Thank you so much, Bryan. Bokeh is absolutely amazing, and you guys do a phenomenal job. I’m sorry for the too-vague bug report.
I come at the problem when I visit the Interactive Tutorial Notebooks link in the center of the page:
https://docs.bokeh.org/en/latest/. I think this is Bokeh 3.3.4, from the page title.
The link it takes me to is this page. It’s the one that seems to crash. I’m not sure about which version of jupyter
https://mybinder.org/v2/gh/bokeh/bokeh-notebooks/HEAD?labpath=index.ipynb
Here is the print of the build logs:
Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockerynx4hbxd'...
HEAD is now at 0153bf1 Update README.md
Building conda environment for python=3.10
Using CondaBuildPack builder
Step 1/52 : FROM docker.io/library/buildpack-deps:jammy
---> 0d3eb68a64eb
Step 2/52 : ENV DEBIAN_FRONTEND=noninteractive
---> Using cache
---> 188010f9eb3c
Step 3/52 : 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
---> 8cfc6e7fec81
Step 4/52 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen
---> Using cache
---> 7d8248eb31ad
Step 5/52 : ENV LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 LANGUAGE=en_US.UTF-8
---> Using cache
---> e0166d0f1a5f
Step 6/52 : ENV SHELL=/bin/bash
---> Using cache
---> 752a602d2b1c
Step 7/52 : ARG NB_USER
---> Using cache
---> 0c534a237b77
Step 8/52 : ARG NB_UID
---> Using cache
---> b8399681d390
Step 9/52 : ENV USER=${NB_USER} HOME=/home/${NB_USER}
---> Using cache
---> 798328141c3c
Step 10/52 : 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} ${NB_USER}
---> Using cache
---> 2acfa13db9ce
Step 11/52 : RUN apt-get -qq update && apt-get -qq install --yes --no-install-recommends gettext-base less unzip > /dev/null && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
---> Using cache
---> 916ada9e56a4
Step 12/52 : EXPOSE 8888
---> Using cache
---> 39c3e9eb1d35
Step 13/52 : ENV APP_BASE=/srv
---> Using cache
---> fb18474dd9ed
Step 14/52 : ENV CONDA_DIR=${APP_BASE}/conda
---> Using cache
---> 27f5b690acac
Step 15/52 : ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/notebook
---> Using cache
---> 318d413c9378
Step 16/52 : ENV NPM_DIR=${APP_BASE}/npm
---> Using cache
---> cf3cf4363f8e
Step 17/52 : ENV NPM_CONFIG_GLOBALCONFIG=${NPM_DIR}/npmrc
---> Using cache
---> bf306dd97043
Step 18/52 : ENV NB_ENVIRONMENT_FILE=/tmp/env/environment.lock
---> Using cache
---> 34e46cef830c
Step 19/52 : ENV MAMBA_ROOT_PREFIX=${CONDA_DIR}
---> Using cache
---> dfca566d8e48
Step 20/52 : ENV MAMBA_EXE=${CONDA_DIR}/bin/mamba
---> Using cache
---> dbf268809d11
Step 21/52 : ENV CONDA_PLATFORM=linux-64
---> Using cache
---> 3c97d3f0c42a
Step 22/52 : ENV KERNEL_PYTHON_PREFIX=${NB_PYTHON_PREFIX}
---> Using cache
---> 716c34490b84
Step 23/52 : ENV PATH=${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
---> Using cache
---> 762e4af4fd97
Step 24/52 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-44e764 /etc/profile.d/activate-conda.sh
---> Using cache
---> b7779f5b86e5
Step 25/52 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e10-2dlinux-2d64-2elock-388e0b /tmp/env/environment.lock
---> Using cache
---> 078daca8b772
Step 26/52 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e10-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dbase-2denv-2ebash-e5509f /tmp/install-base-env.bash
---> Using cache
---> 2466320c0b30
Step 27/52 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-base-env.bash' && rm -rf /tmp/install-base-env.bash /tmp/env
---> Using cache
