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Notebook Will Not Launch on Root #7660

Closed greg-amato closed 6 years ago

greg-amato commented 6 years ago

Tried rolling back to previous anaconda version to no effect. Notebook will not launch on root env. At a loss where to go from here...

Traceback (most recent call last): File "C:\Users\grega\Anaconda3\Scripts\jupyter-notebook-script.py", line 10, in sys.exit(main()) File "C:\Users\grega\Anaconda3\lib\site-packages\jupyter_core\application.py", line 266, in launch_instance return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs) File "C:\Users\grega\Anaconda3\lib\site-packages\traitlets\config\application.py", line 657, in launch_instance app.initialize(argv) File "", line 2, in initialize File "C:\Users\grega\Anaconda3\lib\site-packages\traitlets\config\application.py", line 87, in catch_config_error return method(app, *args, **kwargs) File "C:\Users\grega\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 1368, in initialize self.init_webapp() File "C:\Users\grega\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 1161, in init_webapp self.jinja_environment_options File "C:\Users\grega\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 154, in __init__ base_url, default_url, settings_overrides, jinja_env_options) File "C:\Users\grega\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 263, in init_settings nbextensions_path=jupyter_app.nbextensions_path, File "C:\Users\grega\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 874, in nbextensions_path from IPython.paths import get_ipython_dir File "C:\Users\grega\Anaconda3\lib\site-packages\IPython\__init__.py", line 55, in from .terminal.embed import embed File "C:\Users\grega\Anaconda3\lib\site-packages\IPython\terminal\embed.py", line 16, in from IPython.terminal.interactiveshell import TerminalInteractiveShell File "C:\Users\grega\Anaconda3\lib\site-packages\IPython\terminal\interactiveshell.py", line 32, in from .debugger import TerminalPdb, Pdb File "C:\Users\grega\Anaconda3\lib\site-packages\IPython\terminal\debugger.py", line 6, in from IPython.core.completer import IPCompleter File "C:\Users\grega\Anaconda3\lib\site-packages\IPython\core\completer.py", line 146, in import jedi File "C:\Users\grega\Anaconda3\lib\site-packages\jedi\__init__.py", line 41, in from jedi.api import Script, Interpreter, NotFoundError, set_debug_function File "C:\Users\grega\Anaconda3\lib\site-packages\jedi\api\__init__.py", line 23, in from jedi.api import classes File "C:\Users\grega\Anaconda3\lib\site-packages\jedi\api\classes.py", line 14, in from jedi.evaluate import representation as er File "C:\Users\grega\Anaconda3\lib\site-packages\jedi\evaluate\__init__.py", line 69, in from jedi.evaluate import representation as er File "C:\Users\grega\Anaconda3\lib\site-packages\jedi\evaluate\representation.py", line 52, in from jedi.evaluate import docstrings File "C:\Users\grega\Anaconda3\lib\site-packages\jedi\evaluate\docstrings.py", line 46, in from numpydoc.docscrape import NumpyDocString File "C:\Users\grega\Anaconda3\lib\site-packages\numpydoc\__init__.py", line 5, in from .numpydoc import setup File "C:\Users\grega\Anaconda3\lib\site-packages\numpydoc\numpydoc.py", line 28, in if sphinx.__version__ AttributeError: module 'sphinx' has no attribute '__version__'

Also looks like jedi and parso are show 4 resolutions.

C:\Users\grega>conda update --all Fetching package metadata ............. Solving package specifications: . Warning: 4 possible package resolutions (only showing differing packages):

Package plan for installation in environment C:\Users\grega\Anaconda3:

The following packages will be UPDATED:

jedi:  0.10.2-py35h3350e2d_0 --> 0.11.0-py35hc856aec_0

The following packages will be DOWNGRADED:

parso: 0.1.1-py35he39c48a_0  --> 0.1.0-py35hb960d57_0

Proceed ([y]/n)? n

If I run update again it gives the reverse resolution!

jjhelmus commented 6 years ago

Can you provide the output from conda list in the environment which is causing issues?

