{"action":"closed","issue":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/2883","labels_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/2883/labels{/name}","comments_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/2883/comments","events_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/2883/events","html_url":"https://github.com/Homebrew/homebrew-science/issues/2883","id":111270138,"number":2883,"title":"During gubbins install, does not realize that numpy is already installed","user":{"login":"christianparobek","id":2909204,"avatar_url":"https://avatars.githubusercontent.com/u/2909204?v=3","gravatar_id":"","url":"https://api.github.com/users/christianparobek","html_url":"https://github.com/christianparobek","followers_url":"https://api.github.com/users/christianparobek/followers","following_url":"https://api.github.com/users/christianparobek/following{/other_user}","gists_url":"https://api.github.com/users/christianparobek/gists{/gist_id}","starred_url":"https://api.github.com/users/christianparobek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/christianparobek/subscriptions","organizations_url":"https://api.github.com/users/christianparobek/orgs","repos_url":"https://api.github.com/users/christianparobek/repos","events_url":"https://api.github.com/users/christianparobek/events{/privacy}","received_events_url":"https://api.github.com/users/christianparobek/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-13T21:01:12Z","updated_at":"2015-10-14T01:41:53Z","closed_at":"2015-10-14T01:41:53Z","body":"Hi there,\r\nI've been working on this all day and haven't found any guidance on this online, so opening an issue. I'm trying to install [gubbins](http://sanger-pathogens.github.io/gubbins/) using `linuxbrew` in an Ubuntu 14.04 system. As far as I can tell, `numpy` is correctly installed and importable into python2 and python3, but keep getting the following error:\r\n\r\n```\r\nchristian@juliano:~$ brew list\r\nautoconf  check   fasttree  gdbm  libpng   libtool\tm4\t    ncurses  openssl  pkg-config  python3  readline  unzip  xz\r\nautomake  fastml  freetype  jpeg  libtiff  little-cms2\tmakedepend  numpy    pillow   python\t  raxml    sqlite    webp   zlib\r\nchristian@juliano:~$ \r\nchristian@juliano:~$ \r\nchristian@juliano:~$ brew install gubbins\r\n==> Installing gubbins from homebrew/homebrew-science\r\n==> Using a fortran compiler found at /usr/bin/gfortran.\r\nThis may be changed by setting the FC environment variable.\r\n==> Downloading https://github.com/sanger-pathogens/gubbins/archive/v1.4.1.tar.gz\r\nAlready downloaded: /home/christian/.cache/Homebrew/gubbins-1.4.1.tar.gz\r\n==> Downloading https://pypi.python.org/packages/source/n/nose/nose-1.3.7.tar.gz\r\nAlready downloaded: /home/christian/.cache/Homebrew/gubbins--nose-1.3.7.tar.gz\r\n==> python3 -c import setuptools... --no-user-cfg install --prefix=/home/christian/.linuxbrew/Cellar/gubbins/1.4.1_1/libexec/vendor --single-v\r\n==> Downloading https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz\r\nAlready downloaded: /home/christian/.cache/Homebrew/gubbins--biopython-1.65.tar.gz\r\n==> python3 -c import setuptools... --no-user-cfg install --prefix=/home/christian/.linuxbrew/Cellar/gubbins/1.4.1_1/libexec/vendor --single-v\r\nLast 15 lines from /home/christian/.cache/Homebrew/Logs/gubbins/02.python3:\r\n--prefix=/home/christian/.linuxbrew/Cellar/gubbins/1.4.1_1/libexec/vendor\r\n--single-version-externally-managed\r\n--record=installed.txt\r\n\r\nrunning install\r\n\r\nNumerical Python (NumPy) is not installed.\r\n\r\nThis package is required for many Biopython features.  Please install\r\nit before you install Biopython. You can install Biopython anyway, but\r\nanything dependent on NumPy will not work. If you do this, and later\r\ninstall NumPy, you should then re-install Biopython.\r\n\r\nYou can find NumPy at http://www.numpy.org\r\n\r\n\r\nREAD THIS: https://github.com/Homebrew/linuxbrew/blob/master/share/doc/homebrew/Troubleshooting.md#troubleshooting\r\nIf reporting this issue please do so at (not Homebrew/homebrew):\r\n  https://github.com/homebrew/homebrew-science/issues\r\n```  \r\n\r\nAs you can see, `python3` and `numpy` are already installed - in fact , when I open an interactive `python3` session, I can `import numpy` no problem. Despite this, `brew` for some reasson thinks that `numpy` is not installed. I've tried ever combination of uninstalling / installing `python3`, `numpy`, and `biopython` I could think of, but still getting same error, so opening an issue. \r\n\r\nThanks for your help - "}}