{"action":"created","issue":{"url":"https://api.github.com/repos/stan-dev/pystan/issues/219","repository_url":"https://api.github.com/repos/stan-dev/pystan","labels_url":"https://api.github.com/repos/stan-dev/pystan/issues/219/labels{/name}","comments_url":"https://api.github.com/repos/stan-dev/pystan/issues/219/comments","events_url":"https://api.github.com/repos/stan-dev/pystan/issues/219/events","html_url":"https://github.com/stan-dev/pystan/issues/219","id":142776389,"number":219,"title":"distutils.errors.CompileError: command 'gcc' failed with exit status 1","user":{"login":"aeleuterio","id":11207474,"avatar_url":"https://avatars.githubusercontent.com/u/11207474?v=3","gravatar_id":"","url":"https://api.github.com/users/aeleuterio","html_url":"https://github.com/aeleuterio","followers_url":"https://api.github.com/users/aeleuterio/followers","following_url":"https://api.github.com/users/aeleuterio/following{/other_user}","gists_url":"https://api.github.com/users/aeleuterio/gists{/gist_id}","starred_url":"https://api.github.com/users/aeleuterio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aeleuterio/subscriptions","organizations_url":"https://api.github.com/users/aeleuterio/orgs","repos_url":"https://api.github.com/users/aeleuterio/repos","events_url":"https://api.github.com/users/aeleuterio/events{/privacy}","received_events_url":"https://api.github.com/users/aeleuterio/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-03-22T20:50:56Z","updated_at":"2016-03-23T18:43:43Z","closed_at":null,"body":"#### Summary:\r\nCompilation error on Pystan 2.9.0.0 with Stan 2.9.0.\r\n\r\n\r\n#### Description:\r\nI am running Pystan on a Linux environment with no internet connection, so I installed everything from source. I am running Python 2.7.7 and gcc 4.8.3. When trying to run the Eight Schools example, I get the output below.\r\nNotes: The same example runs on my RStan installation and on the previous Pystan installation (2.2.0.0). I have tried building Pystan and running the example with several different compilers. Also, another example (Neal Funnel) gives the same output.\r\nI have debugged the compilation down to the gcc call for the model but it was way over my head. My next steps were to install pieces separately (stan and stan_math) and no combination worked.\r\n\r\n\r\n#### Current Output:\r\n`\r\nINFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_95013624776d537c3cd7cd4d641c30e0 NOW.\r\nTraceback (most recent call last):\r\n  File \"eightschools.py\", line 33, in <module>\r\n    iter=1000, chains=4)\r\n  File \"/home/workgroups/reit/apps/python/2.7.7/pystan/2.9.0.0/lib/python2.7/site-packages/pystan/api.py\", line 368, in stan\r\n    verbose=verbose)\r\n  File \"/home/workgroups/reit/apps/python/2.7.7/pystan/2.9.0.0/lib/python2.7/site-packages/pystan/model.py\", line 312, in __init__\r\n    build_extension.run()\r\n  File \"/apps/python/2.7.7/lib/python2.7/distutils/command/build_ext.py\", line 337, in run\r\n    self.build_extensions()\r\n  File \"/apps/python/2.7.7/lib/python2.7/distutils/command/build_ext.py\", line 446, in build_extensions\r\n    self.build_extension(ext)\r\n  File \"/apps/python/2.7.7/lib/python2.7/distutils/command/build_ext.py\", line 496, in build_extension\r\n    depends=ext.depends)\r\n  File \"/apps/python/2.7.7/lib/python2.7/distutils/ccompiler.py\", line 574, in compile\r\n    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)\r\n  File \"/apps/python/2.7.7/lib/python2.7/distutils/unixccompiler.py\", line 122, in _compile\r\n    raise CompileError, msg\r\ndistutils.errors.CompileError: command 'gcc' failed with exit status 1`\r\n\r\n\r\n#### Expected Output:\r\n`INFO:pystan:COMPILING THE C++ CODE FOR MODEL anon_model_95013624776d537c3cd7cd4d641c30e0 NOW.\r\nINFO:pystan:NOW ON CHAIN 0\r\nINFO:pystan:NOW ON CHAIN 1\r\nINFO:pystan:NOW ON CHAIN 2\r\nINFO:pystan:NOW ON CHAIN 3\r\nIteration: 1000 / 1000 [100%]  (Sampling)\r\nElapsed Time: 0.01 seconds (Warm-up)\r\n              0.01 seconds (Sampling)\r\n              0.02 seconds (Total)\r\n\r\nIteration: 1000 / 1000 [100%]  (Sampling)\r\nElapsed Time: 0.01 seconds (Warm-up)\r\n              0.01 seconds (Sampling)\r\n              0.02 seconds (Total)\r\n\r\nIteration: 1000 / 1000 [100%]  (Sampling)\r\nElapsed Time: 0.01 seconds (Warm-up)\r\n              0.01 seconds (Sampling)\r\n              0.02 seconds (Total)\r\n\r\nIteration: 1000 / 1000 [100%]  (Sampling)\r\nElapsed Time: 0.01 seconds (Warm-up)\r\n              0.02 seconds (Sampling)\r\n              0.03 seconds (Total)`\r\n\r\n\r\n#### PyStan Version:\r\n2.9.0.0\r\n#### Python Version:\r\n2.7.7\r\n#### Operating System:\r\nCentOS\r\n\r\n\r\nThank you in advance\r\n"},"comment":{"url":"https://api.github.com/repos/stan-dev/pystan/issues/comments/200490052","html_url":"https://github.com/stan-dev/pystan/issues/219#issuecomment-200490052","issue_url":"https://api.github.com/repos/stan-dev/pystan/issues/219","id":200490052,"user":{"login":"aeleuterio","id":11207474,"avatar_url":"https://avatars.githubusercontent.com/u/11207474?v=3","gravatar_id":"","url":"https://api.github.com/users/aeleuterio","html_url":"https://github.com/aeleuterio","followers_url":"https://api.github.com/users/aeleuterio/followers","following_url":"https://api.github.com/users/aeleuterio/following{/other_user}","gists_url":"https://api.github.com/users/aeleuterio/gists{/gist_id}","starred_url":"https://api.github.com/users/aeleuterio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aeleuterio/subscriptions","organizations_url":"https://api.github.com/users/aeleuterio/orgs","repos_url":"https://api.github.com/users/aeleuterio/repos","events_url":"https://api.github.com/users/aeleuterio/events{/privacy}","received_events_url":"https://api.github.com/users/aeleuterio/received_events","type":"User","site_admin":false},"created_at":"2016-03-23T18:43:43Z","updated_at":"2016-03-23T18:43:43Z","body":"@ariddell You are correct, it was Cython. As soon as I loaded Cython 0.23.x it worked.\r\nI would also suggest to revise the documentation page; it says Cython >=0.19.\r\nThank you very much for you help"}}