{"action":"opened","issue":{"url":"https://api.github.com/repos/vibansal/hapcut/issues/2","labels_url":"https://api.github.com/repos/vibansal/hapcut/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/vibansal/hapcut/issues/2/comments","events_url":"https://api.github.com/repos/vibansal/hapcut/issues/2/events","html_url":"https://github.com/vibansal/hapcut/issues/2","id":92674656,"number":2,"title":"compilation issues","user":{"login":"inti","id":376997,"avatar_url":"https://avatars.githubusercontent.com/u/376997?v=3","gravatar_id":"","url":"https://api.github.com/users/inti","html_url":"https://github.com/inti","followers_url":"https://api.github.com/users/inti/followers","following_url":"https://api.github.com/users/inti/following{/other_user}","gists_url":"https://api.github.com/users/inti/gists{/gist_id}","starred_url":"https://api.github.com/users/inti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/inti/subscriptions","organizations_url":"https://api.github.com/users/inti/orgs","repos_url":"https://api.github.com/users/inti/repos","events_url":"https://api.github.com/users/inti/events{/privacy}","received_events_url":"https://api.github.com/users/inti/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-07-02T16:10:17Z","updated_at":"2015-07-02T16:10:17Z","closed_at":null,"body":"Hi,\r\nI am finding several problem while trying to compile. firstly, \r\n```\r\n$ uname -a\r\nLinux jimi.biocomputing.cl 3.10.0-123.20.1.el7.x86_64 #1 SMP Thu Jan 29 18:05:33 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux\r\n```\r\n\r\nThen, I got two error because the Makefile expect a folder `hapcut-fosmid/`with the files `print_clusters.c` and `fosmidbam_hairs.c` in it.\r\n```\r\n$ make hairs\r\ngcc -D_GNU_SOURCE -Isamtools -g -O2 bamread.o hapfragments.o hashtable.o readfasta.o readvariant.o -o extractHAIRS extracthairs.c  -Lsamtools -lbam -lm -lz\r\nextracthairs.c:50:92: error fatal: hapcut-fosmid/fosmidbam_hairs.c: Demasiados niveles de enlaces simbólicos\r\n #include \"hapcut-fosmid/fosmidbam_hairs.c\" // code for parsing fosmid pooled sequence data \r\n                                                                                            ^\r\ncompilación terminada.\r\nmake: *** [hairs] Error 1\r\n```\r\nand \r\n```\r\n$ make hairs\r\ngcc -D_GNU_SOURCE -Isamtools -g -O2 bamread.o hapfragments.o hashtable.o readfasta.o readvariant.o -o extractHAIRS extracthairs.c  -Lsamtools -lbam -lm -lz\r\nIn file included from extracthairs.c:50:0:\r\nhapcut-fosmid/fosmidbam_hairs.c:49:28: error fatal: print_clusters.c: No existe el fichero o el directorio\r\n #include \"print_clusters.c\"\r\n                            ^\r\ncompilación terminada.\r\nmake: *** [hairs] Error 1\r\n```\r\nI created the folder and copied the files inside, then I got this error \r\n```\r\n$ make hairs\r\ngcc -D_GNU_SOURCE -Isamtools -c bamread.c\r\ngcc -D_GNU_SOURCE -c hashtable.c\r\ngcc -D_GNU_SOURCE -c readvariant.c \r\ngcc -D_GNU_SOURCE -c readfasta.c\r\ngcc -D_GNU_SOURCE -Isamtools -g -O2 bamread.o hapfragments.o hashtable.o readfasta.o readvariant.o -o extractHAIRS extracthairs.c  -Lsamtools -lbam -lm -lz\r\nextracthairs.c: En la función ‘main’:\r\nextracthairs.c:245:44: error: ‘PRIOR’ no se declaró aquí (primer uso en esta función)\r\n   else if (strcmp(argv[i],\"--prior\") == 0) PRIOR = atoi(argv[i+1]); \r\n                                            ^\r\nextracthairs.c:245:44: nota: cada identificador sin declarar se reporta sólo una vez para cada función en el que aparece\r\nextracthairs.c:246:86: error: ‘COMPARE_PHASE’ no se declaró aquí (primer uso en esta función)\r\n   else if (strcmp(argv[i],\"--comparephase\") == 0 || strcmp(argv[i],\"--compare\") ==0) COMPARE_PHASE = atoi(argv[i+1]); \r\n                                                                                      ^\r\nmake: *** [hairs] Error 1\r\n```\r\nI look forwards to using the software so any help will be much appreciated! \r\n\r\nthanks in advance,"}}