{"action":"closed","issue":{"url":"https://api.github.com/repos/merenlab/homebrew-anvio/issues/1","repository_url":"https://api.github.com/repos/merenlab/homebrew-anvio","labels_url":"https://api.github.com/repos/merenlab/homebrew-anvio/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/merenlab/homebrew-anvio/issues/1/comments","events_url":"https://api.github.com/repos/merenlab/homebrew-anvio/issues/1/events","html_url":"https://github.com/merenlab/homebrew-anvio/issues/1","id":332639317,"node_id":"MDU6SXNzdWUzMzI2MzkzMTc=","number":1,"title":"Linuxbrew installation of Anvio (issues with Pip)","user":{"login":"PlantDr430","id":29610303,"node_id":"MDQ6VXNlcjI5NjEwMzAz","avatar_url":"https://avatars3.githubusercontent.com/u/29610303?v=4","gravatar_id":"","url":"https://api.github.com/users/PlantDr430","html_url":"https://github.com/PlantDr430","followers_url":"https://api.github.com/users/PlantDr430/followers","following_url":"https://api.github.com/users/PlantDr430/following{/other_user}","gists_url":"https://api.github.com/users/PlantDr430/gists{/gist_id}","starred_url":"https://api.github.com/users/PlantDr430/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PlantDr430/subscriptions","organizations_url":"https://api.github.com/users/PlantDr430/orgs","repos_url":"https://api.github.com/users/PlantDr430/repos","events_url":"https://api.github.com/users/PlantDr430/events{/privacy}","received_events_url":"https://api.github.com/users/PlantDr430/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-06-15T04:01:23Z","updated_at":"2018-06-19T16:56:26Z","closed_at":"2018-06-19T16:56:26Z","author_association":"NONE","body":"Hello,\r\nBelow is the error message I am getting after running the installing with linuxbrew. I tested \"brew doctor\" prior to installation and everything was ready to go. I then used the commands \"brew tap meren/anvio\" and then \"brew install anvio\". Everything was going great until the end.\r\n\r\n==> Installing merenlab/anvio/anvio\r\n==> Downloading https://files.pythonhosted.org/packages/63/75/3a79f2474b59bd7edd4485afb102\r\nAlready downloaded: /home/swyka430/.cache/Homebrew/anvio-4.tar.gz\r\n==> Downloading https://files.pythonhosted.org/packages/33/bc/fa0b5347139cd9564f0d44ebd2b1\r\nAlready downloaded: /home/swyka430/.cache/Homebrew/anvio--homebrew-virtualenv-16.0.0.tar.gz\r\n==> python3 -c import setuptools... --no-user-cfg install --prefix=/tmp/anvio--homebrew-vi\r\n==> python3 -s /tmp/anvio--homebrew-virtualenv-20180614-27256-zfmt3w/target/bin/virtualenv\r\n==> Downloading https://files.pythonhosted.org/packages/bd/99/04dc59ced52a8261ee0f965a8968\r\nAlready downloaded: /home/swyka430/.cache/Homebrew/anvio--bottle-0.12.13.tar.gz\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\n==> Downloading https://files.pythonhosted.org/packages/be/70/16cdd6c5ef799b2db2af4fd5f972\r\nAlready downloaded: /home/swyka430/.cache/Homebrew/anvio--pysam-0.11.1.tar.gz\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\n==> Downloading https://files.pythonhosted.org/packages/21/17/3c49b7fafe10ed63bb7904ebf976\r\n################################################################################### 100.0%\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\n==> Downloading https://files.pythonhosted.org/packages/f5/2c/5edf2488897cad4fb8c4ace86369\r\n################################################################################### 100.0%\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\n==> Downloading https://files.pythonhosted.org/packages/21/eb/534ac46e63c51eabbfc768d8c11c\r\n################################################################################### 100.0%\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\n==> Downloading https://files.pythonhosted.org/packages/b7/67/7e2a817f9e9c773ee3995c1e1520\r\n################################################################################### 100.0%\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\n==> Downloading https://files.pythonhosted.org/packages/22/82/64dada5382a60471f85f16eb7d01\r\n################################################################################### 100.0%\r\n==> /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/pip install -v --no-deps --no-bi\r\nLast 15 lines from /home/swyka430/.cache/Homebrew/Logs/anvio/09.pip:\r\n  Removing source in /tmp/pip-req-build-kz6kcjud\r\nCommand \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/python3.6 -u -c \"import setuptools, tokenize;__file__='/tmp/pip-req-build-kz6kcjud/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))\" install --record /tmp/pip-record-z4oowrp2/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/include/site/python3.6/h5py\" failed with error code 1 in /tmp/pip-req-build-kz6kcjud/\r\nException information:\r\nTraceback (most recent call last):\r\n  File \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/lib/python3.6/site-packages/pip/_internal/basecommand.py\", line 228, in main\r\n    status = self.run(options, args)\r\n  File \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/lib/python3.6/site-packages/pip/_internal/commands/install.py\", line 335, in run\r\n    use_user_site=options.use_user_site,\r\n  File \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/lib/python3.6/site-packages/pip/_internal/req/__init__.py\", line 49, in install_given_reqs\r\n    **kwargs\r\n  File \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/lib/python3.6/site-packages/pip/_internal/req/req_install.py\", line 779, in install\r\n    spinner=spinner,\r\n  File \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/lib/python3.6/site-packages/pip/_internal/utils/misc.py\", line 698, in call_subprocess\r\n    % (command_desc, proc.returncode, cwd))\r\npip._internal.exceptions.InstallationError: Command \"/home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/bin/python3.6 -u -c \"import setuptools, tokenize;__file__='/tmp/pip-req-build-kz6kcjud/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))\" install --record /tmp/pip-record-z4oowrp2/install-record.txt --single-version-externally-managed --compile --install-headers /home/linuxbrew/.linuxbrew/Cellar/anvio/4/libexec/include/site/python3.6/h5py\" failed with error code 1 in /tmp/pip-req-build-kz6kcjud/\r\n\r\nI tried to run the test \"anvi-self-test --suite mini\" and I get a command not found error. \r\n\r\nswyka430@swyka430-HP-ENVY-x360-Convertible-15-bq1xx:/home$ anvi-self-test --suite mini\r\nanvi-self-test: command not found\r\n\r\nI am using a fresh install of Ubuntu 18.04 \r\n\r\nHere are the 09.pip log file \r\n\r\n[09.pip.cc.txt](https://github.com/merenlab/homebrew-anvio/files/2104745/09.pip.cc.txt)\r\n[09.pip.txt](https://github.com/merenlab/homebrew-anvio/files/2104746/09.pip.txt)\r\n"}}
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