Binder will not launch due to requirements.txt error

[peterdsharpe]

Hi there,

When I click the "Launch in Binder..." button on the README.md to go here, Binder fails to launch this notebook.

This is apparently due to a dependency error. The full log from Binder is at the end of this issue ticket.

Suggested fix: change requirements.txt to not self-conflict.

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker17sq55eq'...
HEAD is now at a065af7 Merge pull request #15 from Ranlot/dependabot/pip/notebook-6.4.1
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
 ---> c6458e9c218d
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> c4d1f71e725a
Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 6e869a073a8f
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 4e0768284ade
Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> b84128b53634
Step 6/53 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 8eb63be64d02
Step 7/53 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 189b3bb92d24
Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 68ab1aea7cf3
Step 9/53 : ARG NB_USER
 ---> Using cache
 ---> e26b9ce19e19
Step 10/53 : ARG NB_UID
 ---> Using cache
 ---> 75f15cc9d222
Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 838c107ed670
Step 12/53 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3592140fdb53
Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> ba292d45e088
Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_14.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 52150c7cca16
Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 4e4b80062d8f
Step 16/53 : EXPOSE 8888
 ---> Using cache
 ---> c09475a6636d
Step 17/53 : ENV APP_BASE /srv
 ---> Using cache
 ---> 2aaec1d1ae80
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 8d575807387e
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 462ce05c7a16
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 241a8938c3fa
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> c5cda9534a3d
Step 22/53 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 3bd3ab5176cc
Step 23/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 343cd2e03232
Step 24/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
 ---> e10bd1938abc
Step 25/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> 5c4e808639ed
Step 26/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> b1bf3b51077e
Step 27/53 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> ee622a3cb2bf
Step 28/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9b8876093b2f
Step 29/53 : USER ${NB_USER}
 ---> Using cache
 ---> 50543e0edcda
Step 30/53 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> caac4a13b2da
Step 31/53 : USER root
 ---> Using cache
 ---> 197b965a28ed
Step 32/53 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> 801eb1ee3486
Step 33/53 : ARG REPO_DIR=${HOME}
 ---> Using cache
 ---> 4711a5342bc0
Step 34/53 : ENV REPO_DIR ${REPO_DIR}
 ---> Using cache
 ---> 8db4431e1848
Step 35/53 : WORKDIR ${REPO_DIR}
 ---> Using cache
 ---> 250ea143a30f
Step 36/53 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Using cache
 ---> e981c79e8dfb
Step 37/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Using cache
 ---> dc36e52c534c
Step 38/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Using cache
 ---> 3e15fe9e72bd
Step 39/53 : COPY --chown=1000:1000 src/requirements.txt ${REPO_DIR}/requirements.txt
 ---> Using cache
 ---> d4ab1fa8f221
Step 40/53 : USER ${NB_USER}
 ---> Using cache
 ---> 3336b67d3d80
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"
 ---> Running in 2f6add63a4df
Collecting appnope==0.1.0
  Downloading appnope-0.1.0-py2.py3-none-any.whl (4.0 kB)
Collecting attrs==19.1.0
  Downloading attrs-19.1.0-py2.py3-none-any.whl (35 kB)
Collecting backcall==0.1.0
  Downloading backcall-0.1.0.zip (11 kB)
Collecting bleach==3.3.0
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Collecting cycler==0.10.0
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting decorator==4.4.0
  Downloading decorator-4.4.0-py2.py3-none-any.whl (8.3 kB)
Collecting defusedxml==0.6.0
  Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Requirement already satisfied: entrypoints==0.3 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 8)) (0.3)
Collecting ipykernel==5.1.0
  Downloading ipykernel-5.1.0-py3-none-any.whl (113 kB)
Collecting ipython==7.5.0
  Downloading ipython-7.5.0-py3-none-any.whl (770 kB)
Requirement already satisfied: ipython-genutils==0.2.0 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 11)) (0.2.0)
Collecting ipywidgets==7.4.2
  Downloading ipywidgets-7.4.2-py2.py3-none-any.whl (111 kB)
Collecting jedi==0.13.3
  Downloading jedi-0.13.3-py2.py3-none-any.whl (178 kB)
Collecting Jinja2==2.11.3
  Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
Collecting jsonschema==3.0.1
  Downloading jsonschema-3.0.1-py2.py3-none-any.whl (54 kB)
Collecting jupyter==1.0.0
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Collecting jupyter-client==5.2.4
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Collecting jupyter-console==6.0.0
  Downloading jupyter_console-6.0.0-py2.py3-none-any.whl (21 kB)
Collecting jupyter-core==4.4.0
  Downloading jupyter_core-4.4.0-py2.py3-none-any.whl (126 kB)
Collecting kiwisolver==1.1.0
  Downloading kiwisolver-1.1.0-cp37-cp37m-manylinux1_x86_64.whl (90 kB)
Collecting MarkupSafe==1.1.1
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Collecting matplotlib==3.0.3
  Downloading matplotlib-3.0.3-cp37-cp37m-manylinux1_x86_64.whl (13.0 MB)
Requirement already satisfied: mistune==0.8.4 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 23)) (0.8.4)
Collecting mpmath==1.1.0
  Downloading mpmath-1.1.0.tar.gz (512 kB)
Collecting nbconvert==5.5.0
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Collecting nbformat==4.4.0
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Collecting notebook==6.4.1
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Collecting numpy==1.16.3
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Collecting pandas==0.24.2
  Downloading pandas-0.24.2-cp37-cp37m-manylinux1_x86_64.whl (10.1 MB)
