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Jupyter, Cells not showing results. #12434

Open CamAust opened 3 years ago

CamAust commented 3 years ago

Actual Behavior

Opening Jupyter 6.0.2 from Anaconda Navigator 1.9.12. on OSX 10.13.6, Cells in notebooks on "run cell", do not show results.

Downloaded workbooks (eg scipy_con_2019-master.zip, open notebook "2_Gaussian_HMM_INSTRUCTOR.ipynb" ) initially show results from cells, but working through from the beginning using run, as each cell is calculated, the results disappear. They are no longer shown.

Expected Behavior

Downloaded notebooks should work if started from the beginning, to make it easy to explore and learn, and or adopt a similar example using ones own data.

To remove possibility something to do with the downloaded notebooks, a new notebook with basic cell contents like a=10 print(a) in one cell,

or something as simple as 2*3 in a cell, upon run, should show a result. Yet same behaviour.

Number in brackets on far left does increase by 1 with each use of Run (run cell).

A full stop kernal and rerun all cells from the beginning, simply enforces behavour to all cells. ie, all results in a downloaded notebook all disappear.

Noting this behaviour is consistent to a downloaded notebook and a new created notebook, suspect it is local settings, or conflict or set up issue.

Using Safari or Firefox as browser makes no difference to this behaviour. Ensuring downloaded notebooks are "trusted" and then re opened and begin again, also makes no difference.

Search of key words, and key fault line in terminal, on Google search, to stack overflow and Superuser, were not successful in finding a relatable solution. Mind you I seem not good at use of search terms of late. (Or may be that is just a google evolution less helpful search engine phenomena.)

Steps to Reproduce

Do not know what to suggest beyond above, in this case, to reproduce.

Looking in terminal I get the following identified error consistently hence I think this is helpful to resolve the source of this issue.

Traceback (most recent call last): File "/anaconda3/lib/python3.7/site-packages/tornado/websocket.py", line 546, in _run_callback result = callback(*args, **kwargs) File "/anaconda3/lib/python3.7/site-packages/notebook/services/kernels/handlers.py", line 274, in open self.create_stream() File "/anaconda3/lib/python3.7/site-packages/notebook/services/kernels/handlers.py", line 127, in createstream meth = getattr(km, 'connect' + channel) AttributeError: 'MappingKernelManager' object has no attribute 'connect_control'

Hence is seems possible the issue relates to permissions or incompatable component, possibly related to security upgrade in Jupyter (those pages read to seek answer to this), so that the standard output of a cell upon running can not be returned to the notebook in the browser to be displayed. My best guess as a not very competent coder.

Anaconda or Miniconda version:

Anaconda3-2020.11-MacOSX-x86_64.pkg

Operating System:

OSX 10.13.6

conda info
conda info

     active environment : base
    active env location : /opt/anaconda3
            shell level : 2
       user config file : /Users/C01/.condarc
 populated config files : /Users/C01/.condarc
          conda version : 4.9.2
    conda-build version : 3.20.5
         python version : 3.8.5.final.0
       virtual packages : __osx=10.13.6=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/anaconda3  (writable)
           channel URLs : https://conda.anaconda.org/anaconda-fusion/osx-64
                          https://conda.anaconda.org/anaconda-fusion/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/anaconda3/pkgs
                          /Users/C01/.conda/pkgs
       envs directories : /opt/anaconda3/envs
                          /Users/C01/.conda/envs
               platform : osx-64
             user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 502:20
             netrc file : None
           offline mode : False

