{"action":"created","issue":{"url":"https://api.github.com/repos/ekg/freebayes/issues/224","labels_url":"https://api.github.com/repos/ekg/freebayes/issues/224/labels{/name}","comments_url":"https://api.github.com/repos/ekg/freebayes/issues/224/comments","events_url":"https://api.github.com/repos/ekg/freebayes/issues/224/events","html_url":"https://github.com/ekg/freebayes/issues/224","id":117889877,"number":224,"title":"Install error undefined reference to `gzopen64' in tabixx make","user":{"login":"mkortas","id":15931261,"avatar_url":"https://avatars.githubusercontent.com/u/15931261?v=3","gravatar_id":"","url":"https://api.github.com/users/mkortas","html_url":"https://github.com/mkortas","followers_url":"https://api.github.com/users/mkortas/followers","following_url":"https://api.github.com/users/mkortas/following{/other_user}","gists_url":"https://api.github.com/users/mkortas/gists{/gist_id}","starred_url":"https://api.github.com/users/mkortas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkortas/subscriptions","organizations_url":"https://api.github.com/users/mkortas/orgs","repos_url":"https://api.github.com/users/mkortas/repos","events_url":"https://api.github.com/users/mkortas/events{/privacy}","received_events_url":"https://api.github.com/users/mkortas/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-11-19T19:31:46Z","updated_at":"2015-11-19T21:20:23Z","closed_at":null,"body":"freebayes/vcflib/tabixpp/bedidx.c:103: undefined reference to `gzopen64'\r\n\r\n./libtabix.a(bedidx.o): In function `bed_read':\r\n/cm/shared/apps/freebayz/freebayes/vcflib/tabixpp/bedidx.c:103: undefined reference to `gzopen64'\r\ncollect2: ld returned 1 exit status\r\nmake[3]: *** [tabix] Error 1\r\n"},"comment":{"url":"https://api.github.com/repos/ekg/freebayes/issues/comments/158201403","html_url":"https://github.com/ekg/freebayes/issues/224#issuecomment-158201403","issue_url":"https://api.github.com/repos/ekg/freebayes/issues/224","id":158201403,"user":{"login":"ekg","id":145425,"avatar_url":"https://avatars.githubusercontent.com/u/145425?v=3","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":"2015-11-19T21:20:22Z","updated_at":"2015-11-19T21:20:22Z","body":"In tabixpp in the freebayes repo, try `git pull origin master`. Then try\nrebuilding and running freebayes.\nOn Nov 19, 2015 10:09 PM, \"mkortas\" <notifications@github.com> wrote:\n\n> I have descended into the tabixpp directory that is provided under\n> freebayes (/freebayes/vcflib/tabixpp) and run the make from there, but with\n> no success.\n>\n> I then tried installing it independently via “git clone --recursive\n> https://github.com/tseemann/tabixpp.git” which seemed to work. At least\n> no errors were generated.\n>\n> [root@cruncher tabixpp]# /cm/shared/apps/tabixpp/tabixpp/tabix++\n> /cm/shared/apps/tabixpp/tabixpp/tabix++ [file] [ [region] ... ]\n> Writes out regions from bgzf-compressed, tabix-indexed file.\n> Supply 'header' to print out the header, and no regions to\n> print the contents of the entire file.\n>\n>\n> From: Erik Garrison [mailto:notifications@github.com]\n> Sent: Thursday, November 19, 2015 11:45 AM\n> To: ekg/freebayes\n> Cc: Michael C. Kortas\n> Subject: Re: [freebayes] Install error undefined reference to `gzopen64'\n> in tabixx make (#224)\n>\n> Can you build tabixpp independently? There have been some patches against\n> it recently that may address this.\n> On Nov 19, 2015 8:44 PM, \"mkortas\" <notifications@github.com> wrote:\n>\n> > I believe so:\n> >\n> > [root@cruncher bin]# yum list installed|grep zlib\n> > zlib.i686 1.2.3-29.el6 installed\n> > zlib.x86_64 1.2.3-29.el6 @base\n> > zlib-devel.i686 1.2.3-29.el6 @base\n> > zlib-devel.x86_64 1.2.3-29.el6 installed\n> >\n> > From: Erik Garrison [mailto:notifications@github.com]\n> > Sent: Thursday, November 19, 2015 11:36 AM\n> > To: ekg/freebayes\n> > Cc: Michael C. Kortas\n> > Subject: Re: [freebayes] Install error undefined reference to `gzopen64'\n> > in tabixx make (#224)\n> >\n> > Are you certain you have the 64-bit compatible version of zlib\n> installed?\n> > On Nov 19, 2015 8:31 PM, \"mkortas\" <notifications@github.com> wrote:\n> >\n> > > freebayes/vcflib/tabixpp/bedidx.c:103: undefined reference to\n> `gzopen64'\n> > >\n> > > ./libtabix.a(bedidx.o): In function bed_read':\n> > > /cm/shared/apps/freebayz/freebayes/vcflib/tabixpp/bedidx.c:103:\n> > undefined\n> > > reference togzopen64'\n> > > collect2: ld returned 1 exit status\n> > > make[3]: *** [tabix] Error 1\n> > >\n> > > —\n> > > Reply to this email directly or view it on GitHub\n> > > <https://github.com/ekg/freebayes/issues/224>.\n> > >\n> >\n> >\n> > —\n> > Reply to this email directly or view it on GitHub<\n> > https://github.com/ekg/freebayes/issues/224#issuecomment-158170958>.\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <https://github.com/ekg/freebayes/issues/224#issuecomment-158173049>.\n> >\n>\n>\n> —\n> Reply to this email directly or view it on GitHub<\n> https://github.com/ekg/freebayes/issues/224#issuecomment-158173311>.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/ekg/freebayes/issues/224#issuecomment-158198870>.\n>\n"}}