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binder launch not working #431

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bendichter opened this issue Sep 3, 2024 · 1 comment
Open

binder launch not working #431

bendichter opened this issue Sep 3, 2024 · 1 comment

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@bendichter
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I tried launching a notebook using binder: https://mybinder.org/v2/gh/AllenInstitute/openscope_databook/main?urlpath=lab/tree/docs/visualization/visualize_2p_raw.ipynb

but eventually got this error:

...
+ rm -rf /root/.cache
+ chown -R jovyan:jovyan /srv/conda
+ /srv/conda/bin/mamba list -p /srv/conda/envs/notebook
# packages in environment at /srv/conda/envs/notebook:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alembic                   1.13.2             pyhd8ed1ab_0    conda-forge
annotated-types           0.7.0              pyhd8ed1ab_0    conda-forge
anyio                     4.4.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38h01eb140_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
async_generator           1.10               pyhd8ed1ab_1    conda-forge
attrs                     24.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.8.2              pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0            py38h17151c0_1    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2024.7.4           pyhd8ed1ab_0    conda-forge
certipy                   0.1.3              pyhd8ed1ab_1    conda-forge
cffi                      1.17.0           py38heb5c249_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
cryptography              43.0.0           py38hf793753_0    conda-forge
debugpy                   1.8.5            py38h6d02427_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
greenlet                  3.0.3            py38h17151c0_0    conda-forge
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.2             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.8                pyhd8ed1ab_0    conda-forge
importlib-metadata        8.4.0              pyha770c72_0    conda-forge
importlib_metadata        8.4.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.4              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.5             pyh3099207_0    conda-forge
ipython                   8.12.2             pyh41d4057_0    conda-forge
ipython_genutils          0.2.0              pyhd8ed1ab_1    conda-forge
ipywidgets                8.1.5              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.4              pyhd8ed1ab_0    conda-forge
json5                     0.9.25             pyhd8ed1ab_0    conda-forge
jsonpointer               3.0.0            py38h578d9bd_0    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter-offlinenotebook   0.3.1              pyhd8ed1ab_0    conda-forge
jupyter-resource-usage    1.1.0              pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2            py38h578d9bd_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterhub-base           5.1.0              pyh31011fe_0    conda-forge
jupyterhub-singleuser     5.1.0              pyh31011fe_0    conda-forge
jupyterlab                4.2.5              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.40                 hf3520f5_7    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.1.0               h77fa898_1    conda-forge
libgcc-ng                 14.1.0               h69a702a_1    conda-forge
libgomp                   14.1.0               h77fa898_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.46.0               hde9e2c9_0    conda-forge
libstdcxx                 14.1.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.1.0               h4852527_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.48.0               hd590300_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
mako                      1.3.5              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.5            py38h01eb140_0    conda-forge
matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
nbclassic                 1.1.0              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  he02047a_1    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
nodejs                    20.12.2              hc19f0b3_1    conda-forge
notebook                  6.5.7              pyha770c72_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
oauthlib                  3.2.2              pyhd8ed1ab_0    conda-forge
openssl                   3.3.1                hb9d3cd8_3    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pamela                    1.2.0              pyhff2d567_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       24.2               pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.47             pyha770c72_0    conda-forge
prompt_toolkit            3.0.47               hd8ed1ab_0    conda-forge
psutil                    5.9.8            py38h01eb140_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pydantic                  2.8.2              pyhd8ed1ab_0    conda-forge
pydantic-core             2.20.1           py38h4005ec7_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.9.0              pyhd8ed1ab_1    conda-forge
