{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pitchfork/issues/265","repository_url":"https://api.github.com/repos/PacificBiosciences/pitchfork","labels_url":"https://api.github.com/repos/PacificBiosciences/pitchfork/issues/265/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pitchfork/issues/265/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pitchfork/issues/265/events","html_url":"https://github.com/PacificBiosciences/pitchfork/issues/265","id":163916445,"number":265,"title":"Work with gcc newer than version 5","user":{"login":"mhsieh","id":7217130,"avatar_url":"https://avatars.githubusercontent.com/u/7217130?v=3","gravatar_id":"","url":"https://api.github.com/users/mhsieh","html_url":"https://github.com/mhsieh","followers_url":"https://api.github.com/users/mhsieh/followers","following_url":"https://api.github.com/users/mhsieh/following{/other_user}","gists_url":"https://api.github.com/users/mhsieh/gists{/gist_id}","starred_url":"https://api.github.com/users/mhsieh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mhsieh/subscriptions","organizations_url":"https://api.github.com/users/mhsieh/orgs","repos_url":"https://api.github.com/users/mhsieh/repos","events_url":"https://api.github.com/users/mhsieh/events{/privacy}","received_events_url":"https://api.github.com/users/mhsieh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-07-05T18:33:29Z","updated_at":"2016-07-05T19:19:29Z","closed_at":null,"body":"blasr doesn't build on gcc/6 or gcc/7"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pitchfork/issues/comments/230575538","html_url":"https://github.com/PacificBiosciences/pitchfork/issues/265#issuecomment-230575538","issue_url":"https://api.github.com/repos/PacificBiosciences/pitchfork/issues/265","id":230575538,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2016-07-05T19:19:29Z","updated_at":"2016-07-05T19:19:29Z","body":"Well, sort of. Actually, blasr builds fine on gcc/6 and 7 if configured properly. But we cannot use `HFD5_INC=/usr/include`, as we then put that into the include PATH via `-isystem`. That fails as described here:\r\n* https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129\r\n\r\nSo for pitchfork, we will need to avoid `-isystem` in the blasr makefile, since we really cannot avoid using `/usr/include` for pitchfork settings. (Unless you want to strip `/usr/include` from paths that are passed to blasr configure.) I don't think we really need `-isystem` at all, since we are no longer running make-depend (`-MM` etc.), so I'll drop that from blasr. (After lunch...)"}}
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