---> 7ea7583968d0
Step 28/52 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
---> Using cache
---> 50f91ccc2184
Step 29/52 : USER root
---> Using cache
---> 1863101607cc
Step 30/52 : ARG REPO_DIR=${HOME}
---> Using cache
---> ce486fafcaa4
Step 31/52 : ENV REPO_DIR=${REPO_DIR}
---> Using cache
---> a87207fa0d83
Step 32/52 : RUN if [ ! -d "${REPO_DIR}" ]; then /usr/bin/install -o ${NB_USER} -g ${NB_USER} -d "${REPO_DIR}"; fi
---> Using cache
---> 2e5448c39cd8
Step 33/52 : WORKDIR ${REPO_DIR}
---> Using cache
---> 24ec45b47818
Step 34/52 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
---> Using cache
---> 0c15cd0f920f
Step 35/52 : ENV PATH=${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
---> Using cache
---> 583a0a81b688
Step 36/52 : ENV CONDA_DEFAULT_ENV=${KERNEL_PYTHON_PREFIX}
---> Using cache
---> cdbb480ea05d
Step 37/52 : COPY --chown=1000:1000 src/environment.yml ${REPO_DIR}/environment.yml
---> Using cache
---> 2c4d3ec10548
Step 38/52 : USER ${NB_USER}
---> Using cache
---> fb29b4c17eaf
Step 39/52 : RUN TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '
---> Running in 3f2beb82af2a
Looking for: ['python=3.10', 'numpy', 'notebook', "bokeh[version='>=3.0']", 'pandas', 'scipy', 'selenium', 'datashader', 'networkx', 'flask', 'firefox', 'geckodriver', 'holoviews', 'hvplot', 'jupyter_contrib_nbextensions']
Transaction
Prefix: /srv/conda/envs/notebook
Updating specs:
- numpy
- bokeh[version='>=3.0']
- pandas
- scipy
- selenium
- datashader
- networkx
- flask
- firefox
- geckodriver
- holoviews
- hvplot
- jupyter_contrib_nbextensions
- python=3.10
- notebook
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────────────────────
+ selenium-manager 4.17.0 he8a937b_0 conda-forge 2MB
+ firefox 122.0 hd3aeb46_0 conda-forge 72MB
+ geckodriver 0.34.0 h2b8f863_0 conda-forge 3MB
+ libgfortran5 13.2.0 ha4646dd_4 conda-forge 1MB
+ libxcrypt 4.4.36 hd590300_1 conda-forge 100kB
+ libjpeg-turbo 3.0.0 hd590300_1 conda-forge 619kB
+ lerc 4.0.0 h27087fc_0 conda-forge 282kB
+ libdeflate 1.19 hd590300_0 conda-forge 67kB
+ zstd 1.5.5 hfc55251_0 conda-forge 545kB
+ libwebp-base 1.3.2 hd590300_0 conda-forge 402kB
+ libpng 1.6.39 h753d276_0 conda-forge 283kB
+ libllvm14 14.0.6 hcd5def8_4 conda-forge 31MB
+ libiconv 1.17 hd590300_2 conda-forge 706kB
+ xorg-libxau 1.0.11 hd590300_0 conda-forge 14kB
+ libbrotlicommon 1.1.0 hd590300_1 conda-forge 69kB
+ pthread-stubs 0.4 h36c2ea0_1001 conda-forge 6kB
+ xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge 19kB
+ libgfortran-ng 13.2.0 h69a702a_4 conda-forge 24kB
+ libtiff 4.6.0 ha9c0a0a_2 conda-forge 283kB
+ freetype 2.12.1 h267a509_2 conda-forge 635kB
+ libxml2 2.11.5 h0d562d8_0 conda-forge 705kB
+ libbrotlienc 1.1.0 hd590300_1 conda-forge 283kB
+ libbrotlidec 1.1.0 hd590300_1 conda-forge 33kB
+ libxcb 1.15 h0b41bf4_0 conda-forge 384kB
+ libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge 6MB
+ unicodedata2 15.1.0 py310h2372a71_0 conda-forge 374kB
+ kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge 73kB
+ llvmlite 0.41.1 py310h1b8f574_0 conda-forge 3MB
+ openjpeg 2.5.0 h488ebb8_3 conda-forge 357kB
+ lcms2 2.16 hb7c19ff_0 conda-forge 245kB
+ libxslt 1.1.37 h0054252_1 conda-forge 254kB
+ brotli-bin 1.1.0 hd590300_1 conda-forge 19kB
+ libblas 3.9.0 21_linux64_openblas conda-forge 15kB
+ pillow 10.2.0 py310h01dd4db_0 conda-forge 41MB
+ lxml 4.9.3 py310h9b7343a_1 conda-forge 1MB
+ brotli 1.1.0 hd590300_1 conda-forge 19kB
+ libcblas 3.9.0 21_linux64_openblas conda-forge 15kB
