{"action":"created","issue":{"url":"https://api.github.com/repos/tomopy/tomopy/issues/65","labels_url":"https://api.github.com/repos/tomopy/tomopy/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/tomopy/tomopy/issues/65/comments","events_url":"https://api.github.com/repos/tomopy/tomopy/issues/65/events","html_url":"https://github.com/tomopy/tomopy/issues/65","id":54916216,"number":65,"title":"build tomopy with Anaconda Python?","user":{"login":"prjemian","id":2279984,"avatar_url":"https://avatars.githubusercontent.com/u/2279984?v=3","gravatar_id":"","url":"https://api.github.com/users/prjemian","html_url":"https://github.com/prjemian","followers_url":"https://api.github.com/users/prjemian/followers","following_url":"https://api.github.com/users/prjemian/following{/other_user}","gists_url":"https://api.github.com/users/prjemian/gists{/gist_id}","starred_url":"https://api.github.com/users/prjemian/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/prjemian/subscriptions","organizations_url":"https://api.github.com/users/prjemian/orgs","repos_url":"https://api.github.com/users/prjemian/repos","events_url":"https://api.github.com/users/prjemian/events{/privacy}","received_events_url":"https://api.github.com/users/prjemian/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/tomopy/tomopy/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-01-20T17:53:25Z","updated_at":"2015-01-20T22:56:45Z","closed_at":null,"body":"Is it possible to build tomopy using Anaconda Python (from http://continuuum.io)?"},"comment":{"url":"https://api.github.com/repos/tomopy/tomopy/issues/comments/70751962","html_url":"https://github.com/tomopy/tomopy/issues/65#issuecomment-70751962","issue_url":"https://api.github.com/repos/tomopy/tomopy/issues/65","id":70751962,"user":{"login":"gazzar","id":131836,"avatar_url":"https://avatars.githubusercontent.com/u/131836?v=3","gravatar_id":"","url":"https://api.github.com/users/gazzar","html_url":"https://github.com/gazzar","followers_url":"https://api.github.com/users/gazzar/followers","following_url":"https://api.github.com/users/gazzar/following{/other_user}","gists_url":"https://api.github.com/users/gazzar/gists{/gist_id}","starred_url":"https://api.github.com/users/gazzar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gazzar/subscriptions","organizations_url":"https://api.github.com/users/gazzar/orgs","repos_url":"https://api.github.com/users/gazzar/repos","events_url":"https://api.github.com/users/gazzar/events{/privacy}","received_events_url":"https://api.github.com/users/gazzar/received_events","type":"User","site_admin":false},"created_at":"2015-01-20T22:56:45Z","updated_at":"2015-01-20T22:56:45Z","body":"Oops, just noticed there should be a line in the dataexchange instructions:\r\n\r\n# fails complaining cannot find lex utility, but it's part of flex, so\r\n$ sudo apt-get install flex\r\n\r\n\r\n\r\nOn 21 January 2015 at 09:53, gary ruben <gary.ruben@gmail.com> wrote:\r\n\r\n> I did this a couple of days ago. Here is a personal build log. I've also\r\n> included my build log for dataexchange.\r\n>\r\n> Gary\r\n>\r\n> This is in my Linux Mint VM.\r\n>\r\n> Install Python dependencies\r\n>\r\n> $ conda install pillow\r\n> $ pip install PyWavelets\r\n>\r\n>\r\n> Install TomoPy\r\n>\r\n> $ cd git-repos\r\n> $ git clone https://github.com/tomopy/tomopy\r\n> $ cd tomopy\r\n> $ sudo python install.py --boost --fftw            # Install fftw and Boost. Get a coffee while these install.