was unsuccessful. >>> >>> bash-3.2$ /opt/local/bin/swig -I/sw/include/suitesparse/ -python -o >>> >>> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:192: Error: Unable to find >>> 'umfpack.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:193: Error: Unable to find >>> 'umfpack_solve.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:194: Error: Unable to find >>> 'umfpack_defaults.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:195: Error: Unable to find >>> 'umfpack_triplet_to_col.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:196: Error: Unable to find >>> 'umfpack_col_to_triplet.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:197: Error: Unable to find >>> 'umfpack_transpose.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:198: Error: Unable to find >>> 'umfpack_scale.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:200: Error: Unable to find >>> 'umfpack_report_symbolic.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:201: Error: Unable to find >>> 'umfpack_report_numeric.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:202: Error: Unable to find >>> 'umfpack_report_info.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:203: Error: Unable to find >>> 'umfpack_report_control.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:215: Error: Unable to find >>> 'umfpack_symbolic.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:216: Error: Unable to find >>> 'umfpack_numeric.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:225: Error: Unable to find >>> 'umfpack_free_symbolic.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:226: Error: Unable to find >>> 'umfpack_free_numeric.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:248: Error: Unable to find >>> 'umfpack_get_lunz.h' >>> >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i:272: Error: Unable to find >>> 'umfpack_get_numeric.h' >>> >>> >>> bash-3.2$ /opt/local/bin/swig -I/sw/include/suitesparse/ -python -o >>> >>> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i -I/opt/local/include/ >>> >>> swig error : Unrecognized option >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> Use 'swig -help' for available options. >>> >>> >>> bash-3.2$ /opt/local/bin/swig -I/opt/local/include/ -python -o >>> >>> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c >>> -outdir build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack >>> scipy/sparse/linalg/dsolve/umfpack/umfpack.i >>> >>> Unable to open file >>> >>> build/src.macosx-10.5-fat3-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c: >>> No such file or directory >>> >>> bash-3.2$ >>> >>> >>> In fact, I don't have build/src.macosx-10.5-fat3-2.7 >>> >>> I do have >>> build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/ but >>> it >>> is empty: >>> >>> bash-3.2$ ls >>> build/src.macosx-10.8-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/ >>> >>> bash-3.2$ >>> >>> >>> A long way to get it running... :-S >>> >>> paul >>> >>> >>> >>> On 10.08.13 09:39, Edward d'Auvergne wrote: >>> >>> Hi, >>> >>> Maybe the files in /opt would be sufficient. Try copying and pasting the >>> swig command in my previous mail >>> (http://thread.gmane.org/gmane.science.nmr.relax.devel/4339/focus=4351) >>> and >>> add -I/opt/local/include/ as that might just work. Note these >>> compilation >>> commands are for the 'sh' shell, so you need bash or sh to run them. >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On Saturday, 10 August 2013, Paul Schanda wrote: >>> >>> Hi, >>> >>> I guess I'll get there. Eventually. >>> >>> In the meantime I don't find suitesparse on my system. At least not at >>> /sw/include/suitesparse. >>> >>> I have a few instances of SuiteSparse on the system, but none of them >>> contains umfpack files. >>> >>> I have a number of umfpack_*.h files, most of them at /opt/local/include: >>> /opt/local/include/umfpack.h >>> /opt/local/include/umfpack_col_to_triplet.h >>> /opt/local/include/umfpack_defaults.h >>> /opt/local/include/umfpack_free_numeric.h >>> /opt/local/include/umfpack_free_symbolic.h >>> /opt/local/include/umfpack_get_determinant.h >>> /opt/local/include/umfpack_get_lunz.h >>> /opt/local/include/umfpack_get_numeric.h >>> /opt/local/include/umfpack_get_symbolic.h >>> /opt/local/include/umfpack_global.h >>> /opt/local/include/umfpack_load_numeric.h >>> /opt/local/include/umfpack_load_symbolic.h >>> /opt/local/include/umfpack_numeric.h >>> /opt/local/include/umfpack_qsymbolic.h >>> /opt/local/include/umfpack_report_control.h >>> /opt/local/include/umfpack_report_info.h >>> /opt/local/include/umfpack_report_matrix.h >>> /opt/local/include/umfpack_report_numeric.h >>> /opt/local/include/umfpack_report_perm.h >>> /opt/local/include/umfpack_report_status.h >>> /opt/local/include/umfpack_report_symbolic.h >>> /opt/local/include/umfpack_report_triplet.h >>> /opt/local/include/umfpack_report_vector.h >>> /opt/local/include/umfpack_save_numeric.h >>> /opt/local/include/umfpack_save_symbolic.h >>> /opt/local/include/umfpack_scale.h >>> /opt/local/include/umfpack_solve.h >>> /opt/local/include/umfpack_symbolic.h >>> /opt/local/include/umfpack_tictoc.h >>> /opt/local/include/umfpack_timer.h >>> /opt/local/include/umfpack_transpose.h >>> /opt/local/include/umfpack_triplet_to_col.h >>> /opt/local/include/umfpack_wsolve.h >>> >>> >>> >>> Otherwise, I seem to have suitesparse installed via macports: >>> >>> [new-host-2:/Users/paul] root# port installed suitesparse >>> >>> The following ports are currently installed: >>> >>> SuiteSparse @3.4.0_0 >>> >>> SuiteSparse @3.4.0_3 >>> >>> SuiteSparse @4.0.0_0 >>> >>> SuiteSparse @4.1.0_0 (active) >>> >>> >>> In the suitesparse directory that is related to macports, there are no >>> umfpack files. >>> >>> [new-host-2:~] paul% ls >>> >>> /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/files/ >>> >>> UFconfig_UFconfig.mk-patch patch-CHOLMOD_Lib_Makefile.diff >>> >>> makefiles.patch >>> >>> [new-host-2:~] paul% ls >>> >>> /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/Portfile >>> >>> >>> >>> /opt/local/var/macports/sources/rsync.macports.org/release/ports/math/SuiteSparse/Portfile >>> >>> >>> I could probably download SuiteSparse, but this of course comes at the >>> risk of downloading again something that does not talk to the other >>> things >>> required... >>> As you say, it's tough with multiple python versions around... >>> >>> cheers - >>> >>> Paul >>> >>> On 09.08.13 16:30, Edward d'Auvergne wrote: >>> >>> Hi, >>> >>> You're actually almost there. That swig error with umfpack.i is >>> exactly the same problem I had yesterday when I was multiply >>> reinstalling everything on my Mac system. The problem was that it >>> could not find the suitesparse header *.h files. I found these on my >>> system at /sw/include/suitesparse - please make sure you have this >>> directory with umfpack_*.h files in it too - and that is what the >>> C_INCLUDE_PATH variable is for. The rest of the problems is due to >>> the C shell so, for avoiding a lot of pain, I would recommend >>> temporarily switching to bash. C shell issues caused the PATH error >>> message you saw. So please try the following: >>> >>> [gre:~/Downloads/scipy-0.12.0] % bash >>> gre:scipy-0.12.0 $ PATH=/usr/local/bin/:$PATH >>> C_INCLUDE_PATH=/sw/include/ >>> suitesparse/ ~/bin/python2.7 setup.py >>> install >>> >>> It is imperative to have the PATH and C_INCLUDE_PATH environmental >>> variables set this way before the Python command. Otherwise Scipy >>> will not be in a functional state and the import will give exactly the >>> error you saw. And /sw/include/suitesparse/ must exist and contain a >>> pile of umfpack_*.h files in it. We almost have it running now! Life >>> is tough having multiple Python versions around on a Mac! >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> -- >>> Paul Schanda, Ph.D. >>> Biomolecular NMR group >>> Institut de Biologie Structurale Jean-Pierre Ebel (IBS) >>> 41, rue Jules Horowitz >>> F-38027 Grenoble >>> France >>> +33 438 78 95 55 >>> [email protected] >>> http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en >>> >>> >>> >>> -- >>> Paul Schanda, Ph.D. >>> Biomolecular NMR group >>> Institut de Biologie Structurale Jean-Pierre Ebel (IBS) >>> 41, rue Jules Horowitz >>> F-38027 Grenoble >>> France >>> +33 438 78 95 55 >>> [email protected] >>> http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en > > > > -- > Paul Schanda, Ph.D. > Biomolecular NMR group > Institut de Biologie Structurale Jean-Pierre Ebel (IBS) > 41, rue Jules Horowitz > F-38027 Grenoble > France > +33 438 78 95 55 > [email protected] > http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
