{"action":"created","issue":{"url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/10153","repository_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues","labels_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/10153/labels{/name}","comments_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/10153/comments","events_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/10153/events","html_url":"https://github.com/ContinuumIO/anaconda-issues/issues/10153","id":366931647,"node_id":"MDU6SXNzdWUzNjY5MzE2NDc=","number":10153,"title":"R kernel in Jupyter Notebook cannot start!","user":{"login":"Xiajun666","id":38359426,"node_id":"MDQ6VXNlcjM4MzU5NDI2","avatar_url":"https://avatars2.githubusercontent.com/u/38359426?v=4","gravatar_id":"","url":"https://api.github.com/users/Xiajun666","html_url":"https://github.com/Xiajun666","followers_url":"https://api.github.com/users/Xiajun666/followers","following_url":"https://api.github.com/users/Xiajun666/following{/other_user}","gists_url":"https://api.github.com/users/Xiajun666/gists{/gist_id}","starred_url":"https://api.github.com/users/Xiajun666/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Xiajun666/subscriptions","organizations_url":"https://api.github.com/users/Xiajun666/orgs","repos_url":"https://api.github.com/users/Xiajun666/repos","events_url":"https://api.github.com/users/Xiajun666/events{/privacy}","received_events_url":"https://api.github.com/users/Xiajun666/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":10,"created_at":"2018-10-04T19:15:07Z","updated_at":"2018-10-05T01:04:24Z","closed_at":null,"author_association":"NONE","body":"Xiajuns-MacBook-Pro:~ Xiajun$ jupyter notebook\r\n[I 15:08:41.597 NotebookApp] The port 8888 is already in use, trying another port.\r\n[I 15:08:41.620 NotebookApp] Serving notebooks from local directory: /Users/Xiajun\r\n[I 15:08:41.621 NotebookApp] The Jupyter Notebook is running at:\r\n[I 15:08:41.621 NotebookApp] http://localhost:8889/?token=001672bf16962cdb6897004f5452b23417fc59c4d2945cf0\r\n[I 15:08:41.621 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).\r\n[C 15:08:41.623 NotebookApp] \r\n    \r\n    Copy/paste this URL into your browser when you connect for the first time,\r\n    to login with a token:\r\n        http://localhost:8889/?token=001672bf16962cdb6897004f5452b23417fc59c4d2945cf0\r\n[I 15:08:41.850 NotebookApp] Accepting one-time-token-authenticated connection from ::1\r\n[W 15:08:56.521 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20181004150841 (::1) 15.54ms referer=http://localhost:8889/notebooks/Desktop/MTH9875%20Volatility%20Surface/HW/9875HW1_Xiajun_Zhang.ipynb\r\n[I 15:08:57.954 NotebookApp] Kernel started: 459ae7ad-5f15-47ed-8697-82844029b279\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:09:00.952 NotebookApp] KernelRestarter: restarting kernel (1/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:09:03.961 NotebookApp] KernelRestarter: restarting kernel (2/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:09:06.976 NotebookApp] KernelRestarter: restarting kernel (3/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:09:09.987 NotebookApp] KernelRestarter: restarting kernel (4/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[W 15:09:12.997 NotebookApp] KernelRestarter: restart failed\r\n[W 15:09:12.998 NotebookApp] Kernel 459ae7ad-5f15-47ed-8697-82844029b279 died, removing from map.\r\n[W 15:09:58.028 NotebookApp] Timeout waiting for kernel_info reply from 459ae7ad-5f15-47ed-8697-82844029b279\r\n[E 15:09:58.032 NotebookApp] Error opening stream: HTTP 404: Not Found (Kernel does not exist: 459ae7ad-5f15-47ed-8697-82844029b279)\r\n^C[I 15:11:53.469 NotebookApp] interrupted\r\nServing notebooks from local directory: /Users/Xiajun\r\n0 active kernels\r\nThe Jupyter Notebook is running at:\r\nhttp://localhost:8889/?token=001672bf16962cdb6897004f5452b23417fc59c4d2945cf0\r\nShutdown this notebook server (y/[n])? y\r\n[C 15:11:54.739 NotebookApp] Shutdown confirmed\r\n[I 15:11:54.740 NotebookApp] Shutting down 0 kernels\r\nXiajuns-MacBook-Pro:~ Xiajun$ rm -Rf ~/Library/R/\r\nXiajuns-MacBook-Pro:~ Xiajun$ conda install r-irkernel\r\nSolving environment: done\r\n\r\n# All requested packages already installed.\r\n\r\nXiajuns-MacBook-Pro:~ Xiajun$ jupyter notebook\r\n[I 15:13:35.067 NotebookApp] Serving notebooks from local directory: /Users/Xiajun\r\n[I 15:13:35.067 NotebookApp] The Jupyter Notebook is running at:\r\n[I 15:13:35.067 NotebookApp] http://localhost:8888/?token=f5c564816f9e0b9a7f7823bacd412d8ac07e846f0de5a4fd\r\n[I 15:13:35.067 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).