+ liblapack 3.9.0 21_linux64_openblas conda-forge 15kB
+ numpy 1.26.3 py310hb13e2d6_0 conda-forge 7MB
+ contourpy 1.2.0 py310hd41b1e2_0 conda-forge 239kB
+ numba 0.58.1 py310h7dc5dd1_0 conda-forge 4MB
+ scipy 1.12.0 py310hb13e2d6_2 conda-forge 16MB
+ colorama 0.4.6 pyhd8ed1ab_0 conda-forge 25kB
+ uc-micro-py 1.0.2 pyhd8ed1ab_0 conda-forge 11kB
+ mdurl 0.1.2 pyhd8ed1ab_0 conda-forge 15kB
+ markdown 3.5.2 pyhd8ed1ab_0 conda-forge 77kB
+ locket 1.0.0 pyhd8ed1ab_0 conda-forge 8kB
+ xyzservices 2023.10.1 pyhd8ed1ab_0 conda-forge 36kB
+ outcome 1.3.0.post0 pyhd8ed1ab_0 conda-forge 16kB
+ sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge 26kB
+ munkres 1.1.4 pyh9f0ad1d_0 conda-forge 12kB
+ pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge 90kB
+ cycler 0.12.1 pyhd8ed1ab_0 conda-forge 13kB
+ python-tzdata 2023.4 pyhd8ed1ab_0 conda-forge 146kB
+ fsspec 2023.12.2 pyhca7485f_0 conda-forge 127kB
+ cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge 25kB
+ toolz 0.12.1 pyhd8ed1ab_0 conda-forge 52kB
+ multipledispatch 0.6.0 py_0 conda-forge 12kB
+ werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge 242kB
+ click 8.1.7 unix_pyh707e725_0 conda-forge 84kB
+ param 2.0.2 pyhca7485f_0 conda-forge 101kB
+ jupyter_server_terminals 0.5.2 pyhd8ed1ab_0 conda-forge 20kB
+ typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge 14kB
+ itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge 16kB
+ networkx 3.2.1 pyhd8ed1ab_0 conda-forge 1MB
+ tqdm 4.66.1 pyhd8ed1ab_0 conda-forge 89kB
+ linkify-it-py 2.0.2 pyhd8ed1ab_0 conda-forge 24kB
+ markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge 64kB
+ partd 1.4.1 pyhd8ed1ab_0 conda-forge 21kB
+ pyct 0.5.0 pyhd8ed1ab_0 conda-forge 20kB
+ pyviz_comms 3.0.0 pyhd8ed1ab_0 conda-forge 48kB
+ overrides 7.7.0 pyhd8ed1ab_0 conda-forge 30kB
+ h11 0.14.0 pyhd8ed1ab_0 conda-forge 48kB
+ async-lru 2.0.4 pyhd8ed1ab_0 conda-forge 15kB
+ flask 3.0.1 pyhd8ed1ab_0 conda-forge 81kB
+ mdit-py-plugins 0.4.0 pyhd8ed1ab_0 conda-forge 41kB
+ dask-core 2024.1.1 pyhd8ed1ab_0 conda-forge 874kB
+ colorcet 3.0.1 pyhd8ed1ab_0 conda-forge 2MB
+ wsproto 1.2.0 pyhd8ed1ab_0 conda-forge 25kB
+ jupyter-lsp 2.2.2 pyhd8ed1ab_0 conda-forge 55kB
+ jupyter_contrib_core 0.4.0 pyhd8ed1ab_0 conda-forge 18kB
+ jupyter_nbextensions_configurator 0.6.1 pyhd8ed1ab_0 conda-forge 461kB
+ jupyter_latex_envs 1.4.6 pyhd8ed1ab_1002 conda-forge 752kB
+ trio 0.21.0 py310hff52083_0 conda-forge 508kB
+ fonttools 4.47.2 py310h2372a71_0 conda-forge 2MB
+ pandas 2.2.0 py310hcc13569_0 conda-forge 13MB
+ jupyter_highlight_selected_word 0.2.0 py310hff52083_1005 conda-forge 15kB
+ matplotlib-base 3.8.2 py310h62c0568_0 conda-forge 7MB
+ trio-websocket 0.11.1 pyhd8ed1ab_0 conda-forge 31kB
+ xarray 2024.1.1 pyhd8ed1ab_0 conda-forge 731kB
+ jupyter_contrib_nbextensions 0.7.0 pyhd8ed1ab_0 conda-forge 21MB
+ selenium 4.17.2 pyhd8ed1ab_0 conda-forge 289kB
+ datashader 0.16.0 pyhd8ed1ab_0 conda-forge 17MB
+ bokeh 3.3.4 py_0 bokeh 5MB
+ panel 1.3.8 pyhd8ed1ab_0 conda-forge 15MB
+ holoviews 1.18.1 pyhd8ed1ab_0 conda-forge 3MB
+ hvplot 0.9.2 pyhd8ed1ab_0 conda-forge 2MB
Upgrade:
────────────────────────────────────────────────────────────────────────────────────────────────
- libnsl 2.0.0 hd590300_1 conda-forge 33kB
+ libnsl 2.0.1 hd590300_0 conda-forge 33kB
- libsqlite 3.43.2 h2797004_0 conda-forge 840kB
+ libsqlite 3.44.2 h2797004_0 conda-forge 846kB
- openssl 3.1.3 hd590300_0 conda-forge 3MB
+ openssl 3.2.0 hd590300_1 conda-forge 3MB
