{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/167","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/167/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/167/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/167/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/167","id":100631721,"number":167,"title":"NameError: global name 'fn' is not defined","user":{"login":"outpaddling","id":11299711,"avatar_url":"https://avatars.githubusercontent.com/u/11299711?v=3","gravatar_id":"","url":"https://api.github.com/users/outpaddling","html_url":"https://github.com/outpaddling","followers_url":"https://api.github.com/users/outpaddling/followers","following_url":"https://api.github.com/users/outpaddling/following{/other_user}","gists_url":"https://api.github.com/users/outpaddling/gists{/gist_id}","starred_url":"https://api.github.com/users/outpaddling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/outpaddling/subscriptions","organizations_url":"https://api.github.com/users/outpaddling/orgs","repos_url":"https://api.github.com/users/outpaddling/repos","events_url":"https://api.github.com/users/outpaddling/events{/privacy}","received_events_url":"https://api.github.com/users/outpaddling/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-08-12T20:47:23Z","updated_at":"2015-08-13T19:29:01Z","closed_at":"2015-08-12T22:11:42Z","body":"Hi,\r\nWe're eager to get a stable installation of FALCON running at UWM.  I think we're pretty close, but I'm getting this error from fc_run.py.\r\nI have the latest snapshot of pypeFLOW from today, py-rdflib 3.4.0, py-rdfextras 0.4, and the June 15 releases of daligner and dazz_db.\r\nI also tried the FALCON-integrate installation method, but it failed with a missing DB.c, which I presume was caused by grabbiing the wrong versions of daligner and dazz_db.  I'd rather not run in a virtualenv anyway, but install via a package manager (we use mainly pkgsrc on CentOS).\r\nThis might be something as simple as a missing module, but Google has let me down on this one.\r\nBelow is the error in some context.\r\nThanks,\r\n    Jason\r\n~~~~~~~~~~\r\n  File \"/usr/local/lib/python2.7/site-packages/pypeflow/task.py\", line 178, in _\r\nrunTask\r\n    return self._taskFun(self)\r\n  File \"/usr/local/lib/python2.7/site-packages/falcon_kit/run_support.py\", line\r\n279, in make_fofn_abs_raw\r\n    return make_fofn_abs(self)\r\n  File \"/usr/local/lib/python2.7/site-packages/falcon_kit/run_support.py\", line\r\n266, in make_fofn_abs\r\n    i_fofn_fn = fn(self.i_fofn)\r\nNameError: global name 'fn' is not defined\r\n2015-08-12 20:28:32,397 - pypeflow.controller - INFO - #jobsReadyToBeSubmitted:\r\n0\r\n2015-08-12 20:28:32,398 - pypeflow.task - ERROR - PypeTaskBase failed:\r\n{'__class__.__name__': 'PypeThreadTaskBase',\r\n '_status': 'TaskInitialized',\r\n 'inputDataObjs': {'i_fofn': PypeLocalFile('file://localhost/usr/home/bacon/PacB\r\nio-CLI/Falcon/input.fofn', '/usr/home/bacon/PacBio-CLI/Falcon/input.fofn')},\r\n 'mutableDataObjs': {},\r\n 'outputDataObjs': {'o_fofn': PypeLocalFile('file://localhost/usr/home/bacon/Pac\r\nBio-CLI/Falcon/0-rawreads/input.fofn', '/usr/home/bacon/PacBio-CLI/Falcon/0-rawr\r\neads/input.fofn')},\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/130812355","html_url":"https://github.com/PacificBiosciences/FALCON/issues/167#issuecomment-130812355","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/167","id":130812355,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2015-08-13T19:29:01Z","updated_at":"2015-08-13T19:29:01Z","body":"> So, the only real issue is that Makefile is out-of-date. Makefile does contain gcc commands in the latest dazz_db and daligner.\r\n\r\nYeah, I'm trying to keep our fork easily merge-able with Gene Myers'. We're using only GNUmakefile.\r\n\r\n> Should I be using v0.3.0 instead?\r\n\r\nNope! What you have is fine, as the tip of master is preferable. You'll get bug-fixes immediately, so I'll see fewer bug-reports. Don't use a specific release unless you have a reason."}}