\r\n[C 15:13:35.068 NotebookApp] \r\n    \r\n    Copy/paste this URL into your browser when you connect for the first time,\r\n    to login with a token:\r\n        http://localhost:8888/?token=f5c564816f9e0b9a7f7823bacd412d8ac07e846f0de5a4fd\r\n[I 15:13:35.291 NotebookApp] Accepting one-time-token-authenticated connection from ::1\r\n[W 15:13:37.613 NotebookApp] 404 GET /api/kernels/23a8c88f-5dab-4678-a494-6671009c1a72/channels?session_id=5edbfe73fb7c4427ae08e30035956497 (::1): Kernel does not exist: 23a8c88f-5dab-4678-a494-6671009c1a72\r\n[W 15:13:37.626 NotebookApp] 404 GET /api/kernels/23a8c88f-5dab-4678-a494-6671009c1a72/channels?session_id=5edbfe73fb7c4427ae08e30035956497 (::1) 22.04ms referer=None\r\n[W 15:13:37.642 NotebookApp] 404 GET /api/kernels/cc32917f-0fe6-494b-ad8b-7b08bf4a9f59/channels?session_id=d9f6c8379e794d56832ca785d8a8d7d1 (::1): Kernel does not exist: cc32917f-0fe6-494b-ad8b-7b08bf4a9f59\r\n[W 15:13:37.644 NotebookApp] 404 GET /api/kernels/cc32917f-0fe6-494b-ad8b-7b08bf4a9f59/channels?session_id=d9f6c8379e794d56832ca785d8a8d7d1 (::1) 5.45ms referer=None\r\n[W 15:13:37.698 NotebookApp] 404 GET /api/kernels/cd9d29a0-9a9f-48d4-8545-5f59b69ceb02/channels?session_id=da86d69b659d4b3886b046f1d56bdcb2 (::1): Kernel does not exist: cd9d29a0-9a9f-48d4-8545-5f59b69ceb02\r\n[W 15:13:37.699 NotebookApp] 404 GET /api/kernels/cd9d29a0-9a9f-48d4-8545-5f59b69ceb02/channels?session_id=da86d69b659d4b3886b046f1d56bdcb2 (::1) 4.66ms referer=None\r\n[W 15:13:44.168 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20181004151334 (::1) 5.27ms referer=http://localhost:8888/notebooks/Desktop/MTH9875%20Volatility%20Surface/HW/9875HW1_Xiajun_Zhang.ipynb\r\n[I 15:13:45.600 NotebookApp] Kernel started: 982ac107-b10c-4826-ab58-106afde490af\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:13:48.594 NotebookApp] KernelRestarter: restarting kernel (1/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:13:51.603 NotebookApp] KernelRestarter: restarting kernel (2/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:13:54.615 NotebookApp] KernelRestarter: restarting kernel (3/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[I 15:13:57.625 NotebookApp] KernelRestarter: restarting kernel (4/5), new random ports\r\ndyld: Library not loaded: @rpath/libgfortran.3.dylib\r\n  Referenced from: /Users/Xiajun/anaconda/lib/R/lib/libRblas.dylib\r\n  Reason: image not found\r\n[W 15:14:00.638 NotebookApp] KernelRestarter: restart failed\r\n[W 15:14:00.639 NotebookApp] Kernel 982ac107-b10c-4826-ab58-106afde490af died, removing from map.\r\n[W 15:14:45.780 NotebookApp] Timeout waiting for kernel_info reply from 982ac107-b10c-4826-ab58-106afde490af\r\n[E 15:14:45.783 NotebookApp] Error opening stream: HTTP 404: Not Found (Kernel does not exist: 982ac107-b10c-4826-ab58-106afde490af)"},"comment":{"url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/comments/427215628","html_url":"https://github.com/ContinuumIO/anaconda-issues/issues/10153#issuecomment-427215628","issue_url":"https://api.github.com/repos/ContinuumIO/anaconda-issues/issues/10153","id":427215628,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNzIxNTYyOA==","user":{"login":"mingwandroid","id":1042804,"node_id":"MDQ6VXNlcjEwNDI4MDQ=","avatar_url":"https://avatars1.githubusercontent.com/u/1042804?v=4","gravatar_id":"","url":"https://api.github.com/users/mingwandroid","html_url":"https://github.com/mingwandroid","followers_url":"https://api.github.com/users/mingwandroid/followers","following_url":"https://api.github.com/users/mingwandroid/following{/other_user}","gists_url":"https://api.github.com/users/mingwandroid/gists{/gist_id}","starred_url":"https://api.github.com/users/mingwandroid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mingwandroid/subscriptions","organizations_url":"https://api.github.com/users/mingwandroid/orgs","repos_url":"https://api.github.com/users/mingwandroid/repos","events_url":"https://api.github.com/users/mingwandroid/events{/privacy}","received_events_url":"https://api.github.com/users/mingwandroid/received_events","type":"User","site_admin":false},"created_at":"2018-10-05T01:04:24Z","updated_at":"2018-10-05T01:04:24Z","author_association":"MEMBER","body":"I'm pretty much out of ideas, the only thing I can think is that some of the things you installed vis other methods than conda install (pip, running python setup.py) has introduced an incompatibility.\r\n\r\nI tried:\r\n1. Minimal env with just the necessary deps for this test.\r\n2. Adding r-essentials metapackage to that.\r\n3. Adding the latest anaconda 5.3 metapackage to that.\r\n4. Running a final conda update --all.\r\n\r\nAll of these tests worked fine."}}
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