search

conda-forge / pyzmq-feedstock

A conda-smithy repository for pyzmq.
BSD 3-Clause "New" or "Revised" License
1 stars 17 forks source link

Problems with version combinations of pyzmq 17.1.2 and zeromq 4.2.5 (and tornado 4.5.3??) #39

Closed megies closed 5 years ago

megies commented 5 years ago

Issue:

I have another (dependency?) versions clash, resulting in a broken installation. After updating pyzmq (and manually updating libsodium see #38 and manually updating tornado) I am left with versions..

Starting jupyter I get the following errors and the kernel does not start

``` $ jupyter notebook --no-browser [W 13:08:54.191 NotebookApp] Error loading server extension jupyterlab Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/notebook/notebookapp.py", line 1271, in init_server_extensions mod = importlib.import_module(modulename) File "/home/megies/anaconda/envs/default/lib/python2.7/importlib/__init__.py", line 37, in import_module __import__(name) ImportError: No module named jupyterlab [I 13:08:54.194 NotebookApp] Serving notebooks from local directory: /home/megies/notebooks [I 13:08:54.194 NotebookApp] 0 active kernels [I 13:08:54.194 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/?token=b4844e487efd481b837b038ea632356b4bdbe77bd88d6810 [I 13:08:54.194 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 13:08:54.194 NotebookApp] Copy/paste this URL into your browser when you connect for the first time, to login with a token: http://localhost:8888/?token=b4844e487efd481b837b038ea632356b4bdbe77bd88d6810 [I 13:08:57.841 NotebookApp] Kernel started: e1efd357-266e-4540-8eb9-b9908e1940c5 ERROR:tornado.general:Uncaught exception in ZMQStream callback Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback callback(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper return fn(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher return self.dispatch_shell(stream, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell self.pre_handler_hook() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook self.saved_sigint_handler = signal(SIGINT, default_int_handler) ValueError: signal only works in main thread ERROR:tornado.general:Uncaught exception in zmqstream callback Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events self._handle_recv() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv self._run_callback(callback, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback callback(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper return fn(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher return self.dispatch_shell(stream, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell self.pre_handler_hook() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook self.saved_sigint_handler = signal(SIGINT, default_int_handler) ValueError: signal only works in main thread ERROR:tornado.application:Exception in callback ```


Manually downgrading zeromq (which also downgrades pyzmq) resolves the problem

``` (default) wintermute:~/notebooks$ conda install zeromq=4.2.3 Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.5.4 latest version: 4.5.11 Please update conda by running $ conda update -n base conda ## Package Plan ## environment location: /home/megies/anaconda/envs/default added / updated specs: - zeromq=4.2.3 The following packages will be downloaded: package | build ---------------------------|----------------- zeromq-4.2.3 | 2 881 KB conda-forge pyzmq-17.0.0 | py27_3 991 KB conda-forge ------------------------------------------------------------ Total: 1.8 MB The following packages will be DOWNGRADED: pyzmq: 17.1.2-py27hae99301_0 conda-forge --> 17.0.0-py27_3 conda-forge zeromq: 4.2.5-hfc679d8_4 conda-forge --> 4.2.3-2 conda-forge Proceed ([y]/n)? Downloading and Extracting Packages zeromq-4.2.3 | 881 KB | ######################################################################################### | 100% pyzmq-17.0.0 | 991 KB | ######################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (default) wintermute:~/notebooks$ conda list tornado # packages in environment at /home/megies/anaconda/envs/default: # # Name Version Build Channel tornado 4.5.3 py27_0 conda-forge (default) wintermute:~/notebooks$ conda list jupyter # packages in environment at /home/megies/anaconda/envs/default: # # Name Version Build Channel jupyter 1.0.0 py_1 conda-forge jupyter_client 5.0.1 py27_0 conda-forge jupyter_console 5.1.0 py27_0 conda-forge jupyter_core 4.3.0 py27_0 conda-forge ```


After this jupyter runs without problems again.