conda list --show-channel-urls

No packages added since fresh download and install of Anaconda 1 May 2021.

``` conda list --show-channel-urls # packages in environment at /opt/anaconda3: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py38_0 defaults alabaster 0.7.12 py_0 defaults anaconda 2020.11 py38_0 defaults anaconda-client 1.7.2 py38_0 defaults anaconda-navigator 1.10.0 py38_0 defaults anaconda-project 0.8.4 py_0 defaults applaunchservices 0.2.1 py_0 defaults appnope 0.1.0 py38_1001 defaults appscript 1.1.1 py38haf1e3a3_0 defaults argh 0.26.2 py38_0 defaults argon2-cffi 20.1.0 py38haf1e3a3_1 defaults asn1crypto 1.4.0 py_0 defaults astroid 2.4.2 py38_0 defaults astropy 4.0.2 py38haf1e3a3_0 defaults async_generator 1.10 py_0 defaults atomicwrites 1.4.0 py_0 defaults attrs 20.3.0 pyhd3eb1b0_0 defaults autopep8 1.5.4 py_0 defaults babel 2.8.1 pyhd3eb1b0_0 defaults backcall 0.2.0 py_0 defaults backports 1.0 py_2 defaults backports.functools_lru_cache 1.6.1 py_0 defaults backports.shutil_get_terminal_size 1.0.0 py38_2 defaults backports.tempfile 1.0 py_1 defaults backports.weakref 1.0.post1 py_1 defaults beautifulsoup4 4.9.3 pyhb0f4dca_0 defaults bitarray 1.6.1 py38h9ed2024_0 defaults bkcharts 0.2 py38_0 defaults blas 1.0 mkl defaults bleach 3.2.1 py_0 defaults blosc 1.20.1 hab81aa3_0 defaults bokeh 2.2.3 py38_0 defaults boto 2.49.0 py38_0 defaults bottleneck 1.3.2 py38hf1fa96c_1 defaults brotlipy 0.7.0 py38haf1e3a3_1000 defaults bzip2 1.0.8 h1de35cc_0 defaults ca-certificates 2020.10.14 0 defaults certifi 2020.6.20 pyhd3eb1b0_3 defaults cffi 1.14.3 py38hed5b41f_0 defaults chardet 3.0.4 py38_1003 defaults click 7.1.2 py_0 defaults cloudpickle 1.6.0 py_0 defaults clyent 1.2.2 py38_1 defaults colorama 0.4.4 py_0 defaults conda 4.9.2 py38hecd8cb5_0 defaults conda-build 3.20.5 py38_1 defaults conda-env 2.6.0 1 defaults conda-package-handling 1.7.2 py38h22f3db7_0 defaults conda-verify 3.4.2 py_1 defaults contextlib2 0.6.0.post1 py_0 defaults cryptography 3.1.1 py38hddc9c9b_0 defaults curl 7.71.1 hb0a8c7a_1 defaults cycler 0.10.0 py38_0 defaults cython 0.29.21 py38hb1e8313_0 defaults cytoolz 0.11.0 py38haf1e3a3_0 defaults dask 2.30.0 py_0 defaults dask-core 2.30.0 py_0 defaults dbus 1.13.18 h18a8e69_0 defaults decorator 4.4.2 py_0 defaults defusedxml 0.6.0 py_0 defaults diff-match-patch 20200713 py_0 defaults distributed 2.30.1 py38hecd8cb5_0 defaults docutils 0.16 py38_1 defaults entrypoints 0.3 py38_0 defaults et_xmlfile 1.0.1 py_1001 defaults expat 2.2.10 hb1e8313_2 defaults fastcache 1.1.0 py38h1de35cc_0 defaults filelock 3.0.12 py_0 defaults flake8 3.8.4 py_0 defaults flask 1.1.2 py_0 defaults freetype 2.10.4 ha233b18_0 defaults fsspec 0.8.3 py_0 defaults future 0.18.2 py38_1 defaults get_terminal_size 1.0.0 h7520d66_0 defaults gettext 0.19.8.1 hb0f4f8b_2 