- python 3.10.12 hd12c33a_0_cpython conda-forge 26MB
+ python 3.10.13 hd12c33a_1_cpython conda-forge 26MB
- typing_extensions 4.8.0 pyha770c72_0 conda-forge 35kB
+ typing_extensions 4.9.0 pyha770c72_0 conda-forge 36kB
- typing-extensions 4.8.0 hd8ed1ab_0 conda-forge 10kB
+ typing-extensions 4.9.0 hd8ed1ab_0 conda-forge 10kB
- jupyter_server 1.24.0 pyhd8ed1ab_0 conda-forge 244kB
+ jupyter_server 2.10.0 pyhd8ed1ab_0 conda-forge 317kB
- jupyterlab 3.6.6 pyhd8ed1ab_0 conda-forge 5MB
+ jupyterlab 4.0.11 pyhd8ed1ab_0 conda-forge 6MB
- notebook 6.5.6 pyha770c72_0 conda-forge 307kB
+ notebook 7.0.7 pyhd8ed1ab_0 conda-forge 3MB
Summary:
Install: 97 packages
Upgrade: 9 packages
Total download: 329MB
────────────────────────────────────────────────────────────────────────────────────────────────
Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
from ._compat.nbextensions import BaseNBExtensionApp
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
from ._compat.nbextensions import BaseNBExtensionApp
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'
Traceback (most recent call last):
File "/srv/conda/envs/notebook/bin/jupyter-nbextensions_configurator", line 6, in <module>
from jupyter_nbextensions_configurator.application import main
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_nbextensions_configurator/__init__.py", line 17, in <module>
from notebook import version_info as nb_version_info
ImportError: cannot import name 'version_info' from 'notebook' (/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/__init__.py)
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/srv/conda/envs/notebook/bin/jupyter-contrib-nbextension", line 6, in <module>
from jupyter_contrib_nbextensions.application import main
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_nbextensions/application.py", line 7, in <module>
from jupyter_contrib_core.notebook_compat.nbextensions import ArgumentConflict
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
from ._compat.nbextensions import BaseNBExtensionApp
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'
done
Rolling back transaction: ...working... ERROR conda.core.link:_execute(945): An error occurred while installing package 'conda-forge::jupyter_highlight_selected_word-0.2.0-py310hff52083_1005'.
done
LinkError: post-link script failed for package conda-forge::jupyter_highlight_selected_word-0.2.0-py310hff52083_1005
location of failed script: /srv/conda/envs/notebook/bin/.jupyter_highlight_selected_word-post-link.sh
==> script messages <==
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 6, in <module>
from notebook.extensions import BaseExtensionApp
ModuleNotFoundError: No module named 'notebook.extensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 10, in <module>
from notebook.nbextensions import BaseNBExtensionApp
ModuleNotFoundError: No module named 'notebook.nbextensions'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/nbextensions.py", line 12, in <module>
from ._compat.nbextensions import BaseNBExtensionApp
File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_contrib_core/notebook_compat/_compat/nbextensions.py", line 35, in <module>
from notebook.nbextensions import (
ModuleNotFoundError: No module named 'notebook.nbextensions'
==> script output <==
stdout:
stderr:
return code: 1
()
time: 188.313
Removing intermediate container 3f2beb82af2a
The command '/bin/sh -c TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '' returned a non-zero code: 1