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: >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> 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" <nth...@users.sf.net> >>>>>>>>>>>>>> http://Nicolas.Thiery.name/ >>>>>>>>>>>>>> >>>>>>>>>>>>> -- 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.