One option is to install the packages which are defined by the last anaconda release using conda install anaconda=5.0.1. This set of packages has been tested and is known to work well together.

greg-amato commented 6 years ago

(root) C:\Users\grega>conda list

packages in environment at C:\Users\grega\Anaconda3:

# _license 1.1 py35_1 _nb_ext_conf 0.4.0 py35_1 alabaster 0.7.10 py35h3a808de_0 anaconda custom py35h64770cb_0 anaconda-client 1.6.6 py35h690133a_0 anaconda-navigator 1.6.9 py35hfe15c67_0 anaconda-project 0.8.2 py35h06aeb26_0 anyqt 0.0.8 py35_0 argcomplete 1.0.0 py35_1 asn1crypto 0.23.0 py35h65de013_0 astroid 1.5.3 py35h82ecf54_0 astropy 2.0.2 py35h6e1a5eb_4 attrs 17.3.0 py35hdfbe3a1_0 babel 2.5.0 py35hcd66c26_0 backports 1.0 py35he88aa47_1 backports.shutil_get_terminal_size 1.0.0 py35h9d89c8b_2 beautifulsoup4 4.6.0 py35h61fcdcc_1 bitarray 0.8.1 py35ha601307_0 bkcharts 0.2 py35h4704c85_0 blaze 0.11.3 py35hae12140_0 bleach 2.1.1 py35h73b2768_0 bokeh 0.12.11 py35h969371a_0 boto 2.48.0 py35ha0bef00_1 bottleneck 1.2.1 py35h8a3671c_0 bzip2 1.0.6 haa5b126_2 ca-certificates 2017.08.26 h94faf87_0 cachecontrol 0.12.3 py35h3f82863_0 certifi 2017.11.5 py35h456c6ae_0 certifi 2017.11.5 cffi 1.11.2 py35h74ad5ef_0 chardet 3.0.4 py35h177e1b7_1 chest 0.2.3 py35_0 click 6.7 py35h10df73f_0 cloudpickle 0.5.2 py35hd830302_0 clyent 1.2.2 py35h3cd9751_1 colorama 0.3.9 py35h32a752f_0 comtypes 1.1.2 py35hfae9076_0 conda 4.3.30 py35hec795fb_0 conda-build 3.1.0 py35h5a4bd72_0 conda-env 2.6.0 h36134e3_1 conda-verify 2.0.0 py35h84a86bd_0 configobj 5.0.6 py35_0 console_shortcut 0.1.1 h6bb2dd7_3 contextlib2 0.5.5 py35h0a97e54_0 coverage 4.4.2 py35h1d76e2e_0 cryptography 2.1.4 py35h8ead9e0_0 curl 7.55.1 h3b839b5_4 cycler 0.10.0 py35hcc71164_0 cymem 1.31.2 py35h3642f57_0 cython 0.27.3 py35h82876f0_0 cytoolz 0.8.2 py35h6a98e29_0 dask 0.16.0 py35hc436b91_0 dask-core 0.16.0 py35h0988329_0 datashape 0.5.4 py35ha38994c_0 decorator 4.1.2 py35hc7d1f2e_0 dill 0.2.7.1 py35hfe367cb_0 distlib 0.2.5 py35h12c42d7_0 distributed 1.20.1 py35h3ced2a0_0 django 1.11.3 py35_0 docutils 0.14 py35h8ccb97f_0 dynd-python 0.7.2 py35_0 entrypoints 0.2.3 py35hb91ced9_2 et_xmlfile 1.0.1 py35h2c13def_0 fastcache 1.0.2 py35h8710e77_0 filelock 2.0.13 py35hed8fc95_0 flask 0.12.2 py35he898f9a_0 flask-cors 3.0.3 py35h5700fb0_0 freetype 2.8 h51f8f2c_1 ftfy 4.4.3 py35h615266c_0 get_terminal_size 1.0.0 h38e98db_0 gevent 1.2.2 py35hb3d9581_0 glob2 0.6 py35h9eb15d0_0 greenlet 0.4.12 py35h0b77e5a_0 h5py 2.7.1 py35hb2c3add_0 hdf5 1.10.1 h98b8871_1 heapdict 1.0.0 py35h3d1311d_0 html5lib 0.999999999 py35h79d4e7f_0 hypothesis 3.38.5 py35h37a2ca4_0 icc_rt 2017.0.4 h97af966_0 icu 58.2 ha66f8fd_1 