Environment (conda list): (after resolving the problem)

``` $ conda list # packages in environment at /home/megies/anaconda/envs/default: # # Name Version Build Channel alabaster 0.7.10 py27_1 conda-forge attrs 17.4.0 py_0 conda-forge babel 2.5.1 py27_0 conda-forge backports 1.0 py27_1 conda-forge backports.functools-lru-cache 1.3 backports.functools_lru_cache 1.4 py27_1 conda-forge backports.shutil_get_terminal_size 1.0.0 py27_1 conda-forge backports_abc 0.5 py27_0 conda-forge basemap 1.1.0 py27_3 conda-forge basemap-data-hires 1.1.0 0 conda-forge blas 1.0 mkl bleach 1.5.0 py27_0 conda-forge boost 1.64.0 py27_4 conda-forge boost-cpp 1.64.0 1 conda-forge bzip2 1.0.6 1 conda-forge ca-certificates 2018.8.24 ha4d7672_0 conda-forge cairo 1.14.10 0 conda-forge cartopy 0.16.0 py27h81b52dc_1 conda-forge certifi 2018.8.24 py27_1001 conda-forge click 6.7 py27_0 conda-forge click-plugins 1.0.3 py27_0 conda-forge cligj 0.4.0 py27_0 conda-forge configparser 3.5.0 py27_0 conda-forge curl 7.55.1 0 conda-forge cycler 0.10.0 py27_0 conda-forge dbus 1.10.10 3 conda-forge decorator 4.0.11 py27_0 conda-forge descartes 1.1.0 py27_0 conda-forge docker 2.5.1 docker-pycreds 0.2.1 py27_0 conda-forge docutils 0.14 py27_0 conda-forge entrypoints 0.2.2 py27_1 conda-forge enum34 1.1.6 py27_1 conda-forge execnet 1.3.0 py27_1 expat 2.2.5 0 conda-forge fancycompleter 0.7 py27_0 conda-forge fiona 1.7.9 py27_0 conda-forge flake8 3.3.0 py27_0 conda-forge fontconfig 2.12.6 0 conda-forge freetype 2.8.1 0 conda-forge freexl 1.0.2 1 conda-forge funcsigs 1.0.2 py27_0 conda-forge functools32 3.2.3.2 py27_1 conda-forge future 0.16.0 py27_0 conda-forge futures 3.2.0 py27_0 conda-forge gdal 2.0.0 py27_1 geographiclib 1.48 py27_0 conda-forge geojson 2.1.0 py_0 conda-forge geopandas 0.3.0 py27_0 conda-forge geopy 1.11.0 py27_0 conda-forge geos 3.6.2 1 conda-forge geotiff 1.4.2 1 conda-forge gettext 0.19.7 1 conda-forge giflib 5.1.4 0 conda-forge glib 2.55.0 0 conda-forge gmp 6.1.2 0 conda-forge graphite2 1.3.9 0 conda-forge greenlet 0.4.12 py27_0 conda-forge gst-plugins-base 1.8.0 0 conda-forge gstreamer 1.8.0 1 conda-forge harfbuzz 1.7.6 0 conda-forge hdf4 4.2.12 0 conda-forge hdf5 1.10.1 1 conda-forge html5lib 0.999 py27_0 conda-forge icu 58.2 0 conda-forge imagesize 0.7.1 py27_0 conda-forge intel-openmp 2018.0.3 0 ipaddress 1.0.18 py27_0 conda-forge ipykernel 4.6.1 py27_0 conda-forge ipython 5.4.1 py27_0 conda-forge ipython_genutils 0.2.0 py27_0 conda-forge ipywidgets 6.0.0 py27_0 conda-forge jinja2 2.9.5 py27_0 conda-forge jpeg 9b 0 conda-forge json-c 0.12 0 conda-forge jsonschema 2.5.1 py27_0 conda-forge jupyter 1.0.0 py_1 conda-forge jupyter_client 5.0.1 py27_0 conda-forge jupyter_console 5.1.0 py27_0 conda-forge jupyter_core 4.3.0 py27_0 conda-forge kealib 1.4.7 4 conda-forge kiwisolver 1.0.1 py27_1 conda-forge krb5 1.14.2 0 conda-forge libboost 1.65.1 habcd387_4 libconda 4.0.0 py27_0 conda-forge libdap4 3.18.3 2 conda-forge libffi 3.2.1 3 conda-forge libgcc-ng 7.2.0 hdf63c60_3 libgdal 2.1.4 9 conda-forge libgfortran 3.0.0 1 libgfortran-ng 7.2.0 hdf63c60_3 libiconv 1.15 0 conda-forge libkml 1.3.0 h9d32c78_3 libnetcdf 4.4.1.1 10 conda-forge libpng 1.6.34 0 conda-forge libpq 9.5.4 4 conda-forge libsodium 1.0.16 h470a237_1 conda-forge libspatialindex 1.8.5 1 conda-forge libspatialite 4.3.0a 19 conda-forge libssh2 1.8.0 2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 libtiff 4.0.9 0 conda-forge libxcb 1.12 1 conda-forge libxml2 2.9.4 4 conda-forge libxslt 1.1.29 3 conda-forge livereload 2.5.2 py_0 conda-forge lxml 3.7.3 py27_0 conda-forge markdown 2.6.11 py_0 conda-forge markupsafe 0.23 py27_1 conda-forge matplotlib 2.2.2 py27_0 conda-forge mccabe 0.6.1 py27_0 conda-forge mistune 0.7.4 py27_0 conda-forge mkdocs 1.0.2 py_0 conda-forge mkdocs-bootstrap 1.0 py_0 conda-forge mkdocs-bootswatch 1.0 py_0 conda-forge mkl 2018.0.3 1 mkl_fft 1.0.2 py27_0 conda-forge mkl_random 1.0.1 py27_0 conda-forge mock 2.0.0 py27_0 conda-forge mplstereonet 0.6.dev0 msgpack-python 0.4.8 py27_0 conda-forge munch 2.2.0 py27_0 conda-forge nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py27_0 conda-forge nbstripout 0.3.1 py27_0 conda-forge ncurses 5.9 10 conda-forge neovim 0.2.0 py27_0 conda-forge nllgrid 0.1 notebook 5.0.0 py27_0 conda-forge notedown 1.5.0 numpy 1.14.5 py27hcd700cb_0 numpy-base 1.14.5 py27hdbf6ddf_0 obspy 1.1.0 py27_1 conda-forge obspy 1.1.1rc1.post0+42.ge594292a3d.obspy.maintenance.1.1.x olefile 0.44 py27_0 conda-forge openblas 0.2.20 5 conda-forge openjpeg 