{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/poretools/issues/84","repository_url":"https://api.github.com/repos/arq5x/poretools","labels_url":"https://api.github.com/repos/arq5x/poretools/issues/84/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/poretools/issues/84/comments","events_url":"https://api.github.com/repos/arq5x/poretools/issues/84/events","html_url":"https://github.com/arq5x/poretools/issues/84","id":159543029,"number":84,"title":"docker build fails","user":{"login":"Jeltje","id":5482232,"avatar_url":"https://avatars.githubusercontent.com/u/5482232?v=3","gravatar_id":"","url":"https://api.github.com/users/Jeltje","html_url":"https://github.com/Jeltje","followers_url":"https://api.github.com/users/Jeltje/followers","following_url":"https://api.github.com/users/Jeltje/following{/other_user}","gists_url":"https://api.github.com/users/Jeltje/gists{/gist_id}","starred_url":"https://api.github.com/users/Jeltje/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Jeltje/subscriptions","organizations_url":"https://api.github.com/users/Jeltje/orgs","repos_url":"https://api.github.com/users/Jeltje/repos","events_url":"https://api.github.com/users/Jeltje/events{/privacy}","received_events_url":"https://api.github.com/users/Jeltje/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-06-10T01:35:41Z","updated_at":"2016-06-11T01:52:55Z","closed_at":null,"body":"I git cloned today, resulting in `commit 2552313547985c1c7ff52d4301e401f8bada3d13\r\n`\r\n`docker build -t poretools .`\r\nresulted in\r\n```\r\n============================================================================\r\n                        * The following required packages can not be built:\r\n                        * freetype\r\nerror: Setup script exited with 1\r\nThe command '/bin/sh -c cd /tmp/poretools && python setup.py install' returned a non-zero code: 1\r\n\r\n``` \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/arq5x/poretools/issues/comments/225330353","html_url":"https://github.com/arq5x/poretools/issues/84#issuecomment-225330353","issue_url":"https://api.github.com/repos/arq5x/poretools/issues/84","id":225330353,"user":{"login":"omsai","id":166624,"avatar_url":"https://avatars.githubusercontent.com/u/166624?v=3","gravatar_id":"","url":"https://api.github.com/users/omsai","html_url":"https://github.com/omsai","followers_url":"https://api.github.com/users/omsai/followers","following_url":"https://api.github.com/users/omsai/following{/other_user}","gists_url":"https://api.github.com/users/omsai/gists{/gist_id}","starred_url":"https://api.github.com/users/omsai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/omsai/subscriptions","organizations_url":"https://api.github.com/users/omsai/orgs","repos_url":"https://api.github.com/users/omsai/repos","events_url":"https://api.github.com/users/omsai/events{/privacy}","received_events_url":"https://api.github.com/users/omsai/received_events","type":"User","site_admin":false},"created_at":"2016-06-11T01:52:55Z","updated_at":"2016-06-11T01:52:55Z","body":"There's a numpy ABI runtime error with the Docker image:\r\n\r\n```python-traceback\r\n$ docker run -i poretools\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/poretools\", line 9, in <module>\r\n    load_entry_point('poretools==.0.5.1', 'console_scripts', 'poretools')()\r\n  File \"/usr/lib/python2.7/dist-packages/pkg_resources.py\", line 351, in load_entry_point\r\n    return get_distribution(dist).load_entry_point(group, name)\r\n  File \"/usr/lib/python2.7/dist-packages/pkg_resources.py\", line 2363, in load_entry_point\r\n    return ep.load()\r\n  File \"/usr/lib/python2.7/dist-packages/pkg_resources.py\", line 2088, in load\r\n    entry = __import__(self.module_name, globals(),globals(), ['__name__'])\r\n  File \"/usr/local/lib/python2.7/dist-packages/poretools-.0.5.1-py2.7.egg/poretools/__init__.py\", line 4, in <module>\r\n    from Fast5File import *\r\n  File \"/usr/local/lib/python2.7/dist-packages/poretools-.0.5.1-py2.7.egg/poretools/Fast5File.py\", line 6, in <module>\r\n    import h5py\r\n  File \"/usr/local/lib/python2.7/dist-packages/h5py/__init__.py\", line 34, in <module>\r\n    from ._conv import register_converters as _register_converters\r\n  File \"h5t.pxd\", line 14, in init h5py._conv (/tmp/pip_build_root/h5py/h5py/_conv.c:6880)\r\n  File \"numpy.pxd\", line 66, in init h5py.h5t (/tmp/pip_build_root/h5py/h5py/h5t.c:19113)\r\nValueError: numpy.dtype has the wrong size, try recompiling\r\n```\r\n\r\nThe numpy 1.8.2 upgrade to 1.11.0 is triggered when installing poretools' dependencies in `requirements.txt`.  Since `pip` builds all packages before attempting to install them, one would need to upgrade numpy before installing any numpy dependent packages to ensure they all use the same ABI.  One needs to use `easy_install` instead of `pip` to take precedence over the system numpy (see http://askubuntu.com/a/732371)."}}
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