Ok... So when I did sage -b I got a fatal error; here's the end that lists
the error part:
In file included from
*/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin15.6.0/5.4.0/include-fixed/syslimits.h:7:0*
,
from
*/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin15.6.0/5.4.0/include-fixed/limits.h:34*
,
from
*/Applications/SageMath/local/include/python2.7/Python.h:1*,
from
*/Applications/SageMath/src/build/cythonized/sage/algebras/quatalg/quaternion_algebra_element.cpp:60*
:
*/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin15.6.0/5.4.0/include-fixed/limits.h:168:61:*
*fatal
error: *limits.h: No such file or directory
compilation terminated.
[ 2/450] creating
build/temp.macosx-10.9-x86_64-2.7/Applications/SageMath/src/build/cythonized/sage/algebras/letterplace
gcc -fno-strict-aliasing
-I/Applications/SageMath/local/var/tmp/sage/build/python2-2.7.13.p0/include
-DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused
-I/Applications/SageMath/local/include
-I/Applications/SageMath/local/include/python2.7
-I/Applications/SageMath/local/lib/python2.7/site-packages/numpy/core/include
-I/Applications/SageMath/src -I/Applications/SageMath/src/sage/ext
-I/Applications/SageMath/src/build/cythonized
-I/Applications/SageMath/src/build/cythonized/sage/ext
-I/Applications/SageMath/local/include/python2.7 -c
/Applications/SageMath/src/build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.cpp
-o
build/temp.macosx-10.9-x86_64-2.7/Applications/SageMath/src/build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.o
-I/Applications/SageMath/local/include/singular
-I/Applications/SageMath/local/include/
-I/Applications/SageMath/local/include -DSING_NDEBUG -DOM_NDEBUG
-fno-strict-aliasing
error: command 'gcc' failed with exit status 1
In file included from
*/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin15.6.0/5.4.0/include-fixed/syslimits.h:7:0*
,
from
*/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin15.6.0/5.4.0/include-fixed/limits.h:34*
,
from
*/Applications/SageMath/local/include/python2.7/Python.h:1*,
from
*/Applications/SageMath/src/build/cythonized/sage/algebras/letterplace/free_algebra_element_letterplace.cpp:69*
:
*/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin15.6.0/5.4.0/include-fixed/limits.h:168:61:*
*fatal
error: *limits.h: No such file or directory
compilation terminated.
make: *** [sage] Error 1
The checks still show false. Here's the dot2tex installation log:
Found local metadata for dot2tex-2.9.0.p1
Attempting to download package dot2tex-2.9.0.tar.gz from mirrors
Downloading the Sage mirror list
Searching fastest mirror
265ms: http://ftp.iitm.ac.in/sage/
230ms: http://ftp.kaist.ac.kr/sage/
278ms: http://ftp.leg.uct.ac.za/pub/packages/sage/
180ms: http://ftp.ntua.gr/pub/sagemath/
155ms: http://ftp.riken.jp/sagemath/
855ms: http://ftp.tsukuba.wide.ad.jp/software/sage/
341ms: http://ftp.yz.yamagata-u.ac.jp/pub/math/sage/
175ms: http://linorg.usp.br/sage/
208ms: http://mirror.aarnet.edu.au/pub/sage/
249ms: http://mirror.hust.edu.cn/sagemath/
239ms: http://mirror.switch.ch/mirror/sagemath/
313ms: http://mirror.ufs.ac.za/sagemath/
240ms: http://mirror.yandex.ru/mirrors/sage.math.washington.edu/
464ms: http://mirrors-usa.go-parts.com/sage/sagemath/
143ms: http://mirrors.fe.up.pt/pub/sage/
32ms: http://mirrors.mit.edu/sage/
1033ms: http://mirrors.tuna.tsinghua.edu.cn/sagemath/
1010ms: http://mirrors.ustc.edu.cn/sagemath/
46ms: http://mirrors.xmission.com/sage/
800ms: http://sage.mirror.garr.it/mirrors/sage/
810ms: http://sagemath.c3sl.ufpr.br/
662ms: http://sagemath.mirror.ac.za/
385ms: http://sagemath.polytechnic.edu.na/
136ms: http://sunsite.rediris.es/mirror/sagemath/
116ms: http://www-ftp.lip6.fr/pub/math/sagemath/
56ms: http://www.cecm.sfu.ca/sage/
239ms: http://www.mirrorservice.org/sites/www.sagemath.org/
Fastest mirror: http://mirrors.mit.edu/sage/
http://mirrors.mit.edu/sage/spkg/upstream/dot2tex/dot2tex-2.9.0.tar.gz
[......................................................................]
