{"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":20,"created_at":"2015-08-03T14:25:49Z","updated_at":"2015-08-26T23:32:57Z","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/135205239","html_url":"https://github.com/IRkernel/IRkernel/issues/174#issuecomment-135205239","issue_url":"https://api.github.com/repos/IRkernel/IRkernel/issues/174","id":135205239,"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":"2015-08-26T23:32:56Z","updated_at":"2015-08-26T23:32:56Z","body":"@flying-sheep What do you mean? Do you get the correct HTML representation when you tested? Because the last screenshot certainly doesn't look okay.\r\n\r\nHere you can see that the output needs to have its index, similar to the DataFrame representation that is now working correctly:\r\n\r\n![screenshot from 2015-08-26 18 27 05](https://cloud.githubusercontent.com/assets/599274/9509001/9cb1aad6-4c20-11e5-90ac-6204ed38c9d3.png)\r\n\r\n![screenshot from 2015-08-26 18 27 30](https://cloud.githubusercontent.com/assets/599274/9509005/a1d8b644-4c20-11e5-983b-6ef635004daf.png)\r\n"}}