This notebook no longer runs in Binder. When you click the "launch binder" badge, it results in the following error:
Click for Binder error message
```
Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker2roswvck'...
HEAD is now at 133cea6 Merge pull request #27 from genepattern/develop
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
---> 355caeb0ab97
Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
---> Using cache
---> 1e7c54772073
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
---> 531044f4da68
Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
---> Using cache
---> b559af023763
Step 5/53 : ENV LC_ALL en_US.UTF-8
---> Using cache
---> 9d37fb0cbb72
Step 6/53 : ENV LANG en_US.UTF-8
---> Using cache
---> 3fb564bb80ef
Step 7/53 : ENV LANGUAGE en_US.UTF-8
---> Using cache
---> 4c9b29ed02fe
Step 8/53 : ENV SHELL /bin/bash
---> Using cache
---> 68e0e9eee7f4
Step 9/53 : ARG NB_USER
---> Using cache
---> 9a5cb698005e
Step 10/53 : ARG NB_UID
---> Using cache
---> 3669a5cafb5d
Step 11/53 : ENV USER ${NB_USER}
---> Using cache
---> 4d8788674d23
Step 12/53 : ENV HOME /home/${NB_USER}
---> Using cache
---> 41da903a927b
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
---> 513111bb0462
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_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
---> Using cache
---> 8f835683cb04
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
---> 11e7a751300e
Step 16/53 : EXPOSE 8888
---> Using cache
---> 49e543fa80ee
Step 17/53 : ENV APP_BASE /srv
---> Using cache
---> c94966a65919
Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
---> Using cache
---> 0d8a233b5758
Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
---> Using cache
---> 61aa45c6c971
Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
---> Using cache
---> 2dc58c682598
Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
---> Using cache
---> 2149835a73ee
Step 22/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
---> Using cache
---> bbdb9e256b4e
Step 23/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
---> Using cache
---> 2d6dc190d411
Step 24/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-2747be /etc/profile.d/activate-conda.sh
---> Using cache
---> 43eb68e01f71
Step 25/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2efrozen-2eyml-b3d5bc /tmp/environment.yml
---> Using cache
---> 980c670a8308
Step 26/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiconda-2ebash-12d101 /tmp/install-miniconda.bash
---> Using cache
---> 1224e8b8d4c1
Step 27/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
---> Using cache
---> f8028b665ae0
Step 28/53 : USER ${NB_USER}
---> Using cache
---> b479f9b32425
Step 29/53 : RUN npm config --global set prefix ${NPM_DIR}
---> Using cache
---> e1584e0e1556
Step 30/53 : USER root
---> Using cache
---> 510a24722ca6
Step 31/53 : RUN bash /tmp/install-miniconda.bash && rm /tmp/install-miniconda.bash /tmp/environment.yml
---> Using cache
---> acace99e9840
Step 32/53 : ARG REPO_DIR=${HOME}
---> Using cache
---> 417ff8d6e468
Step 33/53 : ENV REPO_DIR ${REPO_DIR}
---> Using cache
---> d632572969aa
Step 34/53 : WORKDIR ${REPO_DIR}
---> Using cache
---> 4725ebc8c631
Step 35/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
---> Using cache
---> b429c43b3cde
Step 36/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
---> Using cache
---> 5bffdaa7224b
Step 37/53 : COPY src/requirements.txt ${REPO_DIR}/requirements.txt
---> 831c78b3c0d7
Step 38/53 : USER root
---> Running in cb79fb0d91d9
Removing intermediate container cb79fb0d91d9
---> 57dfebb53012
Step 39/53 : RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR}
---> Running in 7feb61ac841b
Removing intermediate container 7feb61ac841b
---> 409bacba2599
Step 40/53 : USER ${NB_USER}
---> Running in e3af7911aaf7
Removing intermediate container e3af7911aaf7
---> b7041ba04ff5
Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"
---> Running in 598fa56b5cf2
Collecting cmake==0.9.0 (from -r requirements.txt (line 1))
Downloading https://files.pythonhosted.org/packages/b4/f1/7e9fa0a5ea7004b97cc8f5365fce25462af6e0da0b9f955f629e4655f1af/cmake-0.9.0.tar.gz (34.9MB)
ERROR: Command errored out with exit status 1:
command: /srv/conda/envs/notebook/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dpe75ski/cmake/setup.py'"'"'; __file__='"'"'/tmp/pip-install-dpe75ski/cmake/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
cwd: /tmp/pip-install-dpe75ski/cmake/
Complete output (5 lines):
Traceback (most recent call last):
File "", line 1, in
File "/tmp/pip-install-dpe75ski/cmake/setup.py", line 6, in
from pip.req import parse_requirements
ModuleNotFoundError: No module named 'pip.req'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Removing intermediate container 598fa56b5cf2
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"' returned a non-zero code: 1
```
The root issue is due to a change introduced in pip when going from version 9 to version 10, which makes cmake uninstallable. This happened a while ago, so this has been broken for some time.