dot2tex-2.9.0.p1
====================================================
Setting up build directory for dot2tex-2.9.0.p1
Finished extraction
Applying patches from ../patches...
Applying ../patches/remove_test_semicolon.patch
patching file tests/test_dot2tex.py
****************************************************
Host system:
Darwin ec112.ec26.earlham.edu 15.6.0 Darwin Kernel Version 15.6.0: Wed Nov
2 20:30:56 PDT 2016; root:xnu-3248.60.11.1.2~2/RELEASE_X86_64 x86_64
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/Applications/SageMath/local/libexec/gcc/x86_64-apple-darwin15.6.0/5.4.0/lto-wrapper
Target: x86_64-apple-darwin15.6.0
Configured with: ../src/configure --prefix=/Applications/SageMath/local
--with-local-prefix=/Applications/SageMath/local
--with-gmp=/Applications/SageMath/local
--with-mpfr=/Applications/SageMath/local
--with-mpc=/Applications/SageMath/local --with-system-zlib
--disable-multilib --disable-nls --enable-languages=c,c++,fortran
--disable-libitm --with-build-config=bootstrap-debug --without-isl
--without-cloog
Thread model: posix
gcc version 5.4.0 (GCC)
****************************************************
Installing package dot2tex using pip
Ignoring indexes: https://pypi.python.org/simple
Processing
/Applications/SageMath/local/var/tmp/sage/build/dot2tex-2.9.0.p1/src
Running setup.py
(path:/var/folders/ys/v5hlv3pd7g7_605k791qvd7m0000gp/T/pip-AHL1N2-build/setup.py)
egg_info for package from
file:///Applications/SageMath/local/var/tmp/sage/build/dot2tex-2.9.0.p1/src
Running command python setup.py egg_info
running egg_info
creating pip-egg-info/dot2tex.egg-info
writing requirements to pip-egg-info/dot2tex.egg-info/requires.txt
writing pip-egg-info/dot2tex.egg-info/PKG-INFO
writing top-level names to pip-egg-info/dot2tex.egg-info/top_level.txt
writing dependency_links to
pip-egg-info/dot2tex.egg-info/dependency_links.txt
writing entry points to pip-egg-info/dot2tex.egg-info/entry_points.txt
writing manifest file 'pip-egg-info/dot2tex.egg-info/SOURCES.txt'
warning: manifest_maker: standard file '-c' not found
reading manifest file 'pip-egg-info/dot2tex.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.pyc' found under
directory 'docs'
warning: no previously-included files matching '*.pyo' found under
directory 'docs'
no previously-included directories found matching
'tests/testgraphs/*/*.dot'
warning: no files found matching 'tests/test_comparedotparsing.py'
warning: no files found matching 'tests/test_multirender.py'
warning: no files found matching 'tests/test_buildexamples.py'
no previously-included directories found matching
'examples/*dot2tex-fig*'
no previously-included directories found matching 'docs/_build'
writing manifest file 'pip-egg-info/dot2tex.egg-info/SOURCES.txt'
Source in
/var/folders/ys/v5hlv3pd7g7_605k791qvd7m0000gp/T/pip-AHL1N2-build has
version 2.9.0, which satisfies requirement dot2tex==2.9.0 from
file:///Applications/SageMath/local/var/tmp/sage/build/dot2tex-2.9.0.p1/src
Installing collected packages: dot2tex
Running setup.py install for dot2tex: started
Running command /Applications/SageMath/local/bin/python -u -c "import
setuptools,
tokenize;__file__='/var/folders/ys/v5hlv3pd7g7_605k791qvd7m0000gp/T/pip-AHL1N2-build/setup.py';exec(compile(getattr(tokenize,
'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))"
install --record
