{"action":"created","issue":{"url":"https://api.github.com/repos/pyenv/pyenv/issues/772","repository_url":"https://api.github.com/repos/pyenv/pyenv","labels_url":"https://api.github.com/repos/pyenv/pyenv/issues/772/labels{/name}","comments_url":"https://api.github.com/repos/pyenv/pyenv/issues/772/comments","events_url":"https://api.github.com/repos/pyenv/pyenv/issues/772/events","html_url":"https://github.com/pyenv/pyenv/issues/772","id":194359416,"node_id":"MDU6SXNzdWUxOTQzNTk0MTY=","number":772,"title":"pyenv in combination with anaconda breaks calls to basic functions [$10]","user":{"login":"Jeremias-Brand","id":7797940,"node_id":"MDQ6VXNlcjc3OTc5NDA=","avatar_url":"https://avatars2.githubusercontent.com/u/7797940?v=4","gravatar_id":"","url":"https://api.github.com/users/Jeremias-Brand","html_url":"https://github.com/Jeremias-Brand","followers_url":"https://api.github.com/users/Jeremias-Brand/followers","following_url":"https://api.github.com/users/Jeremias-Brand/following{/other_user}","gists_url":"https://api.github.com/users/Jeremias-Brand/gists{/gist_id}","starred_url":"https://api.github.com/users/Jeremias-Brand/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Jeremias-Brand/subscriptions","organizations_url":"https://api.github.com/users/Jeremias-Brand/orgs","repos_url":"https://api.github.com/users/Jeremias-Brand/repos","events_url":"https://api.github.com/users/Jeremias-Brand/events{/privacy}","received_events_url":"https://api.github.com/users/Jeremias-Brand/received_events","type":"User","site_admin":false},"labels":[{"id":1238105429,"node_id":"MDU6TGFiZWwxMjM4MTA1NDI5","url":"https://api.github.com/repos/pyenv/pyenv/labels/area:%20shims","name":"area: shims","color":"006b75","default":false},{"id":152630340,"node_id":"MDU6TGFiZWwxNTI2MzAzNDA=","url":"https://api.github.com/repos/pyenv/pyenv/labels/bounty","name":"bounty","color":"129e5e","default":false},{"id":397065397,"node_id":"MDU6TGFiZWwzOTcwNjUzOTc=","url":"https://api.github.com/repos/pyenv/pyenv/labels/impl:%20anaconda","name":"impl: anaconda","color":"bfd4f2","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-12-08T15:08:06Z","updated_at":"2019-03-06T01:46:35Z","closed_at":null,"author_association":"NONE","body":"Working on cent OS 6.\r\nI installed anaconda3-4.1.1 through pyenv.\r\nNow when I am not in anaconda calling functions contained in anaconda will cause an error:\r\n\r\n```\r\n$ clear\r\npyenv: clear: command not found\r\n\r\nThe `clear' command exists in these Python versions:\r\n  anaconda3-4.1.1\r\n```\r\nNow I don't even know why anaconda would have its own clear command but that is beside the point. The problem also occurs with user installed functions.\r\n\r\n```\r\n$ TransDecoder.LongOrfs\r\npyenv: TransDecoder.LongOrfs: command not found\r\n\r\nThe `TransDecoder.LongOrfs' command exists in these Python versions:\r\n  anaconda3-4.1.1\r\n\r\n```\r\nI have Transdecoder installed manually and in my path. \r\n\r\nHere are the relevant lines of my .bash_profile in case that is any help:\r\n\r\n ```\r\n# Get the aliases and functions\r\nif [ -f ~/.bashrc ]; then\r\n>---. ~/.bashrc\r\nfi\r\n\r\n\r\n# User specific environment and startup programs\r\nexport PYENV_ROOT=/home/jeremias/.linuxbrew/var/pyenv\r\n# insert shims for pyenv in front of path\r\nPATH=\"$HOME/.pyenv/shims:$PATH\"\r\n\r\nPATH=\"/usr/bin/R:/opt/bib/active/bin:$PATH\"\r\n\r\nPATH=\"$HOME/.linuxbrew/bin:$PATH\"\r\nPATH=\"$HOME/.linuxbrew/sbin:$PATH\"\r\n\r\n\r\nexport