Solution is to bump the dependencies in requirements.txt, but the notebook may also need updating if any APIs have changed.
This notebook no longer runs in Binder. When you click the "launch binder" badge, it results in the following error:
Click for Binder error message
``` Waiting for build to start... Picked Git content provider. Cloning into '/tmp/repo2docker2roswvck'... HEAD is now at 133cea6 Merge pull request #27 from genepattern/develop 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 ---> 355caeb0ab97 Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive ---> Using cache ---> 1e7c54772073 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 ---> 531044f4da68 Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen ---> Using cache ---> b559af023763 Step 5/53 : ENV LC_ALL en_US.UTF-8 ---> Using cache ---> 9d37fb0cbb72 Step 6/53 : ENV LANG en_US.UTF-8 ---> Using cache ---> 3fb564bb80ef Step 7/53 : ENV LANGUAGE en_US.UTF-8 ---> Using cache ---> 4c9b29ed02fe Step 8/53 : ENV SHELL /bin/bash ---> Using cache ---> 68e0e9eee7f4 Step 9/53 : ARG NB_USER ---> Using cache ---> 9a5cb698005e Step 10/53 : ARG NB_UID ---> Using cache ---> 3669a5cafb5d Step 11/53 : ENV USER ${NB_USER} ---> Using cache ---> 4d8788674d23 Step 12/53 : ENV HOME /home/${NB_USER} ---> Using cache ---> 41da903a927b 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 ---> 513111bb0462 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_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list && echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list ---> Using cache ---> 8f835683cb04 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 ---> 11e7a751300e Step 16/53 : EXPOSE 8888 ---> Using cache ---> 49e543fa80ee Step 17/53 : ENV APP_BASE /srv ---> Using cache ---> c94966a65919 Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm ---> Using cache ---> 0d8a233b5758 Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc ---> Using cache ---> 61aa45c6c971 Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda ---> Using cache ---> 2dc58c682598 Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook ---> Using cache ---> 2149835a73ee Step 22/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX} ---> Using cache ---> bbdb9e256b4e Step 23/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH} ---> Using cache ---> 2d6dc190d411 Step 24/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-2747be /etc/profile.d/activate-conda.sh ---> Using cache ---> 43eb68e01f71 Step 25/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2efrozen-2eyml-b3d5bc /tmp/environment.yml ---> Using cache ---> 980c670a8308 Step 26/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiconda-2ebash-12d101 /tmp/install-miniconda.bash ---> Using cache ---> 1224e8b8d4c1 Step 27/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR} ---> Using cache ---> f8028b665ae0 Step 28/53 : USER ${NB_USER} ---> Using cache ---> b479f9b32425 Step 29/53 : RUN npm config --global set prefix ${NPM_DIR} ---> Using cache ---> e1584e0e1556 Step 30/53 : USER root ---> Using cache ---> 510a24722ca6 Step 31/53 : RUN bash /tmp/install-miniconda.bash && rm /tmp/install-miniconda.bash /tmp/environment.yml ---> Using cache ---> acace99e9840 Step 32/53 : ARG REPO_DIR=${HOME} ---> Using cache ---> 417ff8d6e468 Step 33/53 : ENV REPO_DIR ${REPO_DIR} ---> Using cache ---> d632572969aa Step 34/53 : WORKDIR ${REPO_DIR} ---> Using cache ---> 4725ebc8c631 Step 35/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH} ---> Using cache ---> b429c43b3cde Step 36/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX} ---> Using cache ---> 5bffdaa7224b Step 37/53 : COPY src/requirements.txt ${REPO_DIR}/requirements.txt ---> 831c78b3c0d7 Step 38/53 : USER root ---> Running in cb79fb0d91d9 Removing intermediate container cb79fb0d91d9 ---> 57dfebb53012 Step 39/53 : RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} ---> Running in 7feb61ac841b Removing intermediate container 7feb61ac841b ---> 409bacba2599 Step 40/53 : USER ${NB_USER} ---> Running in e3af7911aaf7 Removing intermediate container e3af7911aaf7 ---> b7041ba04ff5 Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt" ---> Running in 598fa56b5cf2 Collecting cmake==0.9.0 (from -r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/b4/f1/7e9fa0a5ea7004b97cc8f5365fce25462af6e0da0b9f955f629e4655f1af/cmake-0.9.0.tar.gz (34.9MB) ERROR: Command errored out with exit status 1: command: /srv/conda/envs/notebook/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dpe75ski/cmake/setup.py'"'"'; __file__='"'"'/tmp/pip-install-dpe75ski/cmake/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info cwd: /tmp/pip-install-dpe75ski/cmake/ Complete output (5 lines): Traceback (most recent call last): File "The root issue is due to a change introduced in pip when going from version 9 to version 10, which makes cmake uninstallable. This happened a while ago, so this has been broken for some time.
Solution is to bump the dependencies in requirements.txt, but the notebook may also need updating if any APIs have changed.