idna 2.6 py35h8dcb9ae_1 imageio 2.2.0 py35hcd4b9a4_0 imagesize 0.7.1 py35h7f87e83_0 intel-openmp 2018.0.0 hd92c6cd_8 ipykernel 4.6.1 py35hab2028a_0 ipython 6.2.1 py35h4a2ac14_1 ipython_genutils 0.2.0 py35ha709e79_0 ipywidgets 7.0.5 py35h49ade1d_0 isort 4.2.15 py35h0bf7b49_0 itsdangerous 0.24 py35h99d45d4_1 jdcal 1.3 py35h49a1460_0 jedi 0.10.2 py35h3350e2d_0 jinja2 2.10 py35hdf652bb_0 joblib 0.11 py35_0 jpeg 9b hb83a4c4_2 jsonschema 2.6.0 py35h27d56d3_0 jupyter 1.0.0 py35hce9caf1_2 jupyter_client 5.1.0 py35hcddec19_0 jupyter_console 5.2.0 py35hf76c22e_1 jupyter_core 4.4.0 py35h629ba7f_0 jupyterlab 0.27.0 py35hf0f7bbb_2 jupyterlab_launcher 0.4.0 py35h7c94a28_0 keyring 10.5.0 py35h82e68d4_0 lazy-object-proxy 1.3.1 py35he996729_0 libdynd 0.7.2 0 libiconv 1.15 h1df5818_7 libpng 1.6.32 h140d38e_4 libssh2 1.8.0 h75d9407_3 libtiff 4.0.9 h0f13578_0 libxml2 2.9.4 h41ea7b2_6 libxslt 1.1.29 h0037b19_6 llvmlite 0.20.0 py35_0 locket 0.2.0 py35h0dfcdd0_1 lockfile 0.12.2 py35h667c6d9_0 lxml 4.1.1 py35ha957a02_0 lzo 2.10 h6df0209_2 markupsafe 1.0 py35hc253e08_1 matplotlib 2.1.0 py35hea29350_0 mccabe 0.6.1 py35hcf31250_1 menuinst 1.4.10 py35hb57c5a5_0 mistune 0.8.1 py35h7e79247_0 mkl 2018.0.1 h2108138_4 mkl-service 1.1.2 py35h051acba_4 mpmath 1.0.0 py35h253b693_2 msgpack-python 0.4.8 py35hdef45cb_0 multipledispatch 0.4.9 py35hfb38682_0 murmurhash 0.26.4 py35h1512bc8_0 navigator-updater 0.1.0 py35h1d043e2_0 nb_anacondacloud 1.4.0 py35_0 nb_conda 2.2.0 py35_0 nb_conda_kernels 2.1.0 py35_0 nbconvert 5.3.1 py35h98d6c46_0 nbformat 4.4.0 py35h908c9d9_0 nbpresent 3.0.2 py35_0 networkx 1.11 py35h097edc8_0 nltk 3.2.5 py35hbbcff45_0 nose 1.3.7 py35h0e9586c_2 notebook 5.2.2 py35h2b96da0_0 numba 0.35.0 np113py35_10 numexpr 2.6.4 py35hb78e28a_0 numpy 1.13.3 py35hb7e80fb_0 numpydoc 0.7.0 py35h72ac4f2_0 odo 0.5.1 py35hc850252_0 olefile 0.44 py35h7ba86d0_0 openpyxl 2.4.9 py35h572dd3b_0 openssl 1.0.2m h093b818_1 orange3 3.4.1 py35_0 packaging 16.8 py35h5fb721f_1 pandas 0.21.0 py35h0510043_1 pandoc 1.19.2.1 hb2460c7_1 pandocfilters 1.4.2 py35h978f723_1 parso 0.1.1 py35he39c48a_0 partd 0.3.8 py35h894d1e4_0 patch 2.5.9 1 path.py 10.5 py35h3b5be1d_0 pathlib 1.0.1 py35_0 pathlib2 2.3.0 py35h4f1e8f6_0 patsy 0.4.1 py35h01e4a18_0 pep8 1.7.0 py35h15aeeed_0 pickleshare 0.7.4 py35h2f9f535_0 pillow 4.3.0 py35h967e314_1 pip 9.0.1 py35h691316f_4 pkginfo 1.4.1 py35hb922f74_1 plac 0.9.6 py35_0 pluggy 0.6.0 py35h717ee57_0 ply 3.10 py35hb60f152_0 preshed 1.0.0 py35h47f38c0_0 progress 1.3 py35ha84af61_0 prompt_toolkit 1.0.15 py35h89c7cb4_0 psutil 5.4.1 py35h5f28cdc_0 py 1.5.2 py35h4fcc378_0 pyasn1 0.4.2 py35hd2f34a6_0 pycodestyle 2.3.1 py35h35694a3_0 pycosat 0.6.3 py35h456c199_0 