{"action":"created","issue":{"url":"https://api.github.com/repos/biopython/biopython/issues/1287","repository_url":"https://api.github.com/repos/biopython/biopython","labels_url":"https://api.github.com/repos/biopython/biopython/issues/1287/labels{/name}","comments_url":"https://api.github.com/repos/biopython/biopython/issues/1287/comments","events_url":"https://api.github.com/repos/biopython/biopython/issues/1287/events","html_url":"https://github.com/biopython/biopython/issues/1287","id":237051171,"node_id":"MDU6SXNzdWUyMzcwNTExNzE=","number":1287,"title":"gcc Error raised during installation","user":{"login":"jsolvason","id":29126182,"node_id":"MDQ6VXNlcjI5MTI2MTgy","avatar_url":"https://avatars0.githubusercontent.com/u/29126182?v=4","gravatar_id":"","url":"https://api.github.com/users/jsolvason","html_url":"https://github.com/jsolvason","followers_url":"https://api.github.com/users/jsolvason/followers","following_url":"https://api.github.com/users/jsolvason/following{/other_user}","gists_url":"https://api.github.com/users/jsolvason/gists{/gist_id}","starred_url":"https://api.github.com/users/jsolvason/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsolvason/subscriptions","organizations_url":"https://api.github.com/users/jsolvason/orgs","repos_url":"https://api.github.com/users/jsolvason/repos","events_url":"https://api.github.com/users/jsolvason/events{/privacy}","received_events_url":"https://api.github.com/users/jsolvason/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2017-06-19T23:25:15Z","updated_at":"2018-12-10T02:43:48Z","closed_at":"2017-06-21T11:00:41Z","author_association":"NONE","body":"I am following the instructions on installing biopython [here](http://biopython.org/wiki/Download). After unzipping, cding into the folder and typing `python setup.py build` the following error is raised:\r\n\r\n```\r\ngcc: error: unrecognized command line option ‘-Qunused-arguments’; did you mean ‘-Wunused-argument’?\r\ngcc: error: unrecognized command line option ‘-Qunused-arguments’; did you mean ‘-Wunused-argument’?\r\nerror: command 'gcc' failed with exit status 1\r\n```\r\n\r\nI have also tried installing with pip, but the following error was raised:\r\n\r\n`failed building wheel for biopython`\r\n\r\nand\r\n\r\n`Command \"/Users/josephsolvason/miniconda3/bin/python -u -c \"import setuptools, tokenize;__file__='/private/var/folders/98/hln2y055423b7bktpx2m_nb40000gn/T/pip-build-dbc_20t2/biopython/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))\" install --record /var/folders/98/hln2y055423b7bktpx2m_nb40000gn/T/pip-qvap070g-record/install-record.txt --single-version-externally-managed --compile\" failed with error code 1 in /private/var/folders/98/hln2y055423b7bktpx2m_nb40000gn/T/pip-build-dbc_20t2/biopython/`\r\n\r\nThoughts?"},"comment":{"url":"https://api.github.com/repos/biopython/biopython/issues/comments/445638754","html_url":"https://github.com/biopython/biopython/issues/1287#issuecomment-445638754","issue_url":"https://api.github.com/repos/biopython/biopython/issues/1287","id":445638754,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NTYzODc1NA==","user":{"login":"mnmelo","id":11721337,"node_id":"MDQ6VXNlcjExNzIxMzM3","avatar_url":"https://avatars1.githubusercontent.com/u/11721337?v=4","gravatar_id":"","url":"https://api.github.com/users/mnmelo","html_url":"https://github.com/mnmelo","followers_url":"https://api.github.com/users/mnmelo/followers","following_url":"https://api.github.com/users/mnmelo/following{/other_user}","gists_url":"https://api.github.com/users/mnmelo/gists{/gist_id}","starred_url":"https://api.github.com/users/mnmelo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mnmelo/subscriptions","organizations_url":"https://api.github.com/users/mnmelo/orgs","repos_url":"https://api.github.com/users/mnmelo/repos","events_url":"https://api.github.com/users/mnmelo/events{/privacy}","received_events_url":"https://api.github.com/users/mnmelo/received_events","type":"User","site_admin":false},"created_at":"2018-12-10T02:43:48Z","updated_at":"2018-12-10T02:43:48Z","author_association":"NONE","body":"I got this error installing on MacOS 10.13.6 and was able to track it to the [compiler version check](https://github.com/biopython/biopython/blob/b1e33b9d7c619dd122bd7e1d6337455273194602/setup.py#L85) in `setup.py`.\r\n\r\nThat check, which reads the output of `cc -v`, ignores environment flags like `$CC`, which will later be used to decide the compiler. In my mac `cc` is the OS-distributed clang, whereas `$CC` is `gcc-7` via Homebrew.\r\n\r\nI opened a [PR in MDAnalysis](https://github.com/MDAnalysis/mdanalysis/pull/2163), which gave me similar problems, where `setup.py` now uses a combination of `distutils`' `new_compiler()` and `customize_compiler()` to get the compiler that'll be used for building. If biopython can use `distutils` at setup-time this might be a good thing to implement. Otherwise, perhaps directly check environment vars?"}}
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