So it seems that cythonize doesn't pick up the dependency for whatever
reason. Can you post your generated cython output, that is,
src/build/cythonized/sage/combinat/partitions.cpp? Maybe there are more
differences that'll tell us whats going on.
On Monday, May 30, 2016 at 10:50:11 PM UTC+2, paulmasson wrote:
>
> Volker:
>
>
> MacBook-Retina:sage Masson$ python
>
> Python 2.7.10 (default, Oct 23 2015, 19:19:21)
>
> [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
>
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> import sys
>
> >>> sys.path.append('src')
>
> >>> from sage_setup.find import find_extra_files
>
> >>> find_extra_files(["sage.combinat"], 'src', 'src/build/cythonized', '.')
>
> [('./sage/combinat', ['src/sage/combinat/combinat_cython.pxd',
> 'src/sage/combinat/enumeration_mod_permgroup.pxd',
> 'src/sage/combinat/permutation_cython.pxd'])]
>
> >>>
>
>
> On Monday, May 30, 2016 at 6:12:16 AM UTC-7, Volker Braun wrote:
>>
>> You can run the script with your system python directly in your Sage
>> directory, e.g.:
>>
>> $ python
>> Python 2.7.11 (default, Mar 31 2016, 20:46:51)
>> [GCC 5.3.1 20151207 (Red Hat 5.3.1-2)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import sys
>> >>> sys.path.append('src')
>> >>> from sage_setup.find import find_extra_files
>> >>> find_extra_files(["sage.combinat"], 'src', 'src/build/cythonized',
>> '.')
>> [('./sage/combinat', ['src/sage/combinat/combinat_cython.pxd',
>> 'src/sage/combinat/enumeration_mod_permgroup.pxd',
>> 'src/sage/combinat/permutation_cython.pxd',
>> 'src/build/cythonized/sage/combinat/partitions_c.h'])]
>>
>>
>>
>> On Monday, May 30, 2016 at 2:57:41 AM UTC+2, paulmasson wrote:
>>>
>>> Volker, the line you have in logs/install.log does not exist for me when
>>> the build halts. Just this:
>>>
>>> $ egrep -r partitions_c.h logs/install.log
>>>
>>> logs/install.log:/Users/Masson/downloads/github/sage/src/build/
>>> cythonized/sage/combinat/partitions.cpp:323:26: fatal error:
>>> partitions_c.h: No such file or directory
>>>
>>> logs/install.log: #include "partitions_c.h"
>>>
>>> I'll save a copy of the install log at the point of halting if you want
>>> that as well.
>>>
>>> There is no sagelib7.3-beta*.log when the build halts. Attaching
>>> sagelib-7.2.log instead if that helps.
>>>
>>> When the build halts I cannot run Sage to give you the other output. In
>>> the working version of 7.2, the output of the indicated commands is exactly
>>> the same as yours, but that is because I manually made sure the missing
>>> files were put in place.
>>>
>>> These nine files are just not getting copied during the build on my
>>> machine.
>>>
>>>
>>> On Sunday, May 29, 2016 at 4:11:41 PM UTC-7, Volker Braun wrote:
>>>>
>>>> These are copied during the build process:
>>>>
>>>> $ egrep -r partitions_c.h logs/install.log
>>>> copying
>>>> /home/vbraun/Sage/git-develop/src/build/cythonized/sage/combinat/partitions_c.h
>>>>
>>>> ->
>>>> /home/vbraun/Sage/git-develop/local/lib/python2.7/site-packages/sage/combinat
>>>>
>>>> Can you post your logs/pkgs/sagelib-7.3.beta2.log and whats the output
>>>> of
>>>>
>>>> sage: from sage_setup.find import find_extra_files
>>>> sage: from sage.env import SAGE_SRC, SAGE_CYTHONIZED
>>>> sage: find_extra_files(["sage.combinat"], SAGE_SRC, SAGE_CYTHONIZED,
>>>> ".")
