{"action":"created","issue":{"url":"https://api.github.com/repos/google/deepvariant/issues/94","repository_url":"https://api.github.com/repos/google/deepvariant","labels_url":"https://api.github.com/repos/google/deepvariant/issues/94/labels{/name}","comments_url":"https://api.github.com/repos/google/deepvariant/issues/94/comments","events_url":"https://api.github.com/repos/google/deepvariant/issues/94/events","html_url":"https://github.com/google/deepvariant/issues/94","id":361100385,"node_id":"MDU6SXNzdWUzNjExMDAzODU=","number":94,"title":"protobuf error","user":{"login":"ramcn","id":2152628,"node_id":"MDQ6VXNlcjIxNTI2Mjg=","avatar_url":"https://avatars2.githubusercontent.com/u/2152628?v=4","gravatar_id":"","url":"https://api.github.com/users/ramcn","html_url":"https://github.com/ramcn","followers_url":"https://api.github.com/users/ramcn/followers","following_url":"https://api.github.com/users/ramcn/following{/other_user}","gists_url":"https://api.github.com/users/ramcn/gists{/gist_id}","starred_url":"https://api.github.com/users/ramcn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramcn/subscriptions","organizations_url":"https://api.github.com/users/ramcn/orgs","repos_url":"https://api.github.com/users/ramcn/repos","events_url":"https://api.github.com/users/ramcn/events{/privacy}","received_events_url":"https://api.github.com/users/ramcn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-09-18T01:20:17Z","updated_at":"2018-09-19T01:48:54Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI am facing the below error when running built_and_test.sh. I have protocol buf built and installed in my home directory.\r\n\r\n(19:11:12) ERROR: /uufs/chpc.utah.edu/common/home/u1142888/deepvariant/bazel_tmp/_bazel_u1142888/bc41070ad1d30708841b968fbd6bc540/external/com_google_protobuf/BUILD:104:1: C++ compilation of rule '@com_google_protobuf//:protobuf' failed (Exit 1): gcc failed: error executing command \r\n\r\nI have built the latest protobuf from source following the instructions [here](https://github.com/protocolbuffers/protobuf/blob/master/src/README.md) and have installed it under $HOME/protobuf and updated my PATH and LD_LIBRARY_PATH accordingly.\r\n\r\nLooking for some pointers on how to resolve this issue by tweaking the build procedure.\r\n\r\nThank  you,\r\nRam\r\n"},"comment":{"url":"https://api.github.com/repos/google/deepvariant/issues/comments/422619015","html_url":"https://github.com/google/deepvariant/issues/94#issuecomment-422619015","issue_url":"https://api.github.com/repos/google/deepvariant/issues/94","id":422619015,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMjYxOTAxNQ==","user":{"login":"pgrosu","id":6555937,"node_id":"MDQ6VXNlcjY1NTU5Mzc=","avatar_url":"https://avatars2.githubusercontent.com/u/6555937?v=4","gravatar_id":"","url":"https://api.github.com/users/pgrosu","html_url":"https://github.com/pgrosu","followers_url":"https://api.github.com/users/pgrosu/followers","following_url":"https://api.github.com/users/pgrosu/following{/other_user}","gists_url":"https://api.github.com/users/pgrosu/gists{/gist_id}","starred_url":"https://api.github.com/users/pgrosu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pgrosu/subscriptions","organizations_url":"https://api.github.com/users/pgrosu/orgs","repos_url":"https://api.github.com/users/pgrosu/repos","events_url":"https://api.github.com/users/pgrosu/events{/privacy}","received_events_url":"https://api.github.com/users/pgrosu/received_events","type":"User","site_admin":false},"created_at":"2018-09-19T01:48:54Z","updated_at":"2018-09-19T01:48:54Z","author_association":"NONE","body":"\r\nHi Ram,\r\n\r\nI see what's happening.  You have protobuf 3.5.1 in your include paths, but this is trying to compile the protobuf 3.6 version.  You will notice in this line:\r\n\r\n```\r\nnew (initial_block_) Block(options_.initial_block_size, NULL);\r\n```\r\n\r\nWhich is only part of `3.6.x`:\r\n\r\nhttps://github.com/protocolbuffers/protobuf/blob/3.6.x/src/google/protobuf/arena.cc#L77\r\n\r\nBasically a bunch of conflicts between declarations and use.\r\n\r\nSo to simplify things, could you remove your protobuf 3.5.1 from your paths.  If you are on a university cluster, it's usually something like `module unload MODULE_NAME`.  After that try rerunning it again.\r\n\r\nThanks,\r\n~p"}}
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