{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/1834","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/1834/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/1834/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/1834/events","html_url":"https://github.com/vgteam/vg/issues/1834","id":352164506,"node_id":"MDU6SXNzdWUzNTIxNjQ1MDY=","number":1834,"title":"vg install issue on Mac AND Linux","user":{"login":"antoine4ucsd","id":18502631,"node_id":"MDQ6VXNlcjE4NTAyNjMx","avatar_url":"https://avatars3.githubusercontent.com/u/18502631?v=4","gravatar_id":"","url":"https://api.github.com/users/antoine4ucsd","html_url":"https://github.com/antoine4ucsd","followers_url":"https://api.github.com/users/antoine4ucsd/followers","following_url":"https://api.github.com/users/antoine4ucsd/following{/other_user}","gists_url":"https://api.github.com/users/antoine4ucsd/gists{/gist_id}","starred_url":"https://api.github.com/users/antoine4ucsd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antoine4ucsd/subscriptions","organizations_url":"https://api.github.com/users/antoine4ucsd/orgs","repos_url":"https://api.github.com/users/antoine4ucsd/repos","events_url":"https://api.github.com/users/antoine4ucsd/events{/privacy}","received_events_url":"https://api.github.com/users/antoine4ucsd/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":51,"created_at":"2018-08-20T14:37:17Z","updated_at":"2018-09-04T21:52:14Z","closed_at":null,"author_association":"NONE","body":"Hi Team\r\nI've been trying to install vg on my Mac and my Linux platform with all the procedures you describe for linux and for OS (using MacPorts or Homebrew). I always got the same kind of error as below... very frustrating. My gut feeling is that it has to do with gcc/g++ compiler which always causes me trouble (conflicting version? conda install vs MacPorts vs Homebrew?). \r\nif it helps, I've installed gcc and g++ using both anaconda2 and sudo port/homebrew \r\n\r\n```\r\n$ which gcc\r\n/usr/local/bin/gcc\r\n\r\n$ gcc -v\r\nUsing built-in specs.\r\nCOLLECT_GCC=gcc\r\nCOLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc@4.9/4.9.4_1/libexec/gcc/x86_64-apple-darwin17.7.0/4.9.4/lto-wrapper\r\nTarget: x86_64-apple-darwin17.7.0\r\nConfigured with: ../configure --build=x86_64-apple-darwin17.7.0 --prefix=/usr/local/Cellar/gcc@4.9/4.9.4_1 --libdir=/usr/local/Cellar/gcc@4.9/4.9.4_1/lib/gcc/4.9 --enable-languages=c,c++,fortran,objc,obj-c++ --program-suffix=-4.9 --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --enable-plugin --with-build-config=bootstrap-debug --disable-werror --with-pkgversion='Homebrew GCC 4.9.4_1' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues MAKEINFO=missing --disable-nls --enable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk\r\nThread model: posix\r\ngcc version 4.9.4 (Homebrew GCC 4.9.4_1) \r\n\r\n```\r\nand the error messages I got is attached - valid for both MAC and LINUX\r\n\r\nI also tried to do it in a new conda environment but I got the same errors.\r\nI am lost in the dark now,.. Is there a pre-compiled version I could use? I should probably restart from scratch after extensive clean up but I think I did it (probably not) without  more luck\r\n\r\nAll advices are welcome and let me know if you need other info (I am using the most recent OS for Mac)\r\nthank you!\r\n\r\nantoine\r\n\r\n[VG_INSTALL_ERROR_MAC.txt](https://github.com/vgteam/vg/files/2302760/VG_INSTALL_ERROR_MAC.txt)\r\n[VG_INSTALL_ERROR_LINUX.txt](https://github.com/vgteam/vg/files/2302761/VG_INSTALL_ERROR_LINUX.txt)\r\n"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/418530185","html_url":"https://github.com/vgteam/vg/issues/1834#issuecomment-418530185","issue_url":"https://api.github.com/repos/vgteam/vg/issues/1834","id":418530185,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODUzMDE4NQ==","user":{"login":"adamnovak","id":5062495,"node_id":"MDQ6VXNlcjUwNjI0OTU=","avatar_url":"https://avatars1.githubusercontent.com/u/5062495?v=4","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"created_at":"2018-09-04T21:52:14Z","updated_at":"2018-09-04T21:52:14Z","author_association":"CONTRIBUTOR","body":"Yep, that looks consistent with a CPU that's too old. You should be able to\nconfirm by doing `cat /proc/cpuinfo` and looking at one of the flags lines;\nI believe we need \"sse4_1\" and possibly also \"sse4_2\" to be listed.\n\nIf they aren't there, the only thing to do is to use a different computer\nthat has a CPU that supports those instructions.\n\nOn Tue, Sep 4, 2018 at 1:16 PM, antoine <notifications@github.com> wrote:\n\n> here's what I got running vg test (stack attached)\n>\n> ./vg test\n>\n> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n> vg test is a Catch v1.8.2 host application.\n> Run with -? for options\n>\n> -------------------------------------------------------------------------------\n> The smart aligner works on very large inserts\n> -------------------------------------------------------------------------------\n> src/unittest/variant_adder.cpp:317\n> ...............................................................................\n>\n> src/unittest/variant_adder.cpp:317: FAILED:\n> due to a fatal error condition:\n>   SIGILL - Illegal instruction signal\n>\n> ===============================================================================\n> test cases:  6 |  5 passed | 1 failed\n> assertions: 12 | 11 passed | 1 failed\n>\n> ERROR: Signal 4 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.\n>\n> stacktrace_vgtest.txt\n> <https://github.com/vgteam/vg/files/2350080/stacktrace_vgtest.txt>\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/vgteam/vg/issues/1834#issuecomment-418503520>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/AE0_XymsyvwIYxPxtpYyaeCEcGTBkL4Oks5uXt-2gaJpZM4WEIUO>\n> .\n>\n"}}
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