{"action":"created","issue":{"url":"https://api.github.com/repos/lomereiter/sambamba/issues/230","repository_url":"https://api.github.com/repos/lomereiter/sambamba","labels_url":"https://api.github.com/repos/lomereiter/sambamba/issues/230/labels{/name}","comments_url":"https://api.github.com/repos/lomereiter/sambamba/issues/230/comments","events_url":"https://api.github.com/repos/lomereiter/sambamba/issues/230/events","html_url":"https://github.com/lomereiter/sambamba/issues/230","id":163587521,"number":230,"title":"Compilation error using Linuxbrew on CentOS 7.2 system","user":{"login":"hartzell","id":312978,"avatar_url":"https://avatars.githubusercontent.com/u/312978?v=3","gravatar_id":"","url":"https://api.github.com/users/hartzell","html_url":"https://github.com/hartzell","followers_url":"https://api.github.com/users/hartzell/followers","following_url":"https://api.github.com/users/hartzell/following{/other_user}","gists_url":"https://api.github.com/users/hartzell/gists{/gist_id}","starred_url":"https://api.github.com/users/hartzell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hartzell/subscriptions","organizations_url":"https://api.github.com/users/hartzell/orgs","repos_url":"https://api.github.com/users/hartzell/repos","events_url":"https://api.github.com/users/hartzell/events{/privacy}","received_events_url":"https://api.github.com/users/hartzell/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-04T00:40:03Z","updated_at":"2016-07-04T02:30:17Z","closed_at":"2016-07-04T02:30:17Z","body":"I'm using Linuxbrew on a CentOS 7.2 system (building from source, not using prebuilt bottles).\r\n\r\nI've seen #157, which has a very similar phenotype.  I'm unfamiliar with D, but I believe that I'm using the LDC based compilers (linuxbrew built ldc and ...) .\r\n\r\nHere's the error I'm seeing.\r\n\r\n```\r\n==> Summary\r\n/home/throgg/test-for-sjackman/Cellar/ldc/0.17.0: 324 files, 91.5M, built in 11 minutes 55 seconds\r\n==> Installing homebrew/science/sambamba\r\n==> Cloning https://github.com/lomereiter/sambamba.git\r\nCloning into '/home/throgg/.cache/Homebrew/sambamba--git'...\r\nremote: Counting objects: 80, done.\r\nremote: Compressing objects: 100% (76/76), done.\r\nremote: Total 80 (delta 2), reused 20 (delta 0), pack-reused 0\r\nUnpacking objects: 100% (80/80), done.\r\nChecking connectivity... done.\r\nNote: checking out '9d761c5d69cfbcd53ceb4cca25b5a6f694ea09ac'.\r\n\r\nYou are in 'detached HEAD' state. You can look around, make experimental\r\nchanges and commit them, and you can discard any commits you make in this\r\nstate without impacting any branches by performing another checkout.\r\n\r\nIf you want to create a new branch to retain commits you create, you may\r\ndo so (now or later) by using -b with the checkout command again. Example:\r\n\r\n  git checkout -b <new-branch-name>\r\n\r\n==> Checking out tag v0.5.6\r\n==> make sambamba-ldmd2-64\r\nLast 15 lines from /home/throgg/.cache/Homebrew/Logs/sambamba/01.make:\r\ncompiling dynamic library 1.6.0\r\ncreating versioned links\r\nmake[1]: Leaving directory `/tmp/sambamba-20160703-29972-1xs9dch/lz4/lib'\r\nmkdir -p build/\r\nldmd2 @sambamba-ldmd-release.rsp\r\nsambamba/utils/common/filtering.d(327): Error: no property 'representation' for type 'string'\r\ncram/reader.d(107): Error: no property 'map' for type 'Zip!(CramSliceDecoder!(UndecodedSliceRange), Repeat!(CramReader), Repeat!(ubyte[] function(ulong)))'\r\ncram/reference.d(91): Error: no property 'map' for type 'Zip!(CramSliceDecoder!(UndecodedSliceRange), Repeat!(PositionChecker), Repeat!(IBamSamReader), Repeat!(ubyte[] function(ulong)))'\r\n/home/throgg/test-for-sjackman/Cellar/ldc/0.17.0/include/dlang/ldc/std/numeric.d(1616): Deprecation: read-modify-write operations are not allowed for shared variables. Use core.atomic.atomicOp!\"+=\"(s, e) instead.\r\n/home/throgg/test-for-sjackman/Cellar/ldc/0.17.0/include/dlang/ldc/std/numeric.d(1642): Deprecation: read-modify-write operations are not allowed for shared variables. Use core.atomic.atomicOp!\"*=\"(e, f) instead.\r\nsambamba/pileup.d(235): Error: module std.format import 'text' not found\r\nsambamba/view.d(320): Error: no [] operator overload for type ReferenceSequence\r\nsambamba/view.d(345): Error: template instance sambamba.view.sambambaMain!(CramReader).sambambaMain.processAlignments!(ReadCountsambamba/view.d(345): Error: template instance sambamba.view.sambambaMain!(CramReader).sambambaMain.processAlignments!(ReadCounter) error instantiating\r\nsambamba/view.d(192):        instantiated from here: sambambaMain!(CramReader)\r\nmake: *** [sambamba-ldmd2-64] Error 1\r\n```\r\n\r\nCan you give me any debugging pointers?\r\n\r\nThanks,\r\n\r\ng."},"comment":{"url":"https://api.github.com/repos/lomereiter/sambamba/issues/comments/230193341","html_url":"https://github.com/lomereiter/sambamba/issues/230#issuecomment-230193341","issue_url":"https://api.github.com/repos/lomereiter/sambamba/issues/230","id":230193341,"user":{"login":"hartzell","id":312978,"avatar_url":"https://avatars.githubusercontent.com/u/312978?v=3","gravatar_id":"","url":"https://api.github.com/users/hartzell","html_url":"https://github.com/hartzell","followers_url":"https://api.github.com/users/hartzell/followers","following_url":"https://api.github.com/users/hartzell/following{/other_user}","gists_url":"https://api.github.com/users/hartzell/gists{/gist_id}","starred_url":"https://api.github.com/users/hartzell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hartzell/subscriptions","organizations_url":"https://api.github.com/users/hartzell/orgs","repos_url":"https://api.github.com/users/hartzell/repos","events_url":"https://api.github.com/users/hartzell/events{/privacy}","received_events_url":"https://api.github.com/users/hartzell/received_events","type":"User","site_admin":false},"created_at":"2016-07-04T02:30:17Z","updated_at":"2016-07-04T02:30:17Z","body":"I updated the Homebrew-science formula to use v0.6.3 and it build nicely.  Sorry for the noise.\r\n"}}
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