{"action":"opened","issue":{"url":"https://api.github.com/repos/joey711/biom/issues/16","labels_url":"https://api.github.com/repos/joey711/biom/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/joey711/biom/issues/16/comments","events_url":"https://api.github.com/repos/joey711/biom/issues/16/events","html_url":"https://github.com/joey711/biom/issues/16","id":89084992,"number":16,"title":"Biom install issue with numpy on Mac OsX 10.10.3","user":{"login":"braukmann","id":12940513,"avatar_url":"https://avatars.githubusercontent.com/u/12940513?v=3","gravatar_id":"","url":"https://api.github.com/users/braukmann","html_url":"https://github.com/braukmann","followers_url":"https://api.github.com/users/braukmann/followers","following_url":"https://api.github.com/users/braukmann/following{/other_user}","gists_url":"https://api.github.com/users/braukmann/gists{/gist_id}","starred_url":"https://api.github.com/users/braukmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/braukmann/subscriptions","organizations_url":"https://api.github.com/users/braukmann/orgs","repos_url":"https://api.github.com/users/braukmann/repos","events_url":"https://api.github.com/users/braukmann/events{/privacy}","received_events_url":"https://api.github.com/users/braukmann/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-06-17T18:04:52Z","updated_at":"2015-06-17T18:04:52Z","closed_at":null,"body":"I recently tried installing qiime on my mac using pip.  I received the following error when trying to install qiime:\r\n\r\n    building 'biom._filter' extension\r\n    creating build/temp.macosx-10.10-x86_64-2.7\r\n    creating build/temp.macosx-10.10-x86_64-2.7/biom\r\n    clang -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy/core/include/numpy -I/usr/local/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c biom/_filter.c -o build/temp.macosx-10.10-x86_64-2.7/biom/_filter.o\r\n    biom/_filter.c:258:10: fatal error: 'numpy/arrayobject.h' file not found\r\n    #include \"numpy/arrayobject.h\"\r\n             ^\r\n    1 error generated.\r\n    error: command 'clang' failed with exit status 1\r\n    \r\n    ----------------------------------------\r\nCommand \"/usr/local/opt/python/bin/python2.7 -c \"import setuptools, tokenize;__file__='/private/var/folders/dd/ymw96sls33lc2pzwtyw3hcn80000gp/T/pip-build-9s6Bz1/biom-format/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))\" install --record /var/folders/dd/ymw96sls33lc2pzwtyw3hcn80000gp/T/pip-reWvgX-record/install-record.txt --single-version-externally-managed --compile\" failed with error code 1 in /private/var/folders/dd/ymw96sls33lc2pzwtyw3hcn80000gp/T/pip-build-9s6Bz1/biom-format\r\n\r\nIt appears that the headers for numpy cannot be located properly and when I tried adding the using CFlags or the following command:\r\n\r\nsudo ln -s /usr/local/lib/python2.7/site-packages/numpy/core/include/numpy\r\n\r\nI have also tried installing reinstalling numpy using either homebrew or pip with little luck.\r\n\r\nThank you,\r\n\r\nThomas\r\n\r\n\r\n\r\n\r\n\r\n"}}