2.3.0 2 conda-forge openssl 1.0.2p h470a237_0 conda-forge owslib 0.16.0 py_0 conda-forge pandas 0.20.3 py27_1 conda-forge pandoc 1.19.2 0 conda-forge pandoc-attributes 0.1.7 py27_0 conda-forge pandocfilters 1.4.1 py27_0 conda-forge pango 1.40.14 0 conda-forge pathlib2 2.2.1 py27_0 conda-forge patsy 0.4.1 py27_0 conda-forge pbr 3.0.0 py27_0 conda-forge pcre 8.39 0 conda-forge pdbpp 0.9.1 py27_0 conda-forge pep8-naming 0.4.1 py27_0 conda-forge pexpect 4.2.1 py27_0 conda-forge pickleshare 0.7.3 py27_0 conda-forge pillow 5.0.0 py27_0 conda-forge pip 9.0.1 py27_0 conda-forge pixman 0.34.0 0 conda-forge pkginfo 1.4.1 py27_0 conda-forge pluggy 0.6.0 py_0 conda-forge poppler 0.63.0 0 conda-forge poppler-data 0.4.7 0 conda-forge proj4 4.9.3 3 conda-forge prompt_toolkit 1.0.14 py27_0 conda-forge psutil 5.2.1 py27_0 conda-forge psycopg2 2.7.3.1 py27_0 conda-forge ptyprocess 0.5.1 py27_0 conda-forge py 1.5.2 py_0 conda-forge pycodestyle 2.3.1 py27_0 conda-forge pycosat 0.6.1 py27_0 conda-forge pyepsg 0.3.2 py_1 conda-forge pyflakes 1.5.0 py27_0 conda-forge pygments 2.2.0 py27_0 conda-forge pyparsing 2.2.0 py27_0 conda-forge pyproj 1.9.5.1 py27_0 conda-forge pyqt 5.6.0 py27_2 conda-forge pyrepl 0.8.4 py27_1 conda-forge pysal 1.14.2 py_0 conda-forge pyshp 1.2.11 py27_0 conda-forge pytest 3.4.2 py27_0 conda-forge pytest-xdist 1.16.0 py27_0 conda-forge python 2.7.14 4 conda-forge python-dateutil 2.6.0 py27_0 conda-forge pytz 2017.2 py27_0 conda-forge pyyaml 3.12 py27_1 conda-forge pyzmq 17.0.0 py27_3 conda-forge qt 5.6.2 7 conda-forge qtconsole 4.3.0 py27_0 conda-forge readline 7.0 0 conda-forge requests 2.13.0 py27_0 conda-forge requests-toolbelt 0.8.0 py27_0 conda-forge rtree 0.8.3 py27_0 conda-forge scandir 1.5 py27_1 conda-forge scipy 1.1.0 py27hfc37229_0 scons 2.5.1 py27_0 conda-forge seaborn 0.8.1 py27_0 conda-forge seedlink-plotter 0.1.0 setuptools 38.4.0 py27_0 conda-forge shapely 1.6.4 py27_0 conda-forge simplegeneric 0.8.1 py27_0 conda-forge singledispatch 3.4.0.3 py27_0 conda-forge sip 4.18 py27_1 conda-forge six 1.10.0 py27_1 conda-forge snowballstemmer 1.2.1 py27_0 conda-forge sphinx 1.6.7 py27_0 conda-forge sphinx_rtd_theme 0.2.4 py27_0 conda-forge sphinxcontrib-websupport 1.0.1 py27_0 conda-forge sqlalchemy 1.1.5 py27_0 conda-forge sqlite 3.20.1 2 conda-forge ssl_match_hostname 3.5.0.1 py27_1 conda-forge statsmodels 0.8.0 py27_0 conda-forge subprocess32 3.2.7 py27_0 conda-forge terminado 0.6 py27_0 conda-forge testpath 0.3 py27_0 conda-forge tk 8.6.7 0 conda-forge tornado 4.5.3 py27_0 conda-forge tqdm 4.19.4 py_0 conda-forge traitlets 4.3.2 py27_0 conda-forge trollius 2.1 py27_0 conda-forge twine 1.9.1 py27_2 conda-forge typing 3.6.2 py27_0 conda-forge util-linux 2.21 0 utm 0.4.2 py27_0 conda-forge wcwidth 0.1.7 py27_0 conda-forge webencodings 0.5 py27_0 conda-forge websocket-client 0.44.0 py27_0 conda-forge wheel 0.29.0 py27_0 conda-forge widgetsnbextension 2.0.0 py27_0 conda-forge wmctrl 0.3 py27_0 conda-forge xerces-c 3.2.0 0 conda-forge xorg-libxau 1.0.8 3 conda-forge xorg-libxdmcp 1.1.2 3 conda-forge xz 5.2.2 0 conda-forge yaml 0.1.6 0 conda-forge zeromq 4.2.3 2 conda-forge zlib 1.2.11 0 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active environment : default active env location : /home/megies/anaconda/envs/default shell level : 2 user config file : /home/megies/.condarc populated config files : /home/megies/.condarc conda version : 4.5.4 conda-build version : 3.7.1 python version : 2.7.11.final.0 base environment : /home/megies/anaconda (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch https://conda.anaconda.org/obspy/linux-64 https://conda.anaconda.org/obspy/noarch package cache : /home/megies/anaconda/pkgs /home/megies/.conda/pkgs envs directories : /home/megies/anaconda/envs /home/megies/.conda/envs platform : linux-64 user-agent : conda/4.5.4 requests/2.13.0 CPython/2.7.11 Linux/4.9.0-6-amd64 debian/9 glibc/2.24 UID:GID : 1043:100 netrc file : /home/megies/.netrc offline mode : False ```
minrk commented 5 years ago

Closing as duplicate of #38

minrk commented 5 years ago

Reopening since I didn't see that the error was hidden in the details, and is in fact a different issue.

minrk commented 5 years ago

Do you have conda list for an env that can reproduce the problem?

megies commented 5 years ago

Just a minute, I'll try to reproduce one, sorry for only listing the env after resolution above..

minrk commented 5 years ago

FWIW, this conda environment does not have an issue:

conda list

