{"action":"created","issue":{"url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks/issues/65","repository_url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks","labels_url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks/issues/65/comments","events_url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks/issues/65/events","html_url":"https://github.com/cole-trapnell-lab/cufflinks/issues/65","id":162941063,"number":65,"title":"Building Cufflinks from source fails due to undefined reference to 'sam_read1'","user":{"login":"fa-vio","id":12551630,"avatar_url":"https://avatars.githubusercontent.com/u/12551630?v=3","gravatar_id":"","url":"https://api.github.com/users/fa-vio","html_url":"https://github.com/fa-vio","followers_url":"https://api.github.com/users/fa-vio/followers","following_url":"https://api.github.com/users/fa-vio/following{/other_user}","gists_url":"https://api.github.com/users/fa-vio/gists{/gist_id}","starred_url":"https://api.github.com/users/fa-vio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fa-vio/subscriptions","organizations_url":"https://api.github.com/users/fa-vio/orgs","repos_url":"https://api.github.com/users/fa-vio/repos","events_url":"https://api.github.com/users/fa-vio/events{/privacy}","received_events_url":"https://api.github.com/users/fa-vio/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-06-29T14:33:10Z","updated_at":"2016-08-16T14:57:30Z","closed_at":null,"body":"Building cuffilnks from source on Ubuntu 14.04 fails with the following:\r\n`libcufflinks.a(hits.o): In function 'samread':\r\n/usr/local/include/bam/sam.h:95: undefined reference to 'sam_read1'`\r\n\r\nBoost 1.55 installed in `/usr/local`; Eigen installed and headers placed in `/usr/local/include/Eigen`; SAMtools compiled with `CFLAGS=-fPIC` option, so that `libbam.a` was generated and copied to `/usr/local/lib`.  SAMtools headers copied in `/usr/local/include/bam`.\r\n\r\n`-- cufflinks 2.2.2 Configuration Results --\r\n C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3  -DNDEBUG  -pthread -I/usr/local/include -I/usr/local/include    -L/usr/lib\r\n GCC version:         gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4\r\nHost System type:    x86_64-unknown-linux-gnu\r\nInstall prefix:      /usr/local\r\nInstall eprefix:     ${prefix}`\r\n\r\nany idea on how to fix it?\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks/issues/comments/240128416","html_url":"https://github.com/cole-trapnell-lab/cufflinks/issues/65#issuecomment-240128416","issue_url":"https://api.github.com/repos/cole-trapnell-lab/cufflinks/issues/65","id":240128416,"user":{"login":"mestia","id":1309483,"avatar_url":"https://avatars.githubusercontent.com/u/1309483?v=3","gravatar_id":"","url":"https://api.github.com/users/mestia","html_url":"https://github.com/mestia","followers_url":"https://api.github.com/users/mestia/followers","following_url":"https://api.github.com/users/mestia/following{/other_user}","gists_url":"https://api.github.com/users/mestia/gists{/gist_id}","starred_url":"https://api.github.com/users/mestia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mestia/subscriptions","organizations_url":"https://api.github.com/users/mestia/orgs","repos_url":"https://api.github.com/users/mestia/repos","events_url":"https://api.github.com/users/mestia/events{/privacy}","received_events_url":"https://api.github.com/users/mestia/received_events","type":"User","site_admin":false},"created_at":"2016-08-16T14:57:30Z","updated_at":"2016-08-16T14:57:30Z","body":"But why not using the packaged versions ? \r\nhere are the steps to build cufflinks debian package which you later can install with dpkg -i $package\r\n\r\nyou'll need devscripts package installed and all dependencies\r\n\r\napt-get install devscripts\r\nmkdir cufflinks && cd cufflinks\r\ndget -ux http://http.debian.net/debian/pool/non-free/c/cufflinks/cufflinks_2.2.1-1.dsc\r\ncd cufflinks-2.2.1/\r\nas root\r\ncd <pathto>cufflinks-2.2.1/\r\ndebuild  -us -uc\r\ninstall the missing dependencies in case debuild complains... \r\nand repeat  debuild -us -uc\r\n"}}
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