/var/folders/ys/v5hlv3pd7g7_605k791qvd7m0000gp/T/pip-lnn0oo-record/install-record.txt
--single-version-externally-managed --compile
running install
running build
running build_py
creating build
creating build/lib
creating build/lib/dot2tex
copying dot2tex/__init__.py -> build/lib/dot2tex
copying dot2tex/dot2tex.py -> build/lib/dot2tex
copying dot2tex/dotparsing.py -> build/lib/dot2tex
running build_scripts
creating build/scripts-2.7
copying and adjusting dot2tex/dot2tex -> build/scripts-2.7
changing mode of build/scripts-2.7/dot2tex from 644 to 755
running install_lib
creating
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex
copying build/lib/dot2tex/__init__.py ->
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex
copying build/lib/dot2tex/dot2tex.py ->
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex
copying build/lib/dot2tex/dotparsing.py ->
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex
byte-compiling
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex/__init__.py
to __init__.pyc
byte-compiling
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex/dot2tex.py
to dot2tex.pyc
byte-compiling
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex/dotparsing.py
to dotparsing.pyc
running install_egg_info
running egg_info
writing requirements to dot2tex.egg-info/requires.txt
writing dot2tex.egg-info/PKG-INFO
writing top-level names to dot2tex.egg-info/top_level.txt
writing dependency_links to dot2tex.egg-info/dependency_links.txt
writing entry points to dot2tex.egg-info/entry_points.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'dot2tex.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.pyc' found under
directory 'docs'
warning: no previously-included files matching '*.pyo' found under
directory 'docs'
no previously-included directories found matching
'tests/testgraphs/*/*.dot'
warning: no files found matching 'tests/test_comparedotparsing.py'
warning: no files found matching 'tests/test_multirender.py'
warning: no files found matching 'tests/test_buildexamples.py'
no previously-included directories found matching
'examples/*dot2tex-fig*'
no previously-included directories found matching 'docs/_build'
writing manifest file 'dot2tex.egg-info/SOURCES.txt'
Copying dot2tex.egg-info to
/Applications/SageMath/local/lib/python2.7/site-packages/dot2tex-2.9.0-py2.7.egg-info
running install_scripts
copying build/scripts-2.7/dot2tex -> /Applications/SageMath/local/bin
changing mode of /Applications/SageMath/local/bin/dot2tex to 755
Installing dot2tex script to /Applications/SageMath/local/bin
writing list of installed files to
'/var/folders/ys/v5hlv3pd7g7_605k791qvd7m0000gp/T/pip-lnn0oo-record/install-record.txt'
Running setup.py install for dot2tex: finished with status 'done'
Removing source in
/var/folders/ys/v5hlv3pd7g7_605k791qvd7m0000gp/T/pip-AHL1N2-build
Successfully installed dot2tex-2.9.0
Cleaning up...
real 0m2.014s
user 0m1.493s
sys 0m0.465s
Successfully installed dot2tex-2.9.0.p1
Deleting temporary build directory
/Applications/SageMath/local/var/tmp/sage/build/dot2tex-2.9.0.p1
Finished installing dot2tex-2.9.0.p1.spkg
On Saturday, June 3, 2017 at 4:02:19 AM UTC-4, Dima Pasechnik wrote:
>
> also, could you please post here the logfile of dot2tex installation:
> it is SAGEROOT/logs/pkgs/dot2tex-2.9.0.p1.log
>
> On Friday, June 2, 2017 at 11:41:50 PM UTC+1, Julie Beier wrote:
>>
>> This returns false.
