{"action":"created","issue":{"url":"https://api.github.com/repos/IRkernel/IRkernel/issues/174","labels_url":"https://api.github.com/repos/IRkernel/IRkernel/issues/174/labels{/name}","comments_url":"https://api.github.com/repos/IRkernel/IRkernel/issues/174/comments","events_url":"https://api.github.com/repos/IRkernel/IRkernel/issues/174/events","html_url":"https://github.com/IRkernel/IRkernel/issues/174","id":98756101,"number":174,"title":"Calling nycflights13 dataframe hangs kernel","user":{"login":"rsmith31415","id":599274,"avatar_url":"https://avatars.githubusercontent.com/u/599274?v=3","gravatar_id":"","url":"https://api.github.com/users/rsmith31415","html_url":"https://github.com/rsmith31415","followers_url":"https://api.github.com/users/rsmith31415/followers","following_url":"https://api.github.com/users/rsmith31415/following{/other_user}","gists_url":"https://api.github.com/users/rsmith31415/gists{/gist_id}","starred_url":"https://api.github.com/users/rsmith31415/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rsmith31415/subscriptions","organizations_url":"https://api.github.com/users/rsmith31415/orgs","repos_url":"https://api.github.com/users/rsmith31415/repos","events_url":"https://api.github.com/users/rsmith31415/events{/privacy}","received_events_url":"https://api.github.com/users/rsmith31415/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"flying-sheep","id":291575,"avatar_url":"https://avatars.githubusercontent.com/u/291575?v=3","gravatar_id":"","url":"https://api.github.com/users/flying-sheep","html_url":"https://github.com/flying-sheep","followers_url":"https://api.github.com/users/flying-sheep/followers","following_url":"https://api.github.com/users/flying-sheep/following{/other_user}","gists_url":"https://api.github.com/users/flying-sheep/gists{/gist_id}","starred_url":"https://api.github.com/users/flying-sheep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/flying-sheep/subscriptions","organizations_url":"https://api.github.com/users/flying-sheep/orgs","repos_url":"https://api.github.com/users/flying-sheep/repos","events_url":"https://api.github.com/users/flying-sheep/events{/privacy}","received_events_url":"https://api.github.com/users/flying-sheep/received_events","type":"User","site_admin":false},"milestone":null,"comments":10,"created_at":"2015-08-03T14:25:49Z","updated_at":"2015-08-06T19:09:03Z","closed_at":"2015-08-06T15:38:43Z","body":"Running a particular dataframe (from the nycflights13 package) makes the kernel to hang:\r\n\r\n```\r\nlibrary(nycflights13)\r\ndata(flights)\r\nflights\r\n```\r\n\r\nI noticed the last call is not returning a get_shell_msg() and get_iopub_msg() doesn't seem to be finish. This is the output I get using the kernel directly:\r\n\r\n```\r\nIn [9]: kc.execute('library(nycflights13); data(flights); ls()')\r\nOut[9]: '49ff5db7-9400-4ddc-a559-1ae37050c763'\r\n\r\nIn [10]: kc.get_shell_msg(timeout=1)\r\nOut[10]:\r\n{'buffers': [],\r\n 'content': {u'execution_count': 1,\r\n  u'payload': [],\r\n  u'status': u'ok',\r\n  u'user_expressions': {}},\r\n 'header': {u'msg_id': u'9f43398b-0f34-4307-a985-d97c4a8d5916',\r\n  u'msg_type': u'execute_reply',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'9f43398b-0f34-4307-a985-d97c4a8d5916',\r\n 'msg_type': u'execute_reply',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 49, 30, 890131),\r\n  u'msg_id': u'49ff5db7-9400-4ddc-a559-1ae37050c763',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [11]: kc.get_iopub_msg(timeout=1)\r\nOut[11]:\r\n{'buffers': [],\r\n 'content': {u'execution_state': u'busy'},\r\n 'header': {u'msg_id': u'7023fb15-c445-44f7-9251-452b16b9d9d4',\r\n  u'msg_type': u'status',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'7023fb15-c445-44f7-9251-452b16b9d9d4',\r\n 