``` # packages in environment at /opt/conda: # # Name Version Build Channel asn1crypto 0.24.0 py27_0 backports 1.0 py_2 conda-forge backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge backports_abc 0.5 py_1 conda-forge bleach 3.0.0 py_0 conda-forge ca-certificates 2018.8.24 ha4d7672_0 conda-forge certifi 2018.8.24 py27_1001 conda-forge cffi 1.11.5 py27he75722e_1 chardet 3.0.4 py27_1 conda 4.5.11 py27_0 conda-forge conda-env 2.6.0 1 configparser 3.5.0 py27_1001 conda-forge cryptography 2.3.1 py27hc365091_0 decorator 4.3.0 py_0 conda-forge entrypoints 0.2.3 py27_1002 conda-forge enum34 1.1.6 py27_1 functools32 3.2.3.2 py_3 conda-forge futures 3.2.0 py27_0 gmp 6.1.2 hfc679d8_0 conda-forge html5lib 1.0.1 py_0 conda-forge idna 2.7 py27_0 ipaddress 1.0.22 py27_0 ipykernel 4.10.0 py27_1 conda-forge ipython 5.8.0 py27_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jinja2 2.10 py_1 conda-forge jsonschema 2.6.0 py27_1002 conda-forge jupyter_client 5.2.3 py_1 conda-forge jupyter_core 4.4.0 py_0 conda-forge libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc-ng 8.2.0 hdf63c60_1 libsodium 1.0.16 h470a237_1 conda-forge libstdcxx-ng 8.2.0 hdf63c60_1 markupsafe 1.0 py27h470a237_1 conda-forge mistune 0.8.3 py27h470a237_2 conda-forge nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py_1 conda-forge ncurses 6.1 hf484d3e_0 notebook 5.7.0 py27_1000 conda-forge openssl 1.0.2p h470a237_0 conda-forge pandoc 2.3.1 0 conda-forge pandocfilters 1.4.2 py_1 conda-forge pathlib2 2.3.2 py27_1000 conda-forge pexpect 4.6.0 py27_1000 conda-forge pickleshare 0.7.5 py27_1000 conda-forge pip 10.0.1 py27_0 prometheus_client 0.4.0 py_0 conda-forge prompt_toolkit 1.0.15 py_1 conda-forge ptyprocess 0.6.0 py27_1000 conda-forge pycosat 0.6.3 py27h14c3975_0 pycparser 2.18 py27_1 pygments 2.2.0 py_1 conda-forge pyopenssl 18.0.0 py27_0 pysocks 1.6.8 py27_0 python 2.7.15 h1571d57_0 python-dateutil 2.7.3 py_0 conda-forge pyzmq 17.1.2 py27hae99301_0 conda-forge readline 7.0 h7b6447c_5 requests 2.19.1 py27_0 ruamel_yaml 0.15.46 py27h14c3975_0 scandir 1.9.0 py27h470a237_0 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 40.2.0 py27_0 simplegeneric 0.8.1 py_1 conda-forge singledispatch 3.4.0.3 py27_0 conda-forge six 1.11.0 py27_1 sqlite 3.24.0 h84994c4_0 ssl_match_hostname 3.5.0.1 py27_1001 conda-forge terminado 0.8.1 py27_1001 conda-forge testpath 0.4.2 py27_1000 conda-forge tk 8.6.8 hbc83047_0 tornado 4.5.3 py27_0 conda-forge traitlets 4.3.2 py27_1000 conda-forge urllib3 1.23 py27_0 wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.31.1 py27_0 yaml 0.1.7 had09818_2 zeromq 4.2.5 hfc679d8_6 conda-forge zlib 1.2.11 ha838bed_2 ```