pycparser 2.18 py35h15a15da_1 pycrypto 2.6.1 py35h8890bb5_1 pycurl 7.43.0 py35hd6f0fee_3 pyflakes 1.6.0 py35hb7fdafe_0 pygments 2.2.0 py35h24c0941_0 pylint 1.7.4 py35h717b2e0_0 pymongo 3.4.0 py35_0 pympler 0.5 py35h0fea292_0 pyodbc 4.0.21 py35h20c60d8_0 pyopenssl 17.5.0 py35h75c5b16_0 pyparsing 2.2.0 py35hcabcaab_1 pyqt 5.6.0 py35hd46907b_5 pyqtgraph 0.10.0 py35_0 pyreadline 2.1 py35h9d47d9c_1 pysocks 1.6.7 py35hb30ac0d_1 pytables 3.4.2 py35h9e98cc6_2 pytest 3.3.0 py35h465e706_0 python 3.5.4 h1357f44_23 python-dateutil 2.6.1 py35h6b299a3_1 pytz 2017.3 py35hb294b1a_0 pywavelets 0.5.2 py35h7c47ace_0 pywin32 221 py35h14ddfd5_0 pyyaml 3.12 py35h4bf9689_1 pyzmq 16.0.3 py35h1861011_0 qt 5.6.2 vc14h6f8c307_12 [vc14] qtawesome 0.4.4 py35h639d0ff_0 qtconsole 4.3.1 py35hc47b0dd_0 qtpy 1.3.1 py35h4918c39_0 regex 2017.11.09 py35h3dee244_0 requests 2.18.4 py35h54a615f_1 rope 0.10.7 py35h5756fe0_0 ruamel_yaml 0.11.14 py35h7ef29f8_2 scikit-image 0.13.1 py35ha2243b5_0 scikit-learn 0.19.1 py35h2037775_0 scipy 1.0.0 py35h75710e8_0 seaborn 0.8.1 py35hc73483e_0 semver 2.4.1 py35_0 spacy setuptools 36.5.0 py35h21a22e4_0 simplegeneric 0.8.1 py35h6406082_0 singledispatch 3.4.0.3 py35h33f66b4_0 sip 4.18.1 py35h01cbaa7_2 six 1.11.0 py35hc1da2df_1 snowballstemmer 1.2.1 py35h4c55bfa_0 sockjs-tornado 1.0.3 py35_0 sortedcollections 0.5.3 py35h4a7ff62_0 sortedcontainers 1.5.7 py35h9857911_0 spacy 1.9.0 py35_vc14hcdb467c_1 [vc14] sphinx 1.6.3 py35heeac824_0 sphinx_rtd_theme 0.2.4 py35_0 sphinxcontrib 1.0 py35h45f5ca3_1 sphinxcontrib-websupport 1.0.1 py35ha3690eb_1 sputnik 0.9.3 py35_0 spacy spyder 3.2.4 py35h467e5b4_0 sqlalchemy 1.1.13 py35h5463dee_0 sqlite 3.20.1 h9eeafa9_2 statsmodels 0.8.0 py35hfa6034c_0 sympy 1.1.1 py35ha5375ed_0 tblib 1.3.2 py35hd2cf7e1_0 termcolor 1.1.0 py35_0 testpath 0.3.1 py35h06cf69e_0 thinc 6.5.2 py35_vc14h2607e83_0 [vc14] tk 8.6.7 hcb92d03_3 toolz 0.8.2 py35h7afdc4e_0 tornado 4.5.2 py35h03246f3_0 tqdm 4.19.4 py35h1d89acb_0 traitlets 4.3.2 py35h09b975b_0 typing 3.6.2 py35h37628ea_0 ujson 1.35 py35_0 unicodecsv 0.14.1 py35h0d88516_0 urllib3 1.22 py35h8cc84eb_0 vc 14 h2379b0c_2 vs2015_runtime 14.0.25123 hd4c4e62_2 wcwidth 0.1.7 py35h6e80d8a_0 webencodings 0.5.1 py35h5d527fb_1 werkzeug 0.12.2 py35hc854123_0 wheel 0.30.0 py35h38a90bc_1 widgetsnbextension 3.0.8 py35hdf37555_0 win_inet_pton 1.0.1 py35hbef1270_1 win_unicode_console 0.5 py35h56988b5_0 wincertstore 0.2 py35hfebbdb8_0 wrapt 1.10.11 py35h54666f7_0 xlrd 1.1.0 py35h22b952b_1 xlsxwriter 1.0.2 py35h6052a16_0 xlwings 0.11.4 py35he637782_0 xlwt 1.3.0 py35hd04410a_0 yaml 0.1.7 hc54c509_2 zict 0.1.3 py35hf5542e0_0 zlib 1.2.11 h8395fce_2 zope 1.0 py35_0 zope.interface 4.4.3 py35h57d3274_0

