{"action":"created","issue":{"url":"https://api.github.com/repos/PyTables/PyTables/issues/219","labels_url":"https://api.github.com/repos/PyTables/PyTables/issues/219/labels{/name}","comments_url":"https://api.github.com/repos/PyTables/PyTables/issues/219/comments","events_url":"https://api.github.com/repos/PyTables/PyTables/issues/219/events","html_url":"https://github.com/PyTables/PyTables/issues/219","id":12116780,"number":219,"title":"pip tables install fails, HDF5 library not found","user":{"login":"nehalecky","id":1455590,"avatar_url":"https://avatars.githubusercontent.com/u/1455590?v=3","gravatar_id":"","url":"https://api.github.com/users/nehalecky","html_url":"https://github.com/nehalecky","followers_url":"https://api.github.com/users/nehalecky/followers","following_url":"https://api.github.com/users/nehalecky/following{/other_user}","gists_url":"https://api.github.com/users/nehalecky/gists{/gist_id}","starred_url":"https://api.github.com/users/nehalecky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nehalecky/subscriptions","organizations_url":"https://api.github.com/users/nehalecky/orgs","repos_url":"https://api.github.com/users/nehalecky/repos","events_url":"https://api.github.com/users/nehalecky/events{/privacy}","received_events_url":"https://api.github.com/users/nehalecky/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PyTables/PyTables/labels/enhancement","name":"enhancement","color":"207de5"}],"state":"closed","locked":false,"assignee":{"login":"avalentino","id":614554,"avatar_url":"https://avatars.githubusercontent.com/u/614554?v=3","gravatar_id":"","url":"https://api.github.com/users/avalentino","html_url":"https://github.com/avalentino","followers_url":"https://api.github.com/users/avalentino/followers","following_url":"https://api.github.com/users/avalentino/following{/other_user}","gists_url":"https://api.github.com/users/avalentino/gists{/gist_id}","starred_url":"https://api.github.com/users/avalentino/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/avalentino/subscriptions","organizations_url":"https://api.github.com/users/avalentino/orgs","repos_url":"https://api.github.com/users/avalentino/repos","events_url":"https://api.github.com/users/avalentino/events{/privacy}","received_events_url":"https://api.github.com/users/avalentino/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/PyTables/PyTables/milestones/6","html_url":"https://github.com/PyTables/PyTables/milestones/3.1","labels_url":"https://api.github.com/repos/PyTables/PyTables/milestones/6/labels","id":310907,"number":6,"title":"3.1","description":"","creator":{"login":"avalentino","id":614554,"avatar_url":"https://avatars.githubusercontent.com/u/614554?v=3","gravatar_id":"","url":"https://api.github.com/users/avalentino","html_url":"https://github.com/avalentino","followers_url":"https://api.github.com/users/avalentino/followers","following_url":"https://api.github.com/users/avalentino/following{/other_user}","gists_url":"https://api.github.com/users/avalentino/gists{/gist_id}","starred_url":"https://api.github.com/users/avalentino/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/avalentino/subscriptions","organizations_url":"https://api.github.com/users/avalentino/orgs","repos_url":"https://api.github.com/users/avalentino/repos","events_url":"https://api.github.com/users/avalentino/events{/privacy}","received_events_url":"https://api.github.com/users/avalentino/received_events","type":"User","site_admin":false},"open_issues":0,"closed_issues":55,"state":"closed","created_at":"2013-04-14T17:18:56Z","updated_at":"2014-05-22T15:34:07Z","due_on":null,"closed_at":"2014-02-04T23:10:28Z"},"comments":28,"created_at":"2013-03-17T23:51:10Z","updated_at":"2015-12-22T17:03:13Z","closed_at":"2013-07-10T17:32:18Z","body":"Hi PyTables team,\r\n\r\nThanks for an awesome package, and apologies in advance if I am overlooking something simple.\r\n\r\nI've been trying install pytables via pip using `pip install tables`, however, it fails with an error `Could not find a local HDF5 installation.`:\r\n```\r\nDownloading/unpacking tables\r\n  Running setup.py egg_info for package tables\r\n    /tmp/H5closew4kVON.c:1:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]\r\n    main (int argc, char **argv) {\r\n    ^~~~\r\n    /tmp/H5closew4kVON.c:2:5: warning: implicit declaration of function 'H5close' is invalid in C99 [-Wimplicit-function-declaration]\r\n        H5close();\r\n        ^\r\n    2 warnings generated.