Requirement already satisfied: pandocfilters==1.4.2 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 30)) (1.4.2)
Collecting parso==0.4.0
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Collecting pexpect==4.7.0
  Downloading pexpect-4.7.0-py2.py3-none-any.whl (58 kB)
Requirement already satisfied: pickleshare==0.7.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 33)) (0.7.5)
Collecting Pillow==8.3.2
  Downloading Pillow-8.3.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB)
Collecting prometheus-client==0.6.0
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Collecting prompt-toolkit==2.0.9
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Collecting ptyprocess==0.6.0
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Collecting Pygments==2.7.4
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Collecting pyparsing==2.4.0
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Collecting pyrsistent==0.15.1
  Downloading pyrsistent-0.15.1.tar.gz (106 kB)
Collecting python-dateutil==2.8.0
  Downloading python_dateutil-2.8.0-py2.py3-none-any.whl (226 kB)
Collecting pytz==2019.1
  Downloading pytz-2019.1-py2.py3-none-any.whl (510 kB)
Collecting pyzmq==18.0.1
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Collecting qtconsole==4.4.3
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Collecting scikit-learn==0.20.3
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Collecting scipy==1.2.1
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Collecting Send2Trash==1.5.0
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Collecting six==1.12.0
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Collecting sklearn==0.0
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Collecting terminado==0.8.2
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Collecting testpath==0.4.2
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Collecting tornado==6.0.2
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Collecting traitlets==4.3.2
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Collecting wcwidth==0.1.7
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Requirement already satisfied: webencodings==0.5.1 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from -r requirements.txt (line 55)) (0.5.1)
Collecting widgetsnbextension==3.4.2
  Downloading widgetsnbextension-3.4.2-py2.py3-none-any.whl (2.2 MB)
Requirement already satisfied: packaging in /srv/conda/envs/notebook/lib/python3.7/site-packages (from bleach==3.3.0->-r requirements.txt (line 4)) (21.0)
Requirement already satisfied: setuptools>=18.5 in /srv/conda/envs/notebook/lib/python3.7/site-packages (from ipython==7.5.0->-r requirements.txt (line 10)) (58.0.4)
INFO: pip is looking at multiple versions of nbformat to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of nbconvert to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of mpmath to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of mistune to determine which version is compatible with other requirements. This could take a while.
Collecting mistune==0.8.4
  Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB)
INFO: pip is looking at multiple versions of matplotlib to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of markupsafe to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of kiwisolver to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jupyter-core to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jupyter-console to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jupyter-client to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jupyter to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jsonschema to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jinja2 to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of jedi to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of ipywidgets to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of ipython-genutils to determine which version is compatible with other requirements. This could take a while.
Collecting ipython-genutils==0.2.0
  Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
INFO: pip is looking at multiple versions of ipython to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of ipykernel to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of entrypoints to determine which version is compatible with other requirements. This could take a while.
Collecting entrypoints==0.3
  Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB)
INFO: pip is looking at multiple versions of nbformat to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of nbconvert to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of mpmath to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of mistune to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of defusedxml to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of decorator to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of cycler to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of bleach to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of backcall to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of <Python from Requires-Python> to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of attrs to determine which version is compatible with other requirements. This could take a while.
INFO: pip is looking at multiple versions of appnope to determine which version is compatible with other requirements. This could take a while.
�[91mERROR: Cannot install -r requirements.txt (line 18), -r requirements.txt (line 27), -r requirements.txt (line 9) and jupyter-client==5.2.4 because these package versions have conflicting dependencies.
�[0m
The conflict is caused by:
    The user requested jupyter-client==5.2.4
    ipykernel 5.1.0 depends on jupyter-client
    jupyter-console 6.0.0 depends on jupyter-client
    notebook 6.4.1 depends on jupyter-client>=5.3.4

To fix this you could try to:
1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

�[91mERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
�[0mRemoving intermediate container 2f6add63a4df
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"' returned a non-zero code: 1Built image, launching...
Failed to connect to event stream