'msg_type': u'status',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 49, 30, 890131),\r\n  u'msg_id': u'49ff5db7-9400-4ddc-a559-1ae37050c763',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [12]: kc.get_iopub_msg(timeout=1)\r\nOut[12]:\r\n{'buffers': [],\r\n 'content': {u'code': u'library(nycflights13); data(flights); ls()',\r\n  u'execution_count': 1},\r\n 'header': {u'msg_id': u'5d982d5c-823f-4901-8147-62be8e5b5f45',\r\n  u'msg_type': u'execute_input',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'5d982d5c-823f-4901-8147-62be8e5b5f45',\r\n 'msg_type': u'execute_input',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 49, 30, 890131),\r\n  u'msg_id': u'49ff5db7-9400-4ddc-a559-1ae37050c763',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [13]: kc.get_iopub_msg(timeout=1)\r\nOut[13]:\r\n{'buffers': [],\r\n 'content': {u'data': {u'text/html': u\"'flights'\",\r\n   u'text/latex': u\"'flights'\",\r\n   u'text/markdown': u\"'flights'\",\r\n   u'text/plain': u'[1] \"flights\"'},\r\n  u'execution_count': 1,\r\n  u'metadata': {}},\r\n 'header': {u'msg_id': u'd316615b-41aa-4f27-987a-25cdd8d26d5a',\r\n  u'msg_type': u'execute_result',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'd316615b-41aa-4f27-987a-25cdd8d26d5a',\r\n 'msg_type': u'execute_result',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 49, 30, 890131),\r\n  u'msg_id': u'49ff5db7-9400-4ddc-a559-1ae37050c763',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [14]: kc.get_iopub_msg(timeout=1)\r\nOut[14]:\r\n{'buffers': [],\r\n 'content': {u'execution_state': u'idle'},\r\n 'header': {u'msg_id': u'09c6548e-461c-46fe-aa88-fc78b207505e',\r\n  u'msg_type': u'status',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'09c6548e-461c-46fe-aa88-fc78b207505e',\r\n 'msg_type': u'status',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 49, 30, 890131),\r\n  u'msg_id': u'49ff5db7-9400-4ddc-a559-1ae37050c763',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [15]: kc.execute('flights')\r\nOut[15]: 'ddaf08b9-02e3-47a6-8e08-45bd519f79b8'\r\n\r\nIn [16]: kc.get_shell_msg(timeout=1)\r\n---------------------------------------------------------------------------\r\nEmpty                                     Traceback (most recent call last)\r\n<ipython-input-16-0a8619c215d5> in <module>()\r\n----> 1 kc.get_shell_msg(timeout=1)\r\n\r\n/home/user/anaconda/lib/python2.7/site-packages/IPython/kernel/client.pyc in get_shell_msg(self, *args, **kwargs)\r\n     78     def get_shell_msg(self, *args, **kwargs):\r\n     79         \"\"Get a message from the shell channel\"\"\r\n---> 80         return self.shell_channel.get_msg(*args, **kwargs)\r\n     81\r\n     82     def get_iopub_msg(self, *args, **kwargs):\r\n\r\n/home/user/anaconda/lib/python2.7/site-packages/IPython/kernel/blocking/channels.pyc in get_msg(self, block, timeout)\r\n     55             return self._recv()\r\n     56         else:\r\n---> 57             raise Empty\r\n     58\r\n     59     def get_msgs(self):\r\n\r\nEmpty:\r\n\r\nIn [17]: kc.get_iopub_msg(timeout=5)\r\nOut[17]:\r\n{'buffers': [],\r\n 'content': {u'execution_state': u'busy'},\r\n 'header': {u'msg_id': u'34b2fcc4-5244-42d6-9ac8-2b287cbf9a76',\r\n  u'msg_type': u'status',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'34b2fcc4-5244-42d6-9ac8-2b287cbf9a76',\r\n 'msg_type': u'status',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 50, 10, 152110),\r\n  u'msg_id': u'ddaf08b9-02e3-47a6-8e08-45bd519f79b8',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [18]: kc.get_iopub_msg(timeout=5)\r\nOut[18]:\r\n{'buffers': [],\r\n 'content': {u'code': u'flights', u'execution_count': 2},\r\n 'header': {u'msg_id': u'ee48022a-4650-4630-a062-cb5dbdc3370d',\r\n  