defaults gevent 20.9.0 py38haf1e3a3_0 defaults glib 2.66.1 h9bbe63b_0 defaults glob2 0.7 py_0 defaults gmp 6.1.2 hb37e062_1 defaults gmpy2 2.0.8 py38h6ef4df4_3 defaults greenlet 0.4.17 py38haf1e3a3_0 defaults h5py 2.10.0 py38h3134771_0 defaults hdf5 1.10.4 hfa1e0ec_0 defaults heapdict 1.0.1 py_0 defaults html5lib 1.1 py_0 defaults icu 58.2 h0a44026_3 defaults idna 2.10 py_0 defaults imageio 2.9.0 py_0 defaults imagesize 1.2.0 py_0 defaults importlib-metadata 2.0.0 py_1 defaults importlib_metadata 2.0.0 1 defaults iniconfig 1.1.1 py_0 defaults intel-openmp 2019.4 233 defaults intervaltree 3.1.0 py_0 defaults ipykernel 5.3.4 py38h5ca1d4c_0 defaults ipython 7.19.0 py38h01d92e1_0 defaults ipython_genutils 0.2.0 py38_0 defaults ipywidgets 7.5.1 py_1 defaults isort 5.6.4 py_0 defaults itsdangerous 1.1.0 py_0 defaults jbig 2.1 h4d881f8_0 defaults jdcal 1.4.1 py_0 defaults jedi 0.17.1 py38_0 defaults jinja2 2.11.2 py_0 defaults joblib 0.17.0 py_0 defaults jpeg 9b he5867d9_2 defaults json5 0.9.5 py_0 defaults jsonschema 3.2.0 py_2 defaults jupyter 1.0.0 py38_7 defaults jupyter_client 6.1.7 py_0 defaults jupyter_console 6.2.0 py_0 defaults jupyter_core 4.6.3 py38_0 defaults jupyterlab 2.2.6 py_0 defaults jupyterlab_pygments 0.1.2 py_0 defaults jupyterlab_server 1.2.0 py_0 defaults keyring 21.4.0 py38_1 defaults kiwisolver 1.3.0 py38h23ab428_0 defaults krb5 1.18.2 h75d18d8_0 defaults lazy-object-proxy 1.4.3 py38h1de35cc_0 defaults lcms2 2.11 h92f6f08_0 defaults libarchive 3.4.2 haa3ed63_0 defaults libcurl 7.71.1 h8a08a2b_1 defaults libcxx 10.0.0 1 defaults libedit 3.1.20191231 h1de35cc_1 defaults libffi 3.3 hb1e8313_2 defaults libgfortran 3.0.1 h93005f0_2 defaults libiconv 1.16 h1de35cc_0 defaults liblief 0.10.1 h0a44026_0 defaults libllvm10 10.0.1 h76017ad_5 defaults libpng 1.6.37 ha441bb4_0 defaults libsodium 1.0.18 h1de35cc_0 defaults libspatialindex 1.9.3 h0a44026_0 defaults libssh2 1.9.0 ha12b0ac_1 defaults libtiff 4.1.0 hcb84e12_1 defaults libxml2 2.9.10 h7cdb67c_3 defaults libxslt 1.1.34 h83b36ba_0 defaults llvm-openmp 10.0.0 h28b9765_0 defaults llvmlite 0.34.0 py38h739e7dc_4 defaults locket 0.2.0 py38_1 defaults lxml 4.6.1 py38h63b7cb6_0 defaults lz4-c 1.9.2 h79c402e_3 defaults lzo 2.10 haf1e3a3_2 defaults markupsafe 1.1.1 py38h1de35cc_1 defaults matplotlib 3.3.2 0 defaults matplotlib-base 3.3.2 py38h181983e_0 defaults mccabe 0.6.1 py38_1 defaults mistune 0.8.4 py38h1de35cc_1001 defaults mkl 2019.4 233 defaults mkl-service 2.3.0 py38hfbe908c_0 defaults mkl_fft 1.2.0 py38hc64f4ea_0 defaults mkl_random 1.1.1 py38h959d312_0 defaults mock 4.0.2 py_0 defaults more-itertools 8.6.0 pyhd3eb1b0_0 defaults mpc 1.1.0 h6ef4df4_1 defaults mpfr 4.0.2 h9066e36_1 defaults mpmath 1.1.0 py38_0 defaults msgpack-python 1.0.0 py38h04f5b5a_1 defaults multipledispatch 0.6.0 py38_0 defaults