>>>> [('./sage/combinat',
>>>> ['/home/vbraun/Code/sage/src/sage/combinat/combinat_cython.pxd',
>>>>
>>>> '/home/vbraun/Code/sage/src/sage/combinat/enumeration_mod_permgroup.pxd',
>>>> '/home/vbraun/Code/sage/src/sage/combinat/permutation_cython.pxd',
>>>>
>>>>
>>>> '/home/vbraun/Code/sage/src/build/cythonized/sage/combinat/partitions_c.h'])]
>>>>
>>>>
>>>>
>>>> On Monday, May 30, 2016 at 12:02:31 AM UTC+2, paulmasson wrote:
>>>>>
>>>>> Turns out this issue has nothing to do with the Github copy. I
>>>>> downloaded a 7.2 tarball and had the same issue a total of nine times.
>>>>> Here
>>>>> are the successive error messages:
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/combinat/partitions.cpp:323:26:
>>>>>
>>>>> fatal error: partitions_c.h: No such file or directory
>>>>>
>>>>> #include "partitions_c.h"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/combinat/matrices/dancing_links.cpp:319:29:
>>>>>
>>>>> fatal error: dancing_links_c.h: No such file or directory
>>>>>
>>>>> #include "dancing_links_c.h"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/graphs/base/boost_graph.cpp:314:31:
>>>>>
>>>>> fatal error: boost_interface.cpp: No such file or directory
>>>>>
>>>>> #include "boost_interface.cpp"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/libs/ecl.c:324:20:
>>>>> fatal error: eclsig.h: No such file or directory
>>>>>
>>>>> #include "eclsig.h"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/libs/ppl.cpp:336:23:
>>>>> fatal error: ppl_shim.hh: No such file or directory
>>>>>
>>>>> #include "ppl_shim.hh"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/libs/eclib/mwrank.cpp:356:20:
>>>>>
>>>>> fatal error: wrap.cpp: No such file or directory
>>>>>
>>>>> #include "wrap.cpp"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/matroids/matroid.c:296:22:
>>>>>
>>>>> fatal error: minorfix.h: No such file or directory
>>>>>
>>>>> #include "minorfix.h"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/misc/darwin_utilities.c:290:33:
>>>>>
>>>>> fatal error: darwin_memory_usage.h: No such file or directory
>>>>>
>>>>> #include "darwin_memory_usage.h"
>>>>>
>>>>> /Users/Masson/desktop/sage/src/build/cythonized/sage/symbolic/pynac.cpp:334:22:
>>>>>
>>>>> fatal error: pynac_cc.h: No such file or directory
>>>>>
>>>>> #include "pynac_cc.h"
>>>>>
>>>>> After each failed build I manually copied each missing file to the
>>>>> appropriate directory and ran 'make' again. I now have a running build of
>>>>> 7.2. Yippee!
>>>>>
>>>>> A friend has suggested that the errors might be caused by bad line
>>>>> endings that only show up on a Mac. Any other explanations for such
>>>>> apparently random behavior?
>>>>>
>>>>>
>>>>> On Saturday, May 28, 2016 at 5:55:04 PM UTC-7, paulmasson wrote:
>>>>>>
>>>>>> Running OS X El Capitan on a year-old Macbook.
>>>>>>
>>>>>> Deleted my entire Sage directory. Did a clean clone from
>>>>>> github.com/sagemath/sage.git. Immediately changed to Sage directory
>>>>>> and ran make. Same error as previously:
>>>>>>
>>>>>> error: command 'gcc' failed with exit status 1
>>>>>>
>>>>>> /Users/Masson/downloads/github/sage/src/build/cythonized/sage/combinat/partitions.cpp:323:26:
>>>>>>
>>>>>> fatal error: partitions_c.h: No such file or directory
>>>>>>
>>>>>> #include "partitions_c.h"
>>>>>>
>>>>>> ^
>>>>>>
>>>>>> compilation terminated.
>>>>>>
>>>>>> make[3]: *** [sage] Error 1
>>>>>>
>>>>>>
>>>>>> Is there a problem building from the github copy?
>>>>>>
>>>>>
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