u'msg_type': u'execute_input',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'},\r\n 'metadata': {},\r\n 'msg_id': u'ee48022a-4650-4630-a062-cb5dbdc3370d',\r\n 'msg_type': u'execute_input',\r\n 'parent_header': {u'date': datetime.datetime(2015, 8, 3, 8, 50, 10, 152110),\r\n  u'msg_id': u'ddaf08b9-02e3-47a6-8e08-45bd519f79b8',\r\n  u'msg_type': u'execute_request',\r\n  u'session': u'5c784d01-74e0-4831-8753-957b8205b217',\r\n  u'username': u'user',\r\n  u'version': u'5.0'}}\r\n\r\nIn [19]: kc.get_iopub_msg(timeout=5)\r\n---------------------------------------------------------------------------\r\nEmpty                                     Traceback (most recent call last)\r\n<ipython-input-19-c75f27ab609f> in <module>()\r\n----> 1 kc.get_iopub_msg(timeout=5)\r\n\r\n/home/user/anaconda/lib/python2.7/site-packages/IPython/kernel/client.pyc in get_iopub_msg(self, *args, **kwargs)\r\n     82     def get_iopub_msg(self, *args, **kwargs):\r\n     83         \"\"Get a message from the iopub channel\"\"\r\n---> 84         return self.iopub_channel.get_msg(*args, **kwargs)\r\n     85\r\n     86     def get_stdin_msg(self, *args, **kwargs):\r\n\r\n/home/user/anaconda/lib/python2.7/site-packages/IPython/kernel/blocking/channels.pyc in get_msg(self, block, timeout)\r\n     55             return self._recv()\r\n     56         else:\r\n---> 57             raise Empty\r\n     58\r\n     59     def get_msgs(self):\r\n\r\nEmpty:\r\n```\r\n\r\nOthers dataframes are working as expected. \r\n\r\nThe R interpreter works correctly:\r\n\r\n```\r\nflight origin dest air_time distance hour minute\r\n1        1545    EWR  IAH      227     1400    5     17\r\n2        1714    LGA  IAH      227     1416    5     33\r\n3        1141    JFK  MIA      160     1089    5     42\r\n4         725    JFK  BQN      183     1576    5     44\r\n5         461    LGA  ATL      116      762    5     54\r\n6        1696    EWR  ORD      150      719    5     54\r\n7         507    EWR  FLL      158     1065    5     55\r\n8        5708    LGA  IAD       53      229    5     57\r\n9          79    JFK  MCO      140      944    5     57\r\n10        301    LGA  ORD      138      733    5     58\r\n...\r\n```\r\n\r\nI tried this on Ubuntu 15.04, after reinstalling IR kernel and using R version 3.2.1.\r\n"},"comment":{"url":"https://api.github.com/repos/IRkernel/IRkernel/issues/comments/128476424","html_url":"https://github.com/IRkernel/IRkernel/issues/174#issuecomment-128476424","issue_url":"https://api.github.com/repos/IRkernel/IRkernel/issues/174","id":128476424,"user":{"login":"rsmith31415","id":599274,"avatar_url":"https://avatars.githubusercontent.com/u/599274?v=3","gravatar_id":"","url":"https://api.github.com/users/rsmith31415","html_url":"https://github.com/rsmith31415","followers_url":"https://api.github.com/users/rsmith31415/followers","following_url":"https://api.github.com/users/rsmith31415/following{/other_user}","gists_url":"https://api.github.com/users/rsmith31415/gists{/gist_id}","starred_url":"https://api.github.com/users/rsmith31415/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rsmith31415/subscriptions","organizations_url":"https://api.github.com/users/rsmith31415/orgs","repos_url":"https://api.github.com/users/rsmith31415/repos","events_url":"https://api.github.com/users/rsmith31415/events{/privacy}","received_events_url":"https://api.github.com/users/rsmith31415/received_events","type":"User","site_admin":false},"created_at":"2015-08-06T19:09:03Z","updated_at":"2015-08-06T19:09:03Z","body":"Great. Thanks.\r\n\r\n There are still display issues, though:\r\n\r\n![screenshot from 2015-08-06 14 07 28](https://cloud.githubusercontent.com/assets/599274/9120879/8b74fdea-3c44-11e5-92dc-9bef06058573.png)\r\n"}}