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PR depends on:\r\n- https://github.com/vgteam/vcflib/pull/11\r\n- https://github.com/edawson/gfakluge/pull/41\r\n- https://github.com/benedictpaten/sonLib/pull/34\r\n- https://github.com/vgteam/structures/pull/6\r\n- https://github.com/jltsiren/gcsa2/pull/35\r\n- https://github.com/jltsiren/gbwt/pull/1\r\n- https://github.com/yoheirosen/sublinear-Li-Stephens/pull/4\r\n\r\nThis PR will fix #1246 and let vg build with the default Clang compiler on Mac. We should no longer need to instruct Mac users to replace their system compiler, or have epic issue threads in which dueling compilers and standard libraries battle each other for control of our users systems.\r\n\r\n```\r\nVyoma:vg anovak$ bin/vg version\r\nvg version v1.10.0-59-ga061f801 \"Rionero\"\r\nCompiled with Apple LLVM version 9.0.0 (clang-900.0.39.2) on Darwin\r\nBuilt by anovak@Vyoma\r\nVyoma:vg anovak$ bin/vg test\r\nwarning:[BaseAligner::maximum_mapping_quality_exact]: Max score of 0 is the padding score; changing to -10\r\nwarning:[BaseAligner::maximum_mapping_quality_approx]: Max score of 0 is the padding score; changing to -10\r\nindex file /var/folders/ws/t7b9wm2j2b7fy4_xyq0n5vh00000gn/T//vg-2mOnPd/vg-iC10dg.fai not found, generating...\r\nindex file /var/folders/ws/t7b9wm2j2b7fy4_xyq0n5vh00000gn/T//vg-2mOnPd/vg-DdgmBL.fai not found, generating...\r\nGGCTTGGAAATTTTCTGGAGTG\r\n===============================================================================\r\nAll tests passed (282024 assertions in 271 test cases)\r\n```\r\n\r\nStill TODO:\r\n\r\n- [ ] Merge all the above PRs so Jenkins and Travis have a hope of testing this.\r\n- [ ] Update the documentation for Macports builds to include installing libomp and not GNU GCC.\r\n- [ ] Work out the exact package selection to install via Homebrew to do the same thing.\r\n"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/421513859","html_url":"https://github.com/vgteam/vg/pull/1871#issuecomment-421513859","issue_url":"https://api.github.com/repos/vgteam/vg/issues/1871","id":421513859,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMTUxMzg1OQ==","user":{"login":"cgcloud-jenkins","id":12962446,"node_id":"MDQ6VXNlcjEyOTYyNDQ2","avatar_url":"https://avatars2.githubusercontent.com/u/12962446?v=4","gravatar_id":"","url":"https://api.github.com/users/cgcloud-jenkins","html_url":"https://github.com/cgcloud-jenkins","followers_url":"https://api.github.com/users/cgcloud-jenkins/followers","following_url":"https://api.github.com/users/cgcloud-jenkins/following{/other_user}","gists_url":"https://api.github.com/users/cgcloud-jenkins/gists{/gist_id}","starred_url":"https://api.github.com/users/cgcloud-jenkins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cgcloud-jenkins/subscriptions","organizations_url":"https://api.github.com/users/cgcloud-jenkins/orgs","repos_url":"https://api.github.com/users/cgcloud-jenkins/repos","events_url":"https://api.github.com/users/cgcloud-jenkins/events{/privacy}","received_events_url":"https://api.github.com/users/cgcloud-jenkins/received_events","type":"User","site_admin":false},"created_at":"2018-09-15T00:03:35Z","updated_at":"2018-09-15T00:03:35Z","author_association":"NONE","body":"[Jenkins vg tests](http://jenkins.cgcloud.info/job/vg/2186/) never ran ([Check the logs for setup or build errors](http://jenkins.cgcloud.info/job/vg/2186/consoleFull)) for [PR 1871](https://github.com/vgteam/vg/pull/1871).  View the [full report here](http://cgl-pipeline-inputs.s3.amazonaws.com/vg_cgl/vg_ci/jenkins_reports/commit/6eca989c0959411c5d624fcb040db8b29da6fd2a/index.html).\n\n"}}
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