conda info

``` active environment : base active env location : /opt/conda shell level : 1 user config file : /root/.condarc populated config files : conda version : 4.5.11 conda-build version : not installed python version : 2.7.15.final.0 base environment : /opt/conda (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /opt/conda/pkgs /root/.conda/pkgs envs directories : /opt/conda/envs /root/.conda/envs platform : linux-64 user-agent : conda/4.5.11 requests/2.19.1 CPython/2.7.15 Linux/4.9.125-linuxkit debian/9 glibc/2.24 UID:GID : 0:0 netrc file : None offline mode : False ```

I do see that you have pretty outdated notebook 5.0.0, when current is 5.7.0. My guess is that's the issue.

megies commented 5 years ago

I went back with conda install --revision .., this is the env showing the problem (sorry its so bloated, it's my default sandbox env):

conda list --export:

``` $ conda list --export # This file may be used to create an environment using: # $ conda create --name --file # platform: linux-64 alabaster=0.7.10=py27_1 attrs=17.4.0=py_0 babel=2.5.1=py27_0 backports=1.0=py27_1 backports.functools_lru_cache=1.4=py27_1 backports.shutil_get_terminal_size=1.0.0=py27_1 backports_abc=0.5=py27_0 basemap=1.1.0=py27_3 basemap-data-hires=1.1.0=0 blas=1.0=mkl bleach=1.5.0=py27_0 boost=1.64.0=py27_4 boost-cpp=1.64.0=1 bzip2=1.0.6=1 ca-certificates=2018.8.24=ha4d7672_0 cairo=1.14.10=0 cartopy=0.16.0=py27h81b52dc_1 certifi=2018.8.24=py27_1001 click=6.7=py27_0 click-plugins=1.0.3=py27_0 cligj=0.4.0=py27_0 configparser=3.5.0=py27_0 curl=7.55.1=0 cycler=0.10.0=py27_0 dbus=1.10.10=3 decorator=4.0.11=py27_0 descartes=1.1.0=py27_0 docker-pycreds=0.2.1=py27_0 docutils=0.14=py27_0 entrypoints=0.2.2=py27_1 enum34=1.1.6=py27_1 execnet=1.3.0=py27_1 expat=2.2.5=0 fancycompleter=0.7=py27_0 fiona=1.7.9=py27_0 flake8=3.3.0=py27_0 fontconfig=2.12.6=0 freetype=2.8.1=0 freexl=1.0.2=1 funcsigs=1.0.2=py27_0 functools32=3.2.3.2=py27_1 future=0.16.0=py27_0 futures=3.2.0=py27_0 gdal=2.0.0=py27_1 geographiclib=1.48=py27_0 geojson=2.1.0=py_0 geopandas=0.3.0=py27_0 geopy=1.11.0=py27_0 geos=3.6.2=1 geotiff=1.4.2=1 gettext=0.19.7=1 giflib=5.1.4=0 glib=2.55.0=0 gmp=6.1.2=0 graphite2=1.3.9=0 greenlet=0.4.12=py27_0 gst-plugins-base=1.8.0=0 gstreamer=1.8.0=1 harfbuzz=1.7.6=0 hdf4=4.2.12=0 hdf5=1.10.1=1 html5lib=0.999=py27_0 icu=58.2=0 imagesize=0.7.1=py27_0 intel-openmp=2018.0.3=0 ipaddress=1.0.18=py27_0 ipykernel=4.6.1=py27_0 ipython=5.4.1=py27_0 ipython_genutils=0.2.0=py27_0 ipywidgets=6.0.0=py27_0 jinja2=2.9.5=py27_0 jpeg=9b=0 json-c=0.12=0 jsonschema=2.5.1=py27_0 jupyter=1.0.0=py_1 jupyter_client=5.0.1=py27_0 jupyter_console=5.1.0=py27_0 jupyter_core=4.3.0=py27_0 kealib=1.4.7=4 kiwisolver=1.0.1=py27_1 krb5=1.14.2=0 libboost=1.65.1=habcd387_4 libconda=4.0.0=py27_0 libdap4=3.18.3=2 libffi=3.2.1=3 libgcc-ng=7.2.0=hdf63c60_3 libgdal=2.1.4=9 libgfortran=3.0.0=1 libgfortran-ng=7.2.0=hdf63c60_3 libiconv=1.15=0 libkml=1.3.0=h9d32c78_3 libnetcdf=4.4.1.1=10 libpng=1.6.34=0 libpq=9.5.4=4 libsodium=1.0.16=h470a237_1 libspatialindex=1.8.5=1 libspatialite=4.3.0a=19 libssh2=1.8.0=2 libstdcxx-ng=7.2.0=hdf63c60_3 libtiff=4.0.9=0 libxcb=1.12=1 libxml2=2.9.4=4 libxslt=1.1.29=3 livereload=2.5.2=py_0 lxml=3.7.3=py27_0 markdown=2.6.11=py_0 markupsafe=0.23=py27_1 matplotlib=2.2.2=py27_0 mccabe=0.6.1=py27_0 mistune=0.7.4=py27_0 mkdocs=1.0.2=py_0 mkdocs-bootstrap=1.0=py_0 mkdocs-bootswatch=1.0=py_0 mkl=2018.0.3=1 mkl_fft=1.0.2=py27_0 mkl_random=1.0.1=py27_0 mock=2.0.0=py27_0 msgpack-python=0.4.8=py27_0 munch=2.2.0=py27_0 nbconvert=5.3.1=py_1 nbformat=4.4.0=py27_0 nbstripout=0.3.1=py27_0 ncurses=5.9=10 neovim=0.2.0=py27_0 notebook=5.0.0=py27_0 numpy=1.14.5=py27hcd700cb_0 numpy-base=1.14.5=py27hdbf6ddf_0 obspy=1.1.0=py27_1 olefile=0.44=py27_0 openblas=0.2.20=5 openjpeg=2.3.0=2 openssl=1.0.2p=h470a237_0 owslib=0.16.0=py_0 pandas=0.20.3=py27_1 pandoc=1.19.2=0 pandoc-attributes=0.1.7=py27_0 pandocfilters=1.4.1=py27_0 pango=1.40.14=0 pathlib2=2.2.1=py27_0 patsy=0.4.1=py27_0 pbr=3.0.0=py27_0 pcre=8.39=0 pdbpp=0.9.1=py27_0 pep8-naming=0.4.1=py27_0 pexpect=4.2.1=py27_0 pickleshare=0.7.3=py27_0 pillow=5.0.0=py27_0 pip=9.0.1=py27_0 pixman=0.34.0=0 pkginfo=1.4.1=py27_0 pluggy=0.6.0=py_0 poppler=0.63.0=0 poppler-data=0.4.7=0 proj4=4.9.3=3 prompt_toolkit=1.0.14=py27_0 psutil=5.2.1=py27_0 psycopg2=2.7.3.1=py27_0 ptyprocess=0.5.1=py27_0 py=1.5.2=py_0 pycodestyle=2.3.1=py27_0 pycosat=0.6.1=py27_0 pyepsg=0.3.2=py_1 pyflakes=1.5.0=py27_0 pygments=2.2.0=py27_0 pyparsing=2.2.0=py27_0 pyproj=1.9.5.1=py27_0 pyqt=5.6.0=py27_2 pyrepl=0.8.4=py27_1 pysal=1.14.2=py_0 pyshp=1.2.11=py27_0 pytest=3.4.2=py27_0 pytest-xdist=1.16.0=py27_0 python=2.7.14=4 python-dateutil=2.6.0=py27_0 pytz=2017.2=py27_0 pyyaml=3.12=py27_1 pyzmq=17.1.2=py27hae99301_0 qt=5.6.2=7 qtconsole=4.3.0=py27_0 readline=7.0=0 requests=2.13.0=py27_0 requests-toolbelt=0.8.0=py27_0 rtree=0.8.3=py27_0 scandir=1.5=py27_1 scipy=1.1.0=py27hfc37229_0 scons=2.5.1=py27_0 seaborn=0.8.1=py27_0 setuptools=38.4.0=py27_0 shapely=1.6.4=py27_0 simplegeneric=0.8.1=py27_0 singledispatch=3.4.0.3=py27_0 sip=4.18=py27_1 six=1.10.0=py27_1 snowballstemmer=1.2.1=py27_0 sphinx=1.6.7=py27_0 sphinx_rtd_theme=0.2.4=py27_0 sphinxcontrib-websupport=1.0.1=py27_0 sqlalchemy=1.1.5=py27_0 sqlite=3.20.1=2 ssl_match_hostname=3.5.0.1=py27_1 statsmodels=0.8.0=py27_0 subprocess32=3.2.7=py27_0 terminado=0.6=py27_0 testpath=0.3=py27_0 tk=8.6.7=0 tornado=4.5.3=py27_0 tqdm=4.19.4=py_0 traitlets=4.3.2=py27_0 trollius=2.1=py27_0 twine=1.9.1=py27_2 typing=3.6.2=py27_0 util-linux=2.21=0 utm=0.4.2=py27_0 wcwidth=0.1.7=py27_0 webencodings=0.5=py27_0 websocket-client=0.44.0=py27_0 wheel=0.29.0=py27_0 widgetsnbextension=2.0.0=py27_0 wmctrl=0.3=py27_0 xerces-c=3.2.0=0 xorg-libxau=1.0.8=3 xorg-libxdmcp=1.1.2=3 xz=5.2.2=0 yaml=0.1.6=0 zeromq=4.2.5=hfc679d8_4 zlib=1.2.11=0 ```