navigator-updater 0.2.1 py38_0 defaults nbclient 0.5.1 py_0 defaults nbconvert 6.0.7 py38_0 defaults nbformat 5.0.8 py_0 defaults ncurses 6.2 h0a44026_1 defaults nest-asyncio 1.4.2 pyhd3eb1b0_0 defaults networkx 2.5 py_0 defaults nltk 3.5 py_0 defaults nose 1.3.7 py38_1004 defaults notebook 6.1.4 py38_0 defaults numba 0.51.2 py38h6440ff4_1 defaults numexpr 2.7.1 py38hce01a72_0 defaults numpy 1.19.2 py38h456fd55_0 defaults numpy-base 1.19.2 py38hcfb5961_0 defaults numpydoc 1.1.0 pyhd3eb1b0_1 defaults olefile 0.46 py_0 defaults openpyxl 3.0.5 py_0 defaults openssl 1.1.1h haf1e3a3_0 defaults packaging 20.4 py_0 defaults pandas 1.1.3 py38hb1e8313_0 defaults pandoc 2.11 h0dc7051_0 defaults pandocfilters 1.4.3 py38hecd8cb5_1 defaults parso 0.7.0 py_0 defaults partd 1.1.0 py_0 defaults path 15.0.0 py38_0 defaults path.py 12.5.0 0 defaults pathlib2 2.3.5 py38_1 defaults pathtools 0.1.2 py_1 defaults patsy 0.5.1 py38_0 defaults pcre 8.44 hb1e8313_0 defaults pep8 1.7.1 py38_0 defaults pexpect 4.8.0 py38_1 defaults pickleshare 0.7.5 py38_1001 defaults pillow 8.0.1 py38h5270095_0 defaults pip 20.2.4 py38hecd8cb5_0 defaults pkginfo 1.6.1 py38hecd8cb5_0 defaults pluggy 0.13.1 py38_0 defaults ply 3.11 py38_0 defaults prometheus_client 0.8.0 py_0 defaults prompt-toolkit 3.0.8 py_0 defaults prompt_toolkit 3.0.8 0 defaults psutil 5.7.2 py38haf1e3a3_0 defaults ptyprocess 0.6.0 py38_0 defaults py 1.9.0 py_0 defaults py-lief 0.10.1 py38haf313ee_0 defaults pycodestyle 2.6.0 py_0 defaults pycosat 0.6.3 py38h1de35cc_1 defaults pycparser 2.20 py_2 defaults pycurl 7.43.0.6 py38hddc9c9b_0 defaults pydocstyle 5.1.1 py_0 defaults pyflakes 2.2.0 py_0 defaults pygments 2.7.2 pyhd3eb1b0_0 defaults pylint 2.6.0 py38_0 defaults pyodbc 4.0.30 py38h0a44026_0 defaults pyopenssl 19.1.0 py_1 defaults pyparsing 2.4.7 py_0 defaults pyqt 5.9.2 py38h655552a_2 defaults pyrsistent 0.17.3 py38haf1e3a3_0 defaults pysocks 1.7.1 py38_1 defaults pytables 3.6.1 py38h4727e94_0 defaults pytest 6.1.1 py38_0 defaults python 3.8.5 h26836e1_1 defaults python-dateutil 2.8.1 py_0 defaults python-jsonrpc-server 0.4.0 py_0 defaults python-language-server 0.35.1 py_0 defaults python-libarchive-c 2.9 py_0 defaults python.app 2 py38_10 defaults pytz 2020.1 py_0 defaults pywavelets 1.1.1 py38haf1e3a3_2 defaults pyyaml 5.3.1 py38haf1e3a3_1 defaults pyzmq 19.0.2 py38hb1e8313_1 defaults qdarkstyle 2.8.1 py_0 defaults qt 5.9.7 h468cd18_1 defaults qtawesome 1.0.1 py_0 defaults qtconsole 4.7.7 py_0 defaults qtpy 1.9.0 py_0 defaults readline 8.0 h1de35cc_0 defaults regex 2020.10.15 py38haf1e3a3_0 defaults requests 2.24.0 py_0 defaults ripgrep 12.1.1 0 defaults rope 0.18.0 py_0 defaults rtree 0.9.4 py38_1 defaults ruamel_yaml 0.15.87 py38haf1e3a3_1 defaults scikit-image 0.17.2 py38h81aa140_0 defaults scikit-learn 0.23.2 