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2014-11-21 11:11:36 -0600 answered a question %cython in notebook doesn’t work anymore

How the problem was fixed (magic algorithm):

  • i installed the command line tools of xcode (seemingly not included under osx 10.9)
  • started to compile sage-6.4 from source
  • stopped the compilation after around 1h and deleted the whole sage-6.4 folder

    After that, sage-6.3.app recovered its usual %cython behavior in the notebook.

    Could be that only the first step was useful, but no way checking it now.

  • 2014-11-21 11:03:34 -0600 commented answer %cython in notebook doesn’t work anymore

    the original log is lost; all i can say is what happened between the dates "6.3.app doesn't run cython" and "6.3.app does run cython":

  • i installed the command line tools of xcode (seemingly not included under osx 10.9)
  • started to compile sage-6.4 from source
  • stopped the compilation after around 1h and deleted the whole sage-6.4 folder

    this doesn't help me to figure out what the bug is, only greatly restricts the possibilities; thanks for your help!

  • 2014-11-20 10:57:17 -0600 commented answer %cython in notebook doesn’t work anymore

    thanks, and right: so sorry, i run 10.9 not 8 (updated the question); with the 6.1 version of xcode;

    half good news:

    • i started to build sage 6.4 from source but had to interrupt the compilation - so i trashed the 6.4 folder before leaving here; just in case, i tried sage-6.3.app... now it works fine, %cython in notebook has its usual behavior (isn't that magic?)

    • now i have to find some log of the interrupted make (if any) in order to see what could have changed, i guess this might be a compiler problem

    to be followed

    2014-11-20 08:36:55 -0600 received badge  Editor (source)
    2014-11-20 08:25:45 -0600 commented answer %cython in notebook doesn’t work anymore

    thanks for the answer kcrisman;

    i just downloaded the 6.4 version (not the .app this time, in order to eliminate a doubt); exactly the same problem, both with the notebook and the command line;

    recompiling sage? i fear i'll have some problems with xcode anyway... but i'll try;

    now, with which compiler? any gcc would do the job?

    ps: useless to say i'd prefer it would work directly from the downloaded binaries! :))

    2014-11-20 05:58:50 -0600 commented question %cython in notebook doesn’t work anymore

    In the command line, i can load a .sage file but not a .spyx file, for the very same reason as above (same gcc failed error message)

    2014-11-16 11:49:45 -0600 asked a question %cython in notebook doesn’t work anymore

    hello,
    running sage-6.3.app on macosx 10.9.5, i can’t use %cython in the notebook anymore (it used to work some time ago though, with older sage and system versions);
    i get the following: error: command 'gcc' failed with exit status 1
    more precisely, gcc doesn’t find a certain file limits.h (see details below) that, however, exists at the given address - i checked it;
    how can i make it work again?

    PS: same gcc error when loading a .spyx file in the command line
    PS2: same errors with the 6.4 version (sage-6.4-x86_64-Darwin-OSX_10.9_x86_64.dmg)

    gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Sage-6.3.app/Contents/Resources/sage/local/include/csage -I/Applications/Sage-6.3.app/Contents/Resources/sage/local/include -I/Applications/Sage-6.3.app/Contents/Resources/sage/local/include/python2.7 -I/Applications/Sage-6.3.app/Contents/Resources/sage/local/lib/python/site-packages/numpy/core/include -I/Applications/Sage-6.3.app/Contents/Resources/sage/src/sage/ext -I/Applications/Sage-6.3.app/Contents/Resources/sage/src -I/Applications/Sage-6.3.app/Contents/Resources/sage/src/sage/gsl -I/Users/fabrice/.sage/sage_notebook.sagenb/home/admin/123/code -I/Applications/Sage-6.3.app/Contents/Resources/sage/local/include/python2.7 -c _Users_fabrice__sage_sage_notebook_sagenb_home_admin_123_code_sage2_spyx_0.c -o build/temp.macosx-10.9-x86_64-2.7/_Users_fabrice__sage_sage_notebook_sagenb_home_admin_123_code_sage2_spyx_0.o -w -O2
    In file included from /Applications/Sage-6.3.app/Contents/Resources/sage/local/bin/../lib/gcc/x86_64-apple-darwin13.3.0/4.7.3/include-fixed/syslimits.h:7:0,
                     from /Applications/Sage-6.3.app/Contents/Resources/sage/local/bin/../lib/gcc/x86_64-apple-darwin13.3.0/4.7.3/include-fixed/limits.h:34,
                     from /Applications/Sage-6.3.app/Contents/Resources/sage/local/include/python2.7/Python.h:19,
                     from _Users_fabrice__sage_sage_notebook_sagenb_home_admin_123_code_sage2_spyx_0.c:16:
    /Applications/Sage-6.3.app/Contents/Resources/sage/local/bin/../lib/gcc/x86_64-apple-darwin13.3.0/4.7.3/include-fixed/limits.h:169:61: fatal error: limits.h: No such file or directory
    compilation terminated.