Please see https://trac.sagemath.org/ticket/23116 for another way to install dot2tex. Could you please do an experiment: on a fresh binary installation of sage on OSX, do, as in the link above
sage -pip install dot2tex and see if you get working crystals.* latex/view this way. On Saturday, June 3, 2017 at 10:44:41 PM UTC+1, Julie Beier wrote: > > Hi Dima, > > Thanks; I guess I just have to install from source.. I don't really know > what to do differently than what I've already done so I feel like I > basically just have to give up on it again. But thanks so much for all > your help. > > Julie > > On Saturday, June 3, 2017 at 4:27:40 PM UTC-4, Dima Pasechnik wrote: >> >> >> >> On Saturday, June 3, 2017 at 2:55:49 PM UTC+1, Julie Beier wrote: >>> >>> 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 >>> >> >> OK, this means that this binary installation of sage cannot properly >> install some, if not all, optional packages. >> (and "sage -b" might have broken sage installation, so that you might >> need to reinstall) >> >> The usual advice applies: build your sage from source... >> >> >> >>> >>> The checks still show false. >>> >> >> Do you mean that >> >> sage: have_dot2tex() >> >> returns False, right? >> >> How about >> >> sage: import dot2tex >> >> Does this work? >> >> >> Here's the dot2tex installation log: >>> >> >> Thanks. There are some warnings there that perhaps explain what exactly >> goes wrong, >> I am not sure. >> >> TLDR: sage thinks that the package is installed, based on values in some >> configuration files. >> But in fact it is broken. >> >> By the way, I have also noticed that many doctests for dot2tex also >> require graphviz, for a reason I don't understand. >> >> >> >>> >>> 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 d >>>>>>>>>>>>> >>>>>>>>>>>> -- You received this message because you are subscribed to the Google Groups "sage-support" group. 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