I am trying to start a jupyter lab notebook, but suddenly it will not work. I start up jupyter lab from the terminal (using jupyter lab, this is on ubuntu 18.04). I notebooks load normally, but when I try to run a cell, the [ ] to its left is just blank, no number or * appears. There’s a lot of error and stuff in the terminal, but I do not understand what it means:
(base) torkelloman@slpc385:~$ jupyter lab
[I 21:59:16.360 LabApp] Writing notebook server cookie secret to /run/user/1001/jupyter/notebook_cookie_secret
[I 21:59:17.790 LabApp] JupyterLab extension loaded from /home/torkelloman/anaconda3/lib/python3.7/site-packages/jupyterlab
[I 21:59:17.790 LabApp] JupyterLab application directory is /home/torkelloman/anaconda3/share/jupyter/lab
[W 21:59:17.792 LabApp] JupyterLab server extension not enabled, manually loading...
[I 21:59:17.797 LabApp] JupyterLab extension loaded from /home/torkelloman/anaconda3/lib/python3.7/site-packages/jupyterlab
[I 21:59:17.797 LabApp] JupyterLab application directory is /home/torkelloman/anaconda3/share/jupyter/lab
[I 21:59:17.798 LabApp] Serving notebooks from local directory: /home/torkelloman
[I 21:59:17.798 LabApp] The Jupyter Notebook is running at:
[I 21:59:17.798 LabApp] http://localhost:8888/?token=72bd9cd252113081e6096edf4351d8468f8afac774f206f5
[I 21:59:17.798 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 21:59:17.845 LabApp]
To access the notebook, open this file in a browser:
file:///run/user/1001/jupyter/nbserver-4501-open.html
Or copy and paste one of these URLs:
http://localhost:8888/?token=72bd9cd252113081e6096edf4351d8468f8afac774f206f5
[I 21:59:21.946 LabApp] Node v10.13.0
[I 21:59:21.973 LabApp] Build is up to date
[I 21:59:45.061 LabApp] Kernel started: 5e2dc25f-cd20-469b-a5a3-9fe57a55c05d
[I 21:59:45.149 LabApp] Kernel started: e6805dc2-ab37-4a25-bf8e-9cf1f207b42d
ERROR: ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
[I 21:59:48.060 LabApp] KernelRestarter: restarting kernel (1/5), new random ports
[I 21:59:48.148 LabApp] KernelRestarter: restarting kernel (1/5), new random ports
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
[I 21:59:51.071 LabApp] KernelRestarter: restarting kernel (2/5), new random ports
[I 21:59:51.239 LabApp] KernelRestarter: restarting kernel (2/5), new random ports
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
[I 21:59:54.077 LabApp] KernelRestarter: restarting kernel (3/5), new random ports
[I 21:59:54.336 LabApp] KernelRestarter: restarting kernel (3/5), new random ports
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
[I 21:59:57.083 LabApp] KernelRestarter: restarting kernel (4/5), new random ports
ERROR: [I 21:59:57.423 LabApp] KernelRestarter: restarting kernel (4/5), new random ports
LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
ERROR: LoadError: TypeError: in typeassert, expected Vector{Any}, got a value of type Dict{String, Any}
Stacktrace:
[1] explicit_manifest_deps_get(project_file::String, where::Base.UUID, name::String)
@ Base ./loading.jl:498
[2] manifest_deps_get(env::String, where::Base.PkgId, name::String)
@ Base ./loading.jl:379
[3] identify_package(where::Base.PkgId, name::String)
@ Base ./loading.jl:254
[4] stale_cachefile(modpath::String, cachefile::String)
@ Base ./loading.jl:1750
[5] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:736
[6] _require(pkg::Base.PkgId)
@ Base ./loading.jl:998
[7] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:914
[8] require(into::Module, mod::Symbol)
@ Base ./loading.jl:901
in expression starting at /home/torkelloman/.julia/packages/IJulia/e8kqU/src/kernel.jl:1
[W 22:00:00.091 LabApp] KernelRestarter: restart failed
[W 22:00:00.091 LabApp] Kernel 5e2dc25f-cd20-469b-a5a3-9fe57a55c05d died, removing from map.
[W 22:00:00.536 LabApp] KernelRestarter: restart failed
[W 22:00:00.536 LabApp] Kernel e6805dc2-ab37-4a25-bf8e-9cf1f207b42d died, removing from map.
[W 22:00:23.652 LabApp] 404 GET /api/kernels/e6805dc2-ab37-4a25-bf8e-9cf1f207b42d/channels?session_id=97f7f1ff-b96f-4eda-9262-f073d121738b&token=72bd9cd252113081e6096edf4351d8468f8afac774f206f5 (127.0.0.1): Kernel does not exist: e6805dc2-ab37-4a25-bf8e-9cf1f207b42d
[W 22:00:23.680 LabApp] 404 GET /api/kernels/e6805dc2-ab37-4a25-bf8e-9cf1f207b42d/channels?session_id=97f7f1ff-b96f-4eda-9262-f073d121738b&token=72bd9cd252113081e6096edf4351d8468f8afac774f206f5 (127.0.0.1) 29.89ms referer=None
[W 22:00:24.704 LabApp] Replacing stale connection: e6805dc2-ab37-4a25-bf8e-9cf1f207b42d:97f7f1ff-b96f-4eda-9262-f073d121738b
[W 22:00:45.168 LabApp] Timeout waiting for kernel_info reply from 5e2dc25f-cd20-469b-a5a3-9fe57a55c05d
[E 22:00:45.171 LabApp] Error opening stream: HTTP 404: Not Found (Kernel does not exist: 5e2dc25f-cd20-469b-a5a3-9fe57a55c05d)
[E 22:00:45.172 LabApp] Uncaught exception GET /api/kernels/5e2dc25f-cd20-469b-a5a3-9fe57a55c05d/channels?session_id=cd2c5b8c-814a-4e04-b646-300912faf530&token=72bd9cd252113081e6096edf4351d8468f8afac774f206f5 (127.0.0.1)
HTTPServerRequest(protocol='http', host='localhost:8888', method='GET', uri='/api/kernels/5e2dc25f-cd20-469b-a5a3-9fe57a55c05d/channels?session_id=cd2c5b8c-814a-4e04-b646-300912faf530&token=72bd9cd252113081e6096edf4351d8468f8afac774f206f5', version='HTTP/1.1', remote_ip='127.0.0.1')
Traceback (most recent call last):
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/web.py", line 1699, in _execute
result = await result
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 736, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/notebook/services/kernels/handlers.py", line 241, in get
yield super(ZMQChannelsHandler, self).get(kernel_id=kernel_id)
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 729, in run
value = future.result()
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 736, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/notebook/base/zmqhandlers.py", line 297, in get
yield gen.maybe_future(res)
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/gen.py", line 729, in run
value = future.result()
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 278, in get
await self.ws_connection.accept_connection(self)
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 881, in accept_connection
await self._accept_connection(handler)
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 964, in _accept_connection
await self._receive_frame_loop()
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 1118, in _receive_frame_loop
await self._receive_frame()
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 1130, in _receive_frame
data = await self._read_bytes(2)
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 1124, in _read_bytes
data = await self.stream.read_bytes(n)
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/iostream.py", line 436, in read_bytes
future = self._start_read()
File "/home/torkelloman/anaconda3/lib/python3.7/site-packages/tornado/iostream.py", line 797, in _start_read
assert self._read_future is None, "Already reading"
AssertionError: Already reading
[I 22:01:43.704 LabApp] Saving file at /Desktop/Thesis SigV Code/Chapter_SigV/make_figures_old.ipynb