greg-amato commented 6 years ago

More dependency errors trying in install 5.0.1

(root) C:\Users\grega>conda install anaconda=5.0.1 Fetching package metadata ............. Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:

ozancaglayan commented 6 years ago

Constantly having conflicts and downgrades since 3 weeks for networkx and scikit-image. Now jedi and parso came into play as well.

My anaconda version shows as custom and I can't force an install of 5.0.1:

Current conda install:

               platform : linux-64
          conda version : 4.3.30
       conda is private : False
      conda-env version : 4.3.30
    conda-build version : 3.1.0
         python version : 3.6.3.final.0
       requests version : 2.18.4
       root environment : /caglayan/anaconda3  (writable)
    default environment : /caglayan/anaconda3
       envs directories : /caglayan/anaconda3/envs
                          /caglayan/.conda/envs
          package cache : /caglayan/anaconda3/pkgs
                          /caglayan/.conda/pkgs
           channel URLs : https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
Fetching package metadata ...........
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - anaconda 5.0.1*
  - flake8
  - python 3.6*
Use "conda info <package>" to see the dependencies for each package.
greg-amato commented 6 years ago

@ozancaglayan thanks for adding. scope of issues look related... those 4 modules are in disagreement for me (scikit, parso, jedi, networkx).

Interesting that i'm getting "AttributeError: module 'sphinx' has no attribute 'version'" when it's clearly defined reviewing the library.

ozancaglayan commented 6 years ago

I dont have any problem with notebooks or whatsoever but this downgrade and conflict thing is happening since some weeks for me.

jjhelmus commented 6 years ago

The parso and jedi multiple resolution should be fixed now and we are working on a fix for the scikit-image/networkx multiple resolution issue.

Briefly, the latest release of scikit-image requires networkx be to strictly less than version 2.0. Previous releases of scikit-image did not limit the networkx requirement (but should have). Given this, the solver in conda is not sure if it should install the latest version of networkx, which is above 2.0, and an older version of scikit-image, or the latest version of scikit-image and an older release of networkx

@greg-amato I believe the multiple resolution issue was not directly related to the inability to run jupyter notebook. Are you still having issues. If so you might try reinstalling sphinx using conda install --force sphinx. Alternatively you could create a separate conda environment using conda create -n notebook python=3.6 notebook form which you could launch a Notebook.

Updating the root environment to anaconda 5.0.1 may be tricky as you have Python 3.5 installed and 5.0.1 requires Python 3.6. Removing Anaconda entirely and reinstalled the latest version should work if this acceptable

greg-amato commented 6 years ago

Thanks @jjhelmus. Pointing out not being on python 3.6 helped. Not sure why that hadn't updated since becoming the default versions. I was able to follow this article to get python 3.6 and on anaconda 5.0.1 https://support.anaconda.com/customer/en/portal/articles/2797011-updating-anaconda-to-python-3-6 This was able to resolve the issue.