Updating to notebook 5.7.0 still shows the issue:

jupyter error traceback:

``` $ jupyter notebook --no-browser [W 15:19:31.511 NotebookApp] Error loading server extension jupyterlab Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/notebook/notebookapp.py", line 1573, in init_server_extensions mod = importlib.import_module(modulename) File "/home/megies/anaconda/envs/default/lib/python2.7/importlib/__init__.py", line 37, in import_module __import__(name) ImportError: No module named jupyterlab [I 15:19:31.514 NotebookApp] Serving notebooks from local directory: /home/megies/notebooks [I 15:19:31.514 NotebookApp] The Jupyter Notebook is running at: [I 15:19:31.514 NotebookApp] http://localhost:8888/?token=1f8bf2185ea9b3dcf9cc77065c5a6b8c26ab70e3f4893aae [I 15:19:31.514 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation). [C 15:19:31.515 NotebookApp] Copy/paste this URL into your browser when you connect for the first time, to login with a token: http://localhost:8888/?token=1f8bf2185ea9b3dcf9cc77065c5a6b8c26ab70e3f4893aae [W 15:19:34.431 NotebookApp] Clearing invalid/expired login cookie username-localhost-8888 [W 15:19:34.437 NotebookApp] Forbidden [W 15:19:34.444 NotebookApp] 403 GET /api/sessions?_=1539082747837 (::1) 14.72ms referer=http://localhost:8888/tree [W 15:19:34.447 NotebookApp] Clearing invalid/expired login cookie username-localhost-8888 [W 15:19:34.449 NotebookApp] Forbidden [W 15:19:34.450 NotebookApp] 403 GET /api/terminals?_=1539082747838 (::1) 3.51ms referer=http://localhost:8888/tree [I 15:19:34.526 NotebookApp] 302 GET /notebooks/MGSBH_orientation_determination.ipynb (::1) 0.88ms [I 15:19:40.675 NotebookApp] 302 POST /login?next=%2Fnotebooks%2FMGSBH_orientation_determination.ipynb (::1) 2.66ms [I 15:19:41.899 NotebookApp] Kernel started: 2c5e5416-4e44-4a17-8ade-231b8253ac26 ERROR:tornado.general:Uncaught exception in ZMQStream callback Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback callback(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper return fn(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher return self.dispatch_shell(stream, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell self.pre_handler_hook() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook self.saved_sigint_handler = signal(SIGINT, default_int_handler) ValueError: signal only works in main thread ERROR:tornado.general:Uncaught exception in zmqstream callback Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events self._handle_recv() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv self._run_callback(callback, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback callback(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper return fn(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher return self.dispatch_shell(stream, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell self.pre_handler_hook() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook self.saved_sigint_handler = signal(SIGINT, default_int_handler) ValueError: signal only works in main thread ERROR:tornado.application:Exception in callback Traceback (most recent call last): File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/ioloop.py", line 605, in _run_callback ret = callback() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper return fn(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 536, in self.io_loop.add_callback(lambda : self._handle_events(self.socket, 0)) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events self._handle_recv() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv self._run_callback(callback, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback callback(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/tornado/stack_context.py", line 277, in null_wrapper return fn(*args, **kwargs) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 283, in dispatcher return self.dispatch_shell(stream, msg) File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 233, in dispatch_shell self.pre_handler_hook() File "/home/megies/anaconda/envs/default/lib/python2.7/site-packages/ipykernel/kernelbase.py", line 248, in pre_handler_hook self.saved_sigint_handler = signal(SIGINT, default_int_handler) ValueError: signal only works in main thread ```

conda package plan for updating notebook and conda info --export after doing the notebook update to 5.7.0:

``` $ conda install notebook=5.7 Solving environment: done ## Package Plan ## environment location: /home/megies/anaconda/envs/default added / updated specs: - notebook=5.7 The following NEW packages will be INSTALLED: prometheus_client: 0.4.0-py_0 conda-forge send2trash: 1.5.0-py_0 conda-forge The following packages will be UPDATED: jupyter_client: 5.0.1-py27_0 conda-forge --> 5.2.3-py_1 conda-forge jupyter_core: 4.3.0-py27_0 conda-forge --> 4.4.0-py_0 conda-forge notebook: 5.0.0-py27_0 conda-forge --> 5.7.0-py27_1000 conda-forge terminado: 0.6-py27_0 conda-forge --> 0.8.1-py27_1001 conda-forge Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done ```
``` $ conda list --export # This file may be used to create an environment using: # $ conda create --name --file # platform: linux-64 alabaster=0.7.10=py27_1 attrs=17.4.0=py_0 babel=2.5.1=py27_0 backports=1.0=py27_1 backports.functools_lru_cache=1.4=py27_1 backports.shutil_get_terminal_size=1.0.0=py27_1 backports_abc=0.5=py27_0 basemap=1.1.0=py27_3 basemap-data-hires=1.1.0=0 blas=1.0=mkl bleach=1.5.0=py27_0 boost=1.64.0=py27_4 boost-cpp=1.64.0=1 bzip2=1.0.6=1 ca-certificates=2018.8.24=ha4d7672_0 cairo=1.14.10=0 cartopy=0.16.0=py27h81b52dc_1 certifi=2018.8.24=py27_1001 click=6.7=py27_0 click-plugins=1.0.3=py27_0 cligj=0.4.0=py27_0 configparser=3.5.0=py27_0 curl=7.55.1=0 cycler=0.10.0=py27_0 dbus=1.10.10=3 decorator=4.0.11=py27_0 descartes=1.1.0=py27_0 docker-pycreds=0.2.1=py27_0 docutils=0.14=py27_0 entrypoints=0.2.2=py27_1 enum34=1.1.6=py27_1 execnet=1.3.0=py27_1 expat=2.2.5=0 fancycompleter=0.7=py27_0 fiona=1.7.9=py27_0 flake8=3.3.0=py27_0 fontconfig=2.12.6=0 freetype=2.8.1=0 freexl=1.0.2=1 funcsigs=1.0.2=py27_0 functools32=3.2.3.2=py27_1 future=0.16.0=py27_0 futures=3.2.0=py27_0 gdal=2.0.0=py27_1 geographiclib=1.48=py27_0 geojson=2.1.0=py_0 geopandas=0.3.0=py27_0 geopy=1.11.0=py27_0 geos=3.6.2=1 geotiff=1.4.2=1 gettext=0.19.7=1 giflib=5.1.4=0 glib=2.55.0=0 gmp=6.1.2=0 graphite2=1.3.9=0 greenlet=0.4.12=py27_0 gst-plugins-base=1.8.0=0 gstreamer=1.8.0=1 harfbuzz=1.7.6=0 hdf4=4.2.12=0 hdf5=1.10.1=1 html5lib=0.999=py27_0 icu=58.2=0 imagesize=0.7.1=py27_0 intel-openmp=2018.0.3=0 ipaddress=1.0.18=py27_0 ipykernel=4.6.1=py27_0 ipython=5.4.1=py27_0 ipython_genutils=0.2.0=py27_0 ipywidgets=6.0.0=py27_0 jinja2=2.9.5=py27_0 jpeg=9b=0 json-c=0.12=0 jsonschema=2.5.1=py27_0 jupyter=1.0.0=py_1 jupyter_client=5.2.3=py_1 jupyter_console=5.1.0=py27_0 jupyter_core=4.4.0=py_0 kealib=1.4.7=4 kiwisolver=1.0.1=py27_1 krb5=1.14.2=0 libboost=1.65.1=habcd387_4 libconda=4.0.0=py27_0 libdap4=3.18.3=2 libffi=3.2.1=3 libgcc-ng=7.2.0=hdf63c60_3 libgdal=2.1.4=9 libgfortran=3.0.0=1 libgfortran-ng=7.2.0=hdf63c60_3 libiconv=1.15=0 libkml=1.3.0=h9d32c78_3 libnetcdf=4.4.1.1=10 libpng=1.6.34=0 libpq=9.5.4=4 libsodium=1.0.16=h470a237_1 libspatialindex=1.8.5=1 libspatialite=4.3.0a=19 libssh2=1.8.0=2 libstdcxx-ng=7.2.0=hdf63c60_3 libtiff=4.0.9=0 libxcb=1.12=1 libxml2=2.9.4=4 libxslt=1.1.29=3 livereload=2.5.2=py_0 lxml=3.7.3=py27_0 markdown=2.6.11=py_0 markupsafe=0.23=py27_1 matplotlib=2.2.2=py27_0 mccabe=0.6.1=py27_0 mistune=0.7.4=py27_0 mkdocs=1.0.2=py_0 mkdocs-bootstrap=1.0=py_0 mkdocs-bootswatch=1.0=py_0 mkl=2018.0.3=1 mkl_fft=1.0.2=py27_0 mkl_random=1.0.1=py27_0 mock=2.0.0=py27_0 msgpack-python=0.4.8=py27_0 munch=2.2.0=py27_0 nbconvert=5.3.1=py_1 nbformat=4.4.0=py27_0 nbstripout=0.3.1=py27_0 ncurses=5.9=10 neovim=0.2.0=py27_0 notebook=5.7.0=py27_1000 numpy=1.14.5=py27hcd700cb_0 numpy-base=1.14.5=py27hdbf6ddf_0 obspy=1.1.0=py27_1 olefile=0.44=py27_0 openblas=0.2.20=5 openjpeg=2.3.0=2 openssl=1.0.2p=h470a237_0 owslib=0.16.0=py_0 pandas=0.20.3=py27_1 pandoc=1.19.2=0 pandoc-attributes=0.1.7=py27_0 pandocfilters=1.4.1=py27_0 pango=1.40.14=0 pathlib2=2.2.1=py27_0 patsy=0.4.1=py27_0 pbr=3.0.0=py27_0 pcre=8.39=0 pdbpp=0.9.1=py27_0 pep8-naming=0.4.1=py27_0 pexpect=4.2.1=py27_0 pickleshare=0.7.3=py27_0 pillow=5.0.0=py27_0 pip=9.0.1=py27_0 pixman=0.34.0=0 pkginfo=1.4.1=py27_0 pluggy=0.6.0=py_0 poppler=0.63.0=0 poppler-data=0.4.7=0 proj4=4.9.3=3 prometheus_client=0.4.0=py_0 prompt_toolkit=1.0.14=py27_0 psutil=5.2.1=py27_0 psycopg2=2.7.3.1=py27_0 ptyprocess=0.5.1=py27_0 py=1.5.2=py_0 pycodestyle=2.3.1=py27_0 pycosat=0.6.1=py27_0 pyepsg=0.3.2=py_1 pyflakes=1.5.0=py27_0 pygments=2.2.0=py27_0 pyparsing=2.2.0=py27_0 pyproj=1.9.5.1=py27_0 pyqt=5.6.0=py27_2 pyrepl=0.8.4=py27_1 pysal=1.14.2=py_0 pyshp=1.2.11=py27_0 pytest=3.4.2=py27_0 pytest-xdist=1.16.0=py27_0 python=2.7.14=4 python-dateutil=2.6.0=py27_0 pytz=2017.2=py27_0 pyyaml=3.12=py27_1 pyzmq=17.1.2=py27hae99301_0 qt=5.6.2=7 qtconsole=4.3.0=py27_0 readline=7.0=0 requests=2.13.0=py27_0 requests-toolbelt=0.8.0=py27_0 rtree=0.8.3=py27_0 scandir=1.5=py27_1 scipy=1.1.0=py27hfc37229_0 scons=2.5.1=py27_0 seaborn=0.8.1=py27_0 send2trash=1.5.0=py_0 setuptools=38.4.0=py27_0 shapely=1.6.4=py27_0 simplegeneric=0.8.1=py27_0 singledispatch=3.4.0.3=py27_0 sip=4.18=py27_1 six=1.10.0=py27_1 snowballstemmer=1.2.1=py27_0 sphinx=1.6.7=py27_0 sphinx_rtd_theme=0.2.4=py27_0 sphinxcontrib-websupport=1.0.1=py27_0 sqlalchemy=1.1.5=py27_0 sqlite=3.20.1=2 ssl_match_hostname=3.5.0.1=py27_1 statsmodels=0.8.0=py27_0 subprocess32=3.2.7=py27_0 terminado=0.8.1=py27_1001 testpath=0.3=py27_0 tk=8.6.7=0 tornado=4.5.3=py27_0 tqdm=4.19.4=py_0 traitlets=4.3.2=py27_0 trollius=2.1=py27_0 twine=1.9.1=py27_2 typing=3.6.2=py27_0 util-linux=2.21=0 utm=0.4.2=py27_0 wcwidth=0.1.7=py27_0 webencodings=0.5=py27_0 websocket-client=0.44.0=py27_0 wheel=0.29.0=py27_0 widgetsnbextension=2.0.0=py27_0 wmctrl=0.3=py27_0 xerces-c=3.2.0=0 xorg-libxau=1.0.8=3 xorg-libxdmcp=1.1.2=3 xz=5.2.2=0 yaml=0.1.6=0 zeromq=4.2.5=hfc679d8_4 zlib=1.2.11=0 ```
megies commented 5 years ago

I just noticed there are newer builds numer 1000 for pyzmq but they are in a subchannel gcc7 and thus don't get served by conda install -c conda-forge ..?

https://anaconda.org/conda-forge/pyzmq/files

screenshot from 2018-10-09 15 41 32

Anyway, I now got a working env (see below) with pretty much everything on recent version numbers I think, so probably I just ran into a very unlucky combination of package versions (and an old version of one of jupyter_client, jupyter_console, jupyter_core or notebook might have been the culprit) and you might want to close this one, dunno.

jupyter=1.0.0=py_1
jupyter_client=5.2.3=py_1
jupyter_console=5.2.0=py27_1
jupyter_core=4.4.0=py_0
libsodium=1.0.16=h470a237_1
notebook=5.7.0=py27_1000
pyzmq=17.1.2=py27hae99301_0
tornado=4.5.3=py27_0
zeromq=4.2.5=hfc679d8_6

Full env:

``` # This file may be used to create an environment using: # $ conda create --name --file # platform: linux-64 alabaster=0.7.10=py27_1 attrs=17.4.0=py_0 babel=2.5.1=py27_0 backports=1.0=py27_1 backports.functools_lru_cache=1.4=py27_1 backports.shutil_get_terminal_size=1.0.0=py27_1 backports_abc=0.5=py27_0 basemap=1.1.0=py27_3 basemap-data-hires=1.1.0=0 blas=1.0=mkl bleach=1.5.0=py27_0 boost=1.64.0=py27_4 boost-cpp=1.64.0=1 bzip2=1.0.6=1 ca-certificates=2018.8.24=ha4d7672_0 cairo=1.14.10=0 cartopy=0.16.0=py27h81b52dc_1 certifi=2018.8.24=py27_1001 click=6.7=py27_0 click-plugins=1.0.3=py27_0 cligj=0.4.0=py27_0 configparser=3.5.0=py27_0 curl=7.55.1=0 cycler=0.10.0=py27_0 dbus=1.10.10=3 decorator=4.0.11=py27_0 descartes=1.1.0=py27_0 docker-pycreds=0.2.1=py27_0 docutils=0.14=py27_0 entrypoints=0.2.2=py27_1 enum34=1.1.6=py27_1 execnet=1.3.0=py27_1 expat=2.2.5=0 fancycompleter=0.7=py27_0 fiona=1.7.9=py27_0 flake8=3.3.0=py27_0 fontconfig=2.12.6=0 freetype=2.8.1=0 freexl=1.0.2=1 funcsigs=1.0.2=py27_0 functools32=3.2.3.2=py27_1 future=0.16.0=py27_0 futures=3.2.0=py27_0 gdal=2.0.0=py27_1 geographiclib=1.48=py27_0 geojson=2.1.0=py_0 geopandas=0.3.0=py27_0 geopy=1.11.0=py27_0 geos=3.6.2=1 geotiff=1.4.2=1 gettext=0.19.7=1 giflib=5.1.4=0 glib=2.55.0=0 gmp=6.1.2=0 graphite2=1.3.9=0 greenlet=0.4.12=py27_0 gst-plugins-base=1.8.0=0 gstreamer=1.8.0=1 harfbuzz=1.7.6=0 hdf4=4.2.12=0 hdf5=1.10.1=1 html5lib=0.999=py27_0 icu=58.2=0 imagesize=0.7.1=py27_0 intel-openmp=2018.0.3=0 ipaddress=1.0.18=py27_0 ipykernel=4.10.0=py27_1 ipython=5.4.1=py27_0 ipython_genutils=0.2.0=py27_0 ipywidgets=7.4.2=py_0 jinja2=2.9.5=py27_0 jpeg=9b=0 json-c=0.12=0 jsonschema=2.5.1=py27_0 jupyter=1.0.0=py_1 jupyter_client=5.2.3=py_1 jupyter_console=5.2.0=py27_1 jupyter_core=4.4.0=py_0 kealib=1.4.7=4 kiwisolver=1.0.1=py27_1 krb5=1.14.2=0 libboost=1.65.1=habcd387_4 libconda=4.0.0=py27_0 libdap4=3.18.3=2 libffi=3.2.1=3 libgcc-ng=7.2.0=hdf63c60_3 libgdal=2.1.4=9 libgfortran=3.0.0=1 libgfortran-ng=7.2.0=hdf63c60_3 libiconv=1.15=0 libkml=1.3.0=h9d32c78_3 libnetcdf=4.4.1.1=10 libpng=1.6.34=0 libpq=9.5.4=4 libsodium=1.0.16=h470a237_1 libspatialindex=1.8.5=1 libspatialite=4.3.0a=19 libssh2=1.8.0=2 libstdcxx-ng=7.2.0=hdf63c60_3 libtiff=4.0.9=0 libxcb=1.12=1 libxml2=2.9.4=4 libxslt=1.1.29=3 livereload=2.5.2=py_0 lxml=3.7.3=py27_0 markdown=2.6.11=py_0 markupsafe=0.23=py27_1 matplotlib=2.2.2=py27_0 mccabe=0.6.1=py27_0 mistune=0.7.4=py27_0 mkdocs=1.0.2=py_0 mkdocs-bootstrap=1.0=py_0 mkdocs-bootswatch=1.0=py_0 mkl=2018.0.3=1 mkl_fft=1.0.2=py27_0 mkl_random=1.0.1=py27_0 mock=2.0.0=py27_0 msgpack-python=0.4.8=py27_0 munch=2.2.0=py27_0 nbconvert=5.3.1=py_1 nbformat=4.4.0=py27_0 nbstripout=0.3.1=py27_0 ncurses=5.9=10 neovim=0.2.0=py27_0 notebook=5.7.0=py27_1000 numpy=1.14.5=py27hcd700cb_0 numpy-base=1.14.5=py27hdbf6ddf_0 obspy=1.1.0=py27_1 olefile=0.44=py27_0 openblas=0.2.20=5 openjpeg=2.3.0=2 openssl=1.0.2p=h470a237_0 owslib=0.16.0=py_0 pandas=0.20.3=py27_1 pandoc=1.19.2=0 pandoc-attributes=0.1.7=py27_0 pandocfilters=1.4.1=py27_0 pango=1.40.14=0 pathlib2=2.2.1=py27_0 patsy=0.4.1=py27_0 pbr=3.0.0=py27_0 pcre=8.39=0 pdbpp=0.9.1=py27_0 pep8-naming=0.4.1=py27_0 pexpect=4.2.1=py27_0 pickleshare=0.7.3=py27_0 pillow=5.0.0=py27_0 pip=9.0.1=py27_0 pixman=0.34.0=0 pkginfo=1.4.1=py27_0 pluggy=0.6.0=py_0 poppler=0.63.0=0 poppler-data=0.4.7=0 proj4=4.9.3=3 prometheus_client=0.4.0=py_0 prompt_toolkit=1.0.14=py27_0 psutil=5.2.1=py27_0 psycopg2=2.7.3.1=py27_0 ptyprocess=0.5.1=py27_0 py=1.5.2=py_0 pycodestyle=2.3.1=py27_0 pycosat=0.6.1=py27_0 pyepsg=0.3.2=py_1 pyflakes=1.5.0=py27_0 pygments=2.2.0=py27_0 pyparsing=2.2.0=py27_0 pyproj=1.9.5.1=py27_0 pyqt=5.6.0=py27_2 pyrepl=0.8.4=py27_1 pysal=1.14.2=py_0 pyshp=1.2.11=py27_0 pytest=3.4.2=py27_0 pytest-xdist=1.16.0=py27_0 python=2.7.14=4 python-dateutil=2.6.0=py27_0 pytz=2017.2=py27_0 pyyaml=3.12=py27_1 pyzmq=17.1.2=py27hae99301_0 qt=5.6.2=7 qtconsole=4.4.1=py27_1 readline=7.0=0 requests=2.13.0=py27_0 requests-toolbelt=0.8.0=py27_0 rtree=0.8.3=py27_0 scandir=1.5=py27_1 scipy=1.1.0=py27hfc37229_0 scons=2.5.1=py27_0 seaborn=0.8.1=py27_0 send2trash=1.5.0=py_0 setuptools=38.4.0=py27_0 shapely=1.6.4=py27_0 simplegeneric=0.8.1=py27_0 singledispatch=3.4.0.3=py27_0 sip=4.18=py27_1 six=1.10.0=py27_1 snowballstemmer=1.2.1=py27_0 sphinx=1.6.7=py27_0 sphinx_rtd_theme=0.2.4=py27_0 sphinxcontrib-websupport=1.0.1=py27_0 sqlalchemy=1.1.5=py27_0 sqlite=3.20.1=2 ssl_match_hostname=3.5.0.1=py27_1 statsmodels=0.8.0=py27_0 subprocess32=3.2.7=py27_0 terminado=0.8.1=py27_1001 testpath=0.3=py27_0 tk=8.6.7=0 tornado=4.5.3=py27_0 tqdm=4.19.4=py_0 traitlets=4.3.2=py27_0 trollius=2.1=py27_0 twine=1.9.1=py27_2 typing=3.6.2=py27_0 util-linux=2.21=0 utm=0.4.2=py27_0 wcwidth=0.1.7=py27_0 webencodings=0.5=py27_0 websocket-client=0.44.0=py27_0 wheel=0.29.0=py27_0 widgetsnbextension=3.4.2=py27_1000 wmctrl=0.3=py27_0 xerces-c=3.2.0=0 xorg-libxau=1.0.8=3 xorg-libxdmcp=1.1.2=3 xz=5.2.2=0 yaml=0.1.6=0 zeromq=4.2.5=hfc679d8_6 zlib=1.2.11=0 ```
minrk commented 5 years ago

I strongly suspect it was notebook 5.0 that was the culprit. That's from a while back, before some significant changes to tornado and pyzmq that needed updates in the notebook.

The 100X builds are part of the conda-forge transition to new compilers. pyzmq is still building with the old toolchain compilers until the compiler transition is finished (so you should see 1001 on the gcc7 label and 1 on the main label shortly).

I think this can be closed, then.

megies commented 5 years ago

I don't think it was notebook 5.0 alone, since it also happened with 5.7 (see here). But I agree that it's not worth it to put more time into this. Thanks for the help and sorry for stealing your time @minrk.

minrk commented 5 years ago

No problem! Sorry for causing trouble. We can chalk this up to "not sure exactly what combination is the problem, but if your packages are up-to-date it goes away" and move on.