py38h959d312_0 defaults scipy 1.5.2 py38h2515648_0 defaults seaborn 0.11.0 py_0 defaults send2trash 1.5.0 py38_0 defaults setuptools 50.3.1 py38hecd8cb5_1 defaults simplegeneric 0.8.1 py38_2 defaults singledispatch 3.4.0.3 py_1001 defaults sip 4.19.8 py38h0a44026_0 defaults six 1.15.0 py38hecd8cb5_0 defaults snowballstemmer 2.0.0 py_0 defaults sortedcollections 1.2.1 py_0 defaults sortedcontainers 2.2.2 py_0 defaults soupsieve 2.0.1 py_0 defaults sphinx 3.2.1 py_0 defaults sphinxcontrib 1.0 py38_1 defaults sphinxcontrib-applehelp 1.0.2 py_0 defaults sphinxcontrib-devhelp 1.0.2 py_0 defaults sphinxcontrib-htmlhelp 1.0.3 py_0 defaults sphinxcontrib-jsmath 1.0.1 py_0 defaults sphinxcontrib-qthelp 1.0.3 py_0 defaults sphinxcontrib-serializinghtml 1.1.4 py_0 defaults sphinxcontrib-websupport 1.2.4 py_0 defaults spyder 4.1.5 py38_0 defaults spyder-kernels 1.9.4 py38_0 defaults sqlalchemy 1.3.20 py38h9ed2024_0 defaults sqlite 3.33.0 hffcf06c_0 defaults statsmodels 0.12.0 py38haf1e3a3_0 defaults sympy 1.6.2 py38hecd8cb5_1 defaults tblib 1.7.0 py_0 defaults terminado 0.9.1 py38_0 defaults testpath 0.4.4 py_0 defaults threadpoolctl 2.1.0 pyh5ca1d4c_0 defaults tifffile 2020.10.1 py38h0cf3a3e_2 defaults tk 8.6.10 hb0a8c7a_0 defaults toml 0.10.1 py_0 defaults toolz 0.11.1 py_0 defaults tornado 6.0.4 py38h1de35cc_1 defaults tqdm 4.50.2 py_0 defaults traitlets 5.0.5 py_0 defaults typing_extensions 3.7.4.3 py_0 defaults ujson 4.0.1 py38hb1e8313_0 defaults unicodecsv 0.14.1 py38_0 defaults unixodbc 2.3.9 haf1e3a3_0 defaults urllib3 1.25.11 py_0 defaults watchdog 0.10.3 py38haf1e3a3_0 defaults wcwidth 0.2.5 py_0 defaults webencodings 0.5.1 py38_1 defaults werkzeug 1.0.1 py_0 defaults wheel 0.35.1 py_0 defaults widgetsnbextension 3.5.1 py38_0 defaults wrapt 1.11.2 py38h1de35cc_0 defaults wurlitzer 2.0.1 py38_0 defaults xlrd 1.2.0 py_0 defaults xlsxwriter 1.3.7 py_0 defaults xlwings 0.20.8 py38_0 defaults xlwt 1.3.0 py38_0 defaults xmltodict 0.12.0 py_0 defaults xz 5.2.5 h1de35cc_0 defaults yaml 0.2.5 haf1e3a3_0 defaults yapf 0.30.0 py_0 defaults zeromq 4.3.3 hb1e8313_3 defaults zict 2.0.0 py_0 defaults zipp 3.4.0 pyhd3eb1b0_0 defaults zlib 1.2.11 h1de35cc_3 defaults zope 1.0 py38_1 defaults zope.event 4.5.0 py38_0 defaults zope.interface 5.1.2 py38haf1e3a3_0 defaults zstd 1.4.5 h41d2c2f_0 defaults ```
CamAust commented 3 years ago

If this issue arises from some simple evident user error my end, do please just let me know. If such is so, it is not obvious from some hours of research to check so, and find solution.

CamAust commented 3 years ago

Coming to conclusion something big has happened with Anaconda free access version. Nothing either with post on SO. Have now spent 20+ hours, seeking to be able to use Jupyter in the most basic way.

The silence is mysterious. What is happening??