{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/1478","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/1478/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/1478/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/1478/events","html_url":"https://github.com/vgteam/vg/pull/1478","id":301272374,"number":1478,"title":"Try to fix Mac tests","user":{"login":"jltsiren","id":11444026,"avatar_url":"https://avatars0.githubusercontent.com/u/11444026?v=4","gravatar_id":"","url":"https://api.github.com/users/jltsiren","html_url":"https://github.com/jltsiren","followers_url":"https://api.github.com/users/jltsiren/followers","following_url":"https://api.github.com/users/jltsiren/following{/other_user}","gists_url":"https://api.github.com/users/jltsiren/gists{/gist_id}","starred_url":"https://api.github.com/users/jltsiren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jltsiren/subscriptions","organizations_url":"https://api.github.com/users/jltsiren/orgs","repos_url":"https://api.github.com/users/jltsiren/repos","events_url":"https://api.github.com/users/jltsiren/events{/privacy}","received_events_url":"https://api.github.com/users/jltsiren/received_events","type":"User","site_admin":false},"labels":[{"id":280142072,"url":"https://api.github.com/repos/vgteam/vg/labels/in%20progress","name":"in progress","color":"ededed","default":false}],"state":"open","locked":false,"assignee":{"login":"jltsiren","id":11444026,"avatar_url":"https://avatars0.githubusercontent.com/u/11444026?v=4","gravatar_id":"","url":"https://api.github.com/users/jltsiren","html_url":"https://github.com/jltsiren","followers_url":"https://api.github.com/users/jltsiren/followers","following_url":"https://api.github.com/users/jltsiren/following{/other_user}","gists_url":"https://api.github.com/users/jltsiren/gists{/gist_id}","starred_url":"https://api.github.com/users/jltsiren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jltsiren/subscriptions","organizations_url":"https://api.github.com/users/jltsiren/orgs","repos_url":"https://api.github.com/users/jltsiren/repos","events_url":"https://api.github.com/users/jltsiren/events{/privacy}","received_events_url":"https://api.github.com/users/jltsiren/received_events","type":"User","site_admin":false},"assignees":[{"login":"jltsiren","id":11444026,"avatar_url":"https://avatars0.githubusercontent.com/u/11444026?v=4","gravatar_id":"","url":"https://api.github.com/users/jltsiren","html_url":"https://github.com/jltsiren","followers_url":"https://api.github.com/users/jltsiren/followers","following_url":"https://api.github.com/users/jltsiren/following{/other_user}","gists_url":"https://api.github.com/users/jltsiren/gists{/gist_id}","starred_url":"https://api.github.com/users/jltsiren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jltsiren/subscriptions","organizations_url":"https://api.github.com/users/jltsiren/orgs","repos_url":"https://api.github.com/users/jltsiren/repos","events_url":"https://api.github.com/users/jltsiren/events{/privacy}","received_events_url":"https://api.github.com/users/jltsiren/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2018-03-01T04:15:30Z","updated_at":"2018-03-01T10:56:35Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/vgteam/vg/pulls/1478","html_url":"https://github.com/vgteam/vg/pull/1478","diff_url":"https://github.com/vgteam/vg/pull/1478.diff","patch_url":"https://github.com/vgteam/vg/pull/1478.patch"},"body":"I may have figured out why the Travis tests often time out on Mac.\r\n\r\nThe first tests in a freshly cloned repository work fine. They do not clean up properly afterwards. One of the files left behind is `x.gbwt`. On the next time, in `06_vg_index.t`, we run the following line:\r\n\r\n```\r\nvg map -T <(vg sim -s 1337 -n 100 -x x.xg) -d x > x1337.gam\r\n```\r\n\r\nThis loads `x.gbwt`, and then things get out of control. For some reason, the `vg map` command uses tens of gigabytes of memory. Macs don't have that much memory, so they use swap instead.\r\n\r\nThe tests now delete all temporary files that would show up on `git status`. This hopefully fixes the issue.\r\n\r\nAlso, because I was really working on #1475, this PR includes other changes:\r\n\r\n- `vg prune` builds the XG indexes it needs. We should not have to store XG indexes for individual files when indexing multi-file graphs.\r\n- `vg index -g` takes the default values for `--kmer-size` and `--doubling-steps` from GCSA. As a result, it now builds 256-mer indexes by default.\r\n- Temporary files are no longer hidden, and they will be written to the appropriate temp directory instead of the working directory. This is particularly important for the kmer files in `vg index -g`.\r\n"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/369555482","html_url":"https://github.com/vgteam/vg/pull/1478#issuecomment-369555482","issue_url":"https://api.github.com/repos/vgteam/vg/issues/1478","id":369555482,"user":{"login":"ekg","id":145425,"avatar_url":"https://avatars1.githubusercontent.com/u/145425?v=4","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"created_at":"2018-03-01T10:56:35Z","updated_at":"2018-03-01T10:56:35Z","author_association":"COLLABORATOR","body":"I believed I resolved this on the mappering branch, but I still see the timeouts.\r\n\r\nSorry that I have diverged for two weeks so we are duplicating effort."}}
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