\r\n> $ export LD_LIBRARY_PATH=/usr/local/lib\r\n> $ export C_INCLUDE_PATH=/usr/local/include/boost:/usr/local/include\r\n> $ sudo python setup.py install\r\n>\r\n>\r\n> Append to ~/.bashrc this, or updated path if egg name changes:\r\n>\r\n> # Added by me on 20150116 as part of tomopy installation\r\n> export LD_LIBRARY_PATH=~/anaconda/lib/python2.7/site-packages/tomopy-0.0.3-py2.7-linux-x86_64.egg/tomopy/lib:/usr/local/lib\r\n> export C_INCLUDE_PATH=/usr/local/include/boost:/usr/local/include\r\n>\r\n> Make it so\r\n> $ source ~/.bashrc\r\n>\r\n>\r\n> Attempting to import tomopy now results in a glibc compatibility error.\r\n> Here are the last few lines of the traceback in my virtualbox installation,\r\n> where the user is adminuser instead of gary:\r\n>\r\n> /home/adminuser/anaconda/lib/python2.7/ctypes/__init__.pyc in __init__(self, name, mode, handle, use_errno, use_last_error)\r\n>     363\r\n>     364         if handle is None:\r\n> --> 365             self._handle = _dlopen(self._name, mode)\r\n>     366         else:\r\n>     367             self._handle = handle\r\n>\r\n> OSError: /home/adminuser/anaconda/bin/../lib/libm.so.6: version `GLIBC_2.15' not found (required by /usr/local/lib/libfftw3f.so.3)\r\n>\r\n>\r\n> Doga found the solution to this for me a while back:\r\n>\r\n> \"Your source of your problem looks like an fftw import problem. Could you try to remove the soft link which points libm.so.6→libm-2.5.so <http://libm.so.xn--6libm-2-ek9c.5.so> in your $ANACONDA_DIR/lib. According to some discussions in the forums this seems to be a solution for your problem.\"\r\n>\r\n> So\r\n>\r\n> $ cd ~/anaconda/lib\r\n> $ unlink libm.so.6\r\n>\r\n> import tomopy now succeeds without error!\r\n>\r\n> That was the easy part. Now, if you want to build dataexchange, it gets a\r\n> little trickier. This is pretty messy, so read through it and maybe try it\r\n> yourself in a more sensible order:\r\n>\r\n> # install ez_setup\r\n> $ pip install ez_setup\r\n>\r\n> # install conda build environment for pyhdf\r\n> $ conda install conda-build\r\n>\r\n> # pyhdf already has a build recipe\r\n> $ cd ~/git-repos/\r\n> $ git clone https://github.com/conda/conda-recipes\r\n>\r\n> # build pyhdf\r\n> $ conda build pyhdf\r\n> # fails complaining can't find yacc, but it's part of bison, so\r\n> $ sudo apt-get install bison\r\n> $ conda build pyhdf\r\n> # fails complaining cannot find lex utility, but it's part of flex, so\r\n> $ conda build pyhdf\r\n> # error: couldn't find zlib library\r\n> $ sudo apt-get install zlib1g-dev\r\n> # error: couldn't find jpeg library\r\n> $ sudo apt-get install libjpeg8-dev\r\n> $ conda build pyhdf\r\n> $ conda install --use-local pyhdf\r\n>\r\n> # success! upload to binstar to share the love:\r\n> $ binstar upload /home/adminuser/anaconda/conda-bld/linux-64/pyhdf-0.8.3-np19py27_0.tar.bz2\r\n>\r\n> # Apparently nor success yet, as we need netCDF4; install it\r\n> $ conda install netCDF4\r\n>\r\n> # Then I think I broke h5py because import h5py caused an importerror:\r\n> # ImportError: libhdf5.so.8: cannot open shared object file: No such file or directory\r\n> # so\r\n> $ conda update h5py\r\n>\r\n> # Then build data-exchange\r\n> $ python setup.py install\r\n>\r\n> # Success! Apparently.\r\n>\r\n>\r\n>\r\n> On 21 January 2015 at 05:01, Doga Gursoy <notifications@github.com> wrote:\r\n>\r\n>> I think only PyWavelets package is not included in Anaconda distributions.\r\n>>\r\n>> —\r\n>> Reply to this email directly or view it on GitHub\r\n>> <https://github.com/tomopy/tomopy/issues/65#issuecomment-70700981>.\r\n>>\r\n>\r\n>"}}