{"action":"created","issue":{"url":"https://api.github.com/repos/samtools/htslib/issues/420","repository_url":"https://api.github.com/repos/samtools/htslib","labels_url":"https://api.github.com/repos/samtools/htslib/issues/420/labels{/name}","comments_url":"https://api.github.com/repos/samtools/htslib/issues/420/comments","events_url":"https://api.github.com/repos/samtools/htslib/issues/420/events","html_url":"https://github.com/samtools/htslib/issues/420","id":181305899,"number":420,"title":"PTHREAD error when compiling htslib","user":{"login":"jdmontenegro","id":9381306,"avatar_url":"https://avatars.githubusercontent.com/u/9381306?v=3","gravatar_id":"","url":"https://api.github.com/users/jdmontenegro","html_url":"https://github.com/jdmontenegro","followers_url":"https://api.github.com/users/jdmontenegro/followers","following_url":"https://api.github.com/users/jdmontenegro/following{/other_user}","gists_url":"https://api.github.com/users/jdmontenegro/gists{/gist_id}","starred_url":"https://api.github.com/users/jdmontenegro/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdmontenegro/subscriptions","organizations_url":"https://api.github.com/users/jdmontenegro/orgs","repos_url":"https://api.github.com/users/jdmontenegro/repos","events_url":"https://api.github.com/users/jdmontenegro/events{/privacy}","received_events_url":"https://api.github.com/users/jdmontenegro/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"jkbonfield","id":2210525,"avatar_url":"https://avatars.githubusercontent.com/u/2210525?v=3","gravatar_id":"","url":"https://api.github.com/users/jkbonfield","html_url":"https://github.com/jkbonfield","followers_url":"https://api.github.com/users/jkbonfield/followers","following_url":"https://api.github.com/users/jkbonfield/following{/other_user}","gists_url":"https://api.github.com/users/jkbonfield/gists{/gist_id}","starred_url":"https://api.github.com/users/jkbonfield/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jkbonfield/subscriptions","organizations_url":"https://api.github.com/users/jkbonfield/orgs","repos_url":"https://api.github.com/users/jkbonfield/repos","events_url":"https://api.github.com/users/jkbonfield/events{/privacy}","received_events_url":"https://api.github.com/users/jkbonfield/received_events","type":"User","site_admin":false},"assignees":[{"login":"jkbonfield","id":2210525,"avatar_url":"https://avatars.githubusercontent.com/u/2210525?v=3","gravatar_id":"","url":"https://api.github.com/users/jkbonfield","html_url":"https://github.com/jkbonfield","followers_url":"https://api.github.com/users/jkbonfield/followers","following_url":"https://api.github.com/users/jkbonfield/following{/other_user}","gists_url":"https://api.github.com/users/jkbonfield/gists{/gist_id}","starred_url":"https://api.github.com/users/jkbonfield/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jkbonfield/subscriptions","organizations_url":"https://api.github.com/users/jkbonfield/orgs","repos_url":"https://api.github.com/users/jkbonfield/repos","events_url":"https://api.github.com/users/jkbonfield/events{/privacy}","received_events_url":"https://api.github.com/users/jkbonfield/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2016-10-06T01:39:14Z","updated_at":"2016-10-06T08:42:08Z","closed_at":null,"body":"$> autoheader\r\n$> autoconf\r\n$> ./configure\r\n$> make\r\n(...)\r\necho '#define HTS_VERSION \"1.3.2-129-gdaae2ea\"' > version.h\r\ngcc -g -O2 -I.  -c -o hts.o hts.c\r\ngcc -g -O2 -I.  -c -o md5.o md5.c\r\ngcc -g -O2 -I.  -c -o probaln.o probaln.c\r\ngcc -g -O2 -I.  -c -o realn.o realn.c\r\ngcc -g -O2 -I.  -c -o regidx.o regidx.c\r\ngcc -g -O2 -I.  -c -o sam.o sam.c\r\ngcc -g -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c\r\ngcc -g -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c\r\ngcc -g -O2 -I.  -c -o tbx.o tbx.c\r\ngcc -g -O2 -I.  -c -o thread_pool.o thread_pool.c\r\nthread_pool.c: In function ‘hts_tpool_init’:\r\nthread_pool.c:658:38: error: ‘PTHREAD_MUTEX_RECURSIVE’ undeclared (first use in this function)\r\n     pthread_mutexattr_settype(&attr, PTHREAD_MUTEX_RECURSIVE);\r\n                                      ^\r\nthread_pool.c:658:38: note: each undeclared identifier is reported only once for each function it appears in\r\nmake: *** [thread_pool.o] Error 1\r\n\r\ncannot build the development version of htslib in the server:\r\n\r\n$> uname -a\r\n\r\nLinux zeus 3.0.101-80-default #1 SMP Fri Jul 15 14:30:41 UTC 2016 (eb2ba81) x86_64 x86_64 x86_64 GNU/Linux\r\n\r\nAny ideas how to fix it?\r\n\r\nCheers,\r\n"},"comment":{"url":"https://api.github.com/repos/samtools/htslib/issues/comments/251901621","html_url":"https://github.com/samtools/htslib/issues/420#issuecomment-251901621","issue_url":"https://api.github.com/repos/samtools/htslib/issues/420","id":251901621,"user":{"login":"jmarshall","id":70921,"avatar_url":"https://avatars.githubusercontent.com/u/70921?v=3","gravatar_id":"","url":"https://api.github.com/users/jmarshall","html_url":"https://github.com/jmarshall","followers_url":"https://api.github.com/users/jmarshall/followers","following_url":"https://api.github.com/users/jmarshall/following{/other_user}","gists_url":"https://api.github.com/users/jmarshall/gists{/gist_id}","starred_url":"https://api.github.com/users/jmarshall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmarshall/subscriptions","organizations_url":"https://api.github.com/users/jmarshall/orgs","repos_url":"https://api.github.com/users/jmarshall/repos","events_url":"https://api.github.com/users/jmarshall/events{/privacy}","received_events_url":"https://api.github.com/users/jmarshall/received_events","type":"User","site_admin":false},"created_at":"2016-10-06T08:42:08Z","updated_at":"2016-10-06T08:42:08Z","body":"I am aware of the theoretical need to compile as well as link with `-pthread` but had not previously met a system where it makes a difference!  Indeed we should probably be probing for pthread details, and it would be good to fix the problem underlying #255 at the same time.  So I look forward to @jkbonfield's pull request :smile:\r\n\r\nIt would still be interesting to hear more details of your OS and pthread implementation.\r\n\r\nArticles like this [expert's rant](http://www.zaval.org/resources/library/butenhof1.html) suggest that recursive mutexes may not be the best choice in general…"}}
{"actor":{"display_login":"jmarshall"}}