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 >>>>>>>>>>>> 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:<blockquote class="gmail_quote" style="margin:0; >>>>>>>>>>>> >>>>>>>>>>> -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To post to this group, send email to sage-support@googlegroups.com. Visit this group at https://groups.google.com/group/sage-support. For more options, visit https://groups.google.com/d/optout.