\r\n    ld: library not found for -lhdf5\r\n    clang: error: linker command failed with exit code 1 (use -v to see invocation)\r\n    * Found numpy 1.7.0 package installed.\r\n    * Found numexpr 2.0.1 package installed.\r\n    * Found Cython 0.18 package installed.\r\n    ld: library not found for -lhdf5\r\n    clang: error: linker command failed with exit code 1 (use -v to see invocation)\r\n    .. ERROR:: Could not find a local HDF5 installation.\r\n       You may need to explicitly state where your local HDF5 headers and\r\n       library can be found by setting the ``HDF5_DIR`` environment\r\n       variable or by using the ``--hdf5`` command-line option.\r\n    Complete output from command python setup.py egg_info:\r\n    /tmp/H5closew4kVON.c:1:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]\r\n\r\nmain (int argc, char **argv) {\r\n\r\n^~~~\r\n\r\n/tmp/H5closew4kVON.c:2:5: warning: implicit declaration of function 'H5close' is invalid in C99 [-Wimplicit-function-declaration]\r\n\r\n    H5close();\r\n\r\n    ^\r\n\r\n2 warnings generated.\r\n\r\nld: library not found for -lhdf5\r\n\r\nclang: error: linker command failed with exit code 1 (use -v to see invocation)\r\n\r\n* Found numpy 1.7.0 package installed.\r\n\r\n* Found numexpr 2.0.1 package installed.\r\n\r\n* Found Cython 0.18 package installed.\r\n\r\nld: library not found for -lhdf5\r\n\r\nclang: error: linker command failed with exit code 1 (use -v to see invocation)\r\n\r\n.. ERROR:: Could not find a local HDF5 installation.\r\n\r\n   You may need to explicitly state where your local HDF5 headers and\r\n\r\n   library can be found by setting the ``HDF5_DIR`` environment\r\n\r\n   variable or by using the ``--hdf5`` command-line option.\r\n\r\n----------------------------------------\r\nCommand python setup.py egg_info failed with error code 1 in /tmp/pip-build/tables\r\nStoring complete log in /Users/nehalecky/.pip/pip.log\r\n```\r\n\r\nI do, however, have HDF5 installed via MacPorts, and can verify the installation with `port contents hdf5-18`:\r\n```\r\nPort hdf5-18 contains:\r\n  /opt/local/bin/gif2h5\r\n  /opt/local/bin/h52gif\r\n  /opt/local/bin/h5c++\r\n  /opt/local/bin/h5cc\r\n  /opt/local/bin/h5copy\r\n  /opt/local/bin/h5debug  \r\n...\r\n  /opt/local/include/H5ACpublic.h\r\n  /opt/local/include/H5AbstractDs.h\r\n  /opt/local/include/H5Apublic.h\r\n  /opt/local/include/H5ArrayType.h\r\n  /opt/local/include/H5AtomType.h\r\n...\r\n  /opt/local/lib/libhdf5.7.dylib\r\n  /opt/local/lib/libhdf5.a\r\n  /opt/local/lib/libhdf5.dylib\r\n  /opt/local/lib/libhdf5.la\r\n  /opt/local/lib/libhdf5.settings\r\n...\r\n```\r\nI've set env var `HDF5_DIR` in `.bash_profile` with  `export HDF5_DIR=/opt/local`, but still no love from the pytables installation. I've been searching the interwebs for a solution, and finally decided to ask the source. Any help with this would be much appreciated, and thank you for your time!"},"comment":{"url":"https://api.github.com/repos/PyTables/PyTables/issues/comments/166674373","html_url":"https://github.com/PyTables/PyTables/issues/219#issuecomment-166674373","issue_url":"https://api.github.com/repos/PyTables/PyTables/issues/219","id":166674373,"user":{"login":"danielsack","id":4267369,"avatar_url":"https://avatars.githubusercontent.com/u/4267369?v=3","gravatar_id":"","url":"https://api.github.com/users/danielsack","html_url":"https://github.com/danielsack","followers_url":"https://api.github.com/users/danielsack/followers","following_url":"https://api.github.com/users/danielsack/following{/other_user}","gists_url":"https://api.github.com/users/danielsack/gists{/gist_id}","starred_url":"https://api.github.com/users/danielsack/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/danielsack/subscriptions","organizations_url":"https://api.github.com/users/danielsack/orgs","repos_url":"https://api.github.com/users/danielsack/repos","events_url":"https://api.github.com/users/danielsack/events{/privacy}","received_events_url":"https://api.github.com/users/danielsack/received_events","type":"User","site_admin":false},"created_at":"2015-12-22T17:03:13Z","updated_at":"2015-12-22T17:03:13Z","body":"Not sure if this helps anyone, but I got around this by installing `hdf5` via homebrew with:\r\n\r\n```\r\nbrew update\r\nbrew tap homebrew/science\r\nbrew install hdf5\r\n```\r\n\r\nthen just `pip install --upgrade tables`"}}