>>
>> On Friday, June 2, 2017 at 4:59:39 PM UTC-4, Dima Pasechnik wrote:
>>>
>>>
>>>
>>> On Friday, June 2, 2017 at 9:01:08 PM UTC+1, Julie Beier wrote:
>>>>
>>>> Hi Dima,
>>>>
>>>> I get errors when I do this in Sagenb (which is my usual place) and
>>>> when I run it in Terminal. (I've always installed the .dmg and not the
>>>> .app version.) The errors are slightly different but both have to do with
>>>> an inability to compile the tex code. This is why I am so confused. I
>>>> don't really understand why the tex code should be different when all the
>>>> builds are the same.
>>>>
>>>
>>> OSX has its own unique ways to torture developers (and they keep
>>> "improving" them :-)),
>>> that's why it seems that Sage suffers from lack of testing on OSX...
>>>
>>>
>>> Could you check if
>>>
>>> sage: import dot2tex
>>>
>>> works?
>>>
>>> And one more sanity check:
>>>
>>> sage: from sage.graphs.dot2tex_utils import have_dot2tex
>>> sage: have_dot2tex()
>>>
>>> Does this return True? (have_dot2tex() is some old function still used
>>> in that code...)
>>>
>>>
>>>
>>> With sagenb it's not working, and will not work; sagenb is
>>> deprecated---switch to jupyter notebooks
>>> (one advantage is that they can be used on SMC)
>>>
>>>
>>>
>>>
>>>>
>>>> I'll note that I know others who have run into this problem (I've had
>>>> this problem since I updated SAGE in 2013) and they have just given up.
>>>>
>>>> Thanks,
>>>> Julie
>>>>
>>>> On Friday, June 2, 2017 at 4:55:42 AM UTC-4, Dima Pasechnik wrote:
>>>>>
>>>>>
>>>>>
>>>>> On Friday, June 2, 2017 at 1:16:19 AM UTC+1, Julie Beier wrote:
>>>>>>
>>>>>> Current version of SAGE: 7.5.1 though this happened with several
>>>>>> versions, all binary install
>>>>>> Operating System: OSX 10.11.6
>>>>>> Version of Tex: Version 3.14159265-2.6-1.40.17 (TeX Live 2016); All
>>>>>> packages up to date
>>>>>>
>>>>>> As previously mentioned, this was all what matches on the cloud for
>>>>>> SAGE and Tex.
>>>>>>
>>>>>
>>>>> Thanks, I guess I know where the problem is - it is in Sagenb;
>>>>> one more piece of the puzzle: how do you start and run Sage?
>>>>> Possibilities are:
>>>>>
>>>>> Terminal : should work (works for me)
>>>>> OSX app : I don't know
>>>>> Sagenb (the "classical" Sage notebook) : displaying this does not work
>>>>> for me, and most probably won't be fixed
>>>>> jupyter notebook : should work (works for me)
>>>>>
>>>>> Thus, I am able to get an error if I try your code in Sagenb (although
>>>>> the error looks different...)
>>>>>
>>>>> One option for you would be switching to jupyter notebook, but for
>>>>> this you probably needed
>>>>> a newer version of Sage.
>>>>> The other option would be to run the Sage in OSX terminal - then the
>>>>> output should get displayed in a tab of your default browser.
>>>>> Could you try the latter?
>>>>> (if this still fails, to be sure it's not OSX app problem, could you
>>>>> install a non-app version - i.e. the filename should not end with
>>>>> .app.dmg,
>>>>> but just with 64.dmg)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Could you please try this with non-app version of Sage, and run Sage
>>>>> in terminal.
>>>>>
>>>>>
>>>>>>
>>>>>> On Thursday, June 1, 2017 at 4:49:57 PM UTC-4, Dima Pasechnik wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thursday, June 1, 2017 at 8:34:55 PM UTC+1, Julie Beier wrote:
>>>>>>>>
>>>>>>>> So I guess this was the point of my message. What you just posted
>>>>>>>> does *not* work for me. It says True for dot2tex installed, but I
>>>>>>>> get the two different tex files (doing this on my computer versus on
>>>>>>>> the
>>>>>>>> cloud) and on my computer it does not generate something that works.