MANPATH=\"$HOME/.linuxbrew/share/man:$MANPATH\"\r\nexport INFOPATH=\"$HOME/.linuxbrew/share/info:$INFOPATH\"\r\n\r\n#####################################################################################\r\n\r\nPATH=\"$PATH:$HOME/soft/last-658/src:/home/jeremias/soft/TransDecoder-2.0.1:/home/jeremias/soft/BUSCO_v1.1b1\"\r\nPATH=\"$PATH:$HOME/soft/EMBOSS/bin\"\r\nPATH=\"$PATH:$HOME/soft/hmmer-3.1b2-linux-intel-x86_64/binaries\"\r\nPATH=\"$PATH:$HOME/soft/transrate-1.0.2-linux-x86_64\"\r\nPATH=\"$PATH:$HOME/soft/Solexa\"\r\nPATH=\"$PATH:$HOME/soft/sqlite-autoconf-3150100\"\r\nPATH=\"$PATH:$HOME/soft/tmhmm-2.0c/bin\"\r\nPATH=\"$PATH:$HOME/soft/signalp-4.1\"\r\nPATH=\"$PATH:$HOME/soft/rnammer\"\r\nPATH=\"$PATH:$HOME/soft/Trinotate-3.0.1\"\r\nPATH=\"$PATH:$HOME/soft/Trinotate-3.0.1/util/rnammer_support\"\r\nPATH=\"$PATH:$HOME/soft/Trinotate-3.0.1/auto\"\r\nPATH=\"$PATH:$HOME/soft/rcorrector\"\r\n#PATH=\"$PATH:$HOME/soft/Trinotate-3.0.1\" Export the entier PATH\r\nexport PATH=$PATH\r\n\r\n# apparently this should be last\r\nif which pyenv > /dev/null; then eval \"$(pyenv init -)\"; fi\r\neval \"$(pyenv virtualenv-init -)\"\r\nsource /home/jeremias/perl5/perlbrew/etc/bashrc\r\n\r\n```\r\n\r\nAny help would really be appreciated.\r\n\r\n\r\n<bountysource-plugin>\r\n---\r\nThere is a **[$10 open bounty](https://www.bountysource.com/issues/39861664-pyenv-in-combination-with-anaconda-breaks-calls-to-basic-functions?utm_campaign=plugin&utm_content=tracker%2F282009&utm_medium=issues&utm_source=github)** on this issue. Add to the bounty at [Bountysource](https://www.bountysource.com/?utm_campaign=plugin&utm_content=tracker%2F282009&utm_medium=issues&utm_source=github).\r\n</bountysource-plugin>"},"comment":{"url":"https://api.github.com/repos/pyenv/pyenv/issues/comments/469932777","html_url":"https://github.com/pyenv/pyenv/issues/772#issuecomment-469932777","issue_url":"https://api.github.com/repos/pyenv/pyenv/issues/772","id":469932777,"node_id":"MDEyOklzc3VlQ29tbWVudDQ2OTkzMjc3Nw==","user":{"login":"chrahunt","id":2312275,"node_id":"MDQ6VXNlcjIzMTIyNzU=","avatar_url":"https://avatars2.githubusercontent.com/u/2312275?v=4","gravatar_id":"","url":"https://api.github.com/users/chrahunt","html_url":"https://github.com/chrahunt","followers_url":"https://api.github.com/users/chrahunt/followers","following_url":"https://api.github.com/users/chrahunt/following{/other_user}","gists_url":"https://api.github.com/users/chrahunt/gists{/gist_id}","starred_url":"https://api.github.com/users/chrahunt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrahunt/subscriptions","organizations_url":"https://api.github.com/users/chrahunt/orgs","repos_url":"https://api.github.com/users/chrahunt/repos","events_url":"https://api.github.com/users/chrahunt/events{/privacy}","received_events_url":"https://api.github.com/users/chrahunt/received_events","type":"User","site_admin":false},"created_at":"2019-03-06T01:46:35Z","updated_at":"2019-03-06T01:46:35Z","author_association":"MEMBER","body":"Personally I use pyenv as a Python version manager, symlinking `~/bin/python` to `~/.pyenv/shims/python` and keeping `~/bin` on my `PATH` (not `~/.pyenv/shims`). Virtual environments provide all utilities and are activated as-needed.\r\n\r\nIt could save some grief if the shims were opt-in or maybe provided as a plugin, but that's probably just adding an extra step for the large population of users that actually use them."}}
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