>>>>>>>>
>>>>>>>
>>>>>>> We need more details about your computer: Sage version, operating
>>>>>>> system, whether it was compiled from source or installed as a binary,
>>>>>>> what
>>>>>>> version of TeX is installed.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> On Thursday, June 1, 2017 at 3:18:04 PM UTC-4, Dima Pasechnik wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thursday, June 1, 2017 at 7:57:22 PM UTC+1, Julie Beier wrote:
>>>>>>>>>>
>>>>>>>>>> Dima,
>>>>>>>>>>
>>>>>>>>>> Sorry but I'm not sure I understand. I followed the directions
>>>>>>>>>> in the sage help that say to do sage -i 'dot2tex'. That is done.
>>>>>>>>>> But it
>>>>>>>>>> still creates the different tex files, and I still have the problem.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> the following works for me on a local Sage install (it's
>>>>>>>>> 8.0.beta8, but it should not matter)
>>>>>>>>>
>>>>>>>>> sage: is_package_installed("dot2tex") # sanity check
>>>>>>>>> True
>>>>>>>>> sage: B = crystals.Tableaux(['A',2], shape=[2,1])
>>>>>>>>> sage: view(B) # opens a tab in the browser with the picture
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Nicolas's work around makes the small example he posted work,
>>>>>>>>>> but it doesn't work for the crystals. Was I supposed to install
>>>>>>>>>> dot2tex
>>>>>>>>>> differently?
>>>>>>>>>>
>>>>>>>>> you can have more than one Sage install (well, in principle, that
>>>>>>>>> is)
>>>>>>>>> (Or indeed Sage version matters...)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> J
>>>>>>>>>>
>>>>>>>>>> On Thursday, June 1, 2017 at 2:40:04 PM UTC-4, Dima Pasechnik
>>>>>>>>>> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thursday, June 1, 2017 at 7:23:29 PM UTC+1, Julie Beier wrote:
>>>>>>>>>>>>
>>>>>>>>>>>> All,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks all for the help; glad to know it wasn't just something
>>>>>>>>>>>> trivial that I missed.
>>>>>>>>>>>>
>>>>>>>>>>>> This work around doesn't seem to work for whole crystals as
>>>>>>>>>>>> there is no set_latex_options option. Anyway to work around the
>>>>>>>>>>>> problem
>>>>>>>>>>>> there?
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> IMHO you should check if you indeed had installed dot2tex
>>>>>>>>>>> package, for the crystals.* example you posted as not
>>>>>>>>>>> working, works for me after I installed dot2tex (you might
>>>>>>>>>>> have to quit and start your Sage session, at least, after the
>>>>>>>>>>> installation)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>>
>>>>>>>>>>>> Julie
>>>>>>>>>>>>
>>>>>>>>>>>> On Thursday, June 1, 2017 at 2:01:14 PM UTC-4, Nicolas M.
>>>>>>>>>>>> Thiéry wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Jun 01, 2017 at 12:02:19AM -0700, Dima Pasechnik
>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>> > How does one switch to using dot2tex for this example,
>>>>>>>>>>>>> too?
>>>>>>>>>>>>>
>>>>>>>>>>>>> sage: t = StandardTableaux(4).random_element()
>>>>>>>>>>>>> sage: G = DiGraph([[t,t]], loops=True)
>>>>>>>>>>>>> sage: G.set_latex_options(format="dot2tex") #
>>>>>>>>>>>>> <======
>>>>>>>>>>>>> sage: view(G)
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>> Nicolas
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Nicolas M. Thiéry "Isil" <[email protected]>
>>>>>>>>>>>>> http://Nicolas.Thiery.name/
>>>>>>>>>>>>>
>>>>>>>>>>>>
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