pyopenssl                 24.2.1             pyhd8ed1ab_2    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.8.19          hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.20.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      5_cp38    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2            py38h2019614_0    conda-forge
pyzmq                     26.2.0           py38h6c80b9a_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.20.0           py38h4005ec7_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                72.2.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sqlalchemy                2.0.32           py38h2019614_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
tinycss2                  1.3.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4.1            py38hfb59056_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240821     pyhd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_0    conda-forge
typing_extensions         4.12.2             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.2              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 24.8.0             pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.8.0              pyhd8ed1ab_0    conda-forge
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.13             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.5                h75354e8_4    conda-forge
zipp                      3.20.1             pyhd8ed1ab_0    conda-forge
zlib                      1.3.1                h4ab18f5_1    conda-forge
zstandard                 0.23.0           py38h62bed22_0    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge
+ /srv/conda/envs/notebook/bin/npm config --global set prefix /srv/npm
time: 67.660
 ---> Removed intermediate container 8c76b19303e2
 ---> fae223a68c00
Step 28/54 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Running in 5339bbc85f31
 ---> Removed intermediate container 5339bbc85f31
 ---> 778301bc1fba
Step 29/54 : USER root
 ---> Running in 9eb61a09b56a
 ---> Removed intermediate container 9eb61a09b56a
 ---> 5561374cb18f
Step 30/54 : ARG REPO_DIR=${HOME}
 ---> Running in 14f695bdc266
 ---> Removed intermediate container 14f695bdc266
 ---> dfccb088d59c
Step 31/54 : ENV REPO_DIR=${REPO_DIR}
 ---> Running in 62c7117e7082
 ---> Removed intermediate container 62c7117e7082
 ---> 4fe8db1b3068
Step 32/54 : RUN if [ ! -d "${REPO_DIR}" ]; then         /usr/bin/install -o ${NB_USER} -g ${NB_USER} -d "${REPO_DIR}";     fi
 ---> Running in 342e16a2a622
 ---> Removed intermediate container 342e16a2a622
 ---> e37ec096787b
Step 33/54 : WORKDIR ${REPO_DIR}
 ---> Running in c8128d398c2e
 ---> Removed intermediate container c8128d398c2e
 ---> be68bab589bf
Step 34/54 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Running in 6492d0ce396d
 ---> Removed intermediate container 6492d0ce396d
 ---> 4960a8c471f7
Step 35/54 : ENV PATH=${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Running in 9ab0b75b4767
 ---> Removed intermediate container 9ab0b75b4767
 ---> 2d0a897b2a3c
Step 36/54 : ENV CONDA_DEFAULT_ENV=${KERNEL_PYTHON_PREFIX}
 ---> Running in 9d27867eb884
 ---> Removed intermediate container 9d27867eb884
 ---> 31ab84d92015
Step 37/54 : COPY --chown=1000:1000 src/requirements.txt ${REPO_DIR}/requirements.txt
 ---> 06a61711313f
Step 38/54 : RUN apt-get -qq update && apt-get install --yes --no-install-recommends libgl1-mesa-glx && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
 ---> Running in 5ecac6d88319
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
  libdrm2 libgl1 libgl1-mesa-dri libglapi-mesa libglvnd0 libglx-mesa0 libglx0
  libllvm15 libpciaccess0 libsensors-config libsensors5 libx11-xcb1
  libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-randr0
  libxcb-sync1 libxcb-xfixes0 libxfixes3 libxshmfence1 libxxf86vm1
Suggested packages:
  pciutils lm-sensors
Recommended packages:
  libgl1-amber-dri
The following NEW packages will be installed:
  libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
  libdrm2 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglvnd0
  libglx-mesa0 libglx0 libllvm15 libpciaccess0 libsensors-config libsensors5
  libx11-xcb1 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
  libxcb-randr0 libxcb-sync1 libxcb-xfixes0 libxfixes3 libxshmfence1
  libxxf86vm1
0 upgraded, 28 newly installed, 0 to remove and 15 not upgraded.
Need to get 35.0 MB of archives.
After this operation, 154 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libdrm-common all 2.4.113-2~ubuntu0.22.04.1 [5,450 B]
Get:2 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libdrm2 amd64 2.4.113-2~ubuntu0.22.04.1 [38.1 kB]
Get:3 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libdrm-amdgpu1 amd64 2.4.113-2~ubuntu0.22.04.1 [19.9 kB]
Get:4 http://archive.ubuntu.com/ubuntu jammy/main amd64 libpciaccess0 amd64 0.16-3 [19.1 kB]
Get:5 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libdrm-intel1 amd64 2.4.113-2~ubuntu0.22.04.1 [66.7 kB]
Get:6 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libdrm-nouveau2 amd64 2.4.113-2~ubuntu0.22.04.1 [17.5 kB]
Get:7 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libdrm-radeon1 amd64 2.4.113-2~ubuntu0.22.04.1 [21.6 kB]
Get:8 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libglapi-mesa amd64 23.2.1-1ubuntu3.1~22.04.2 [37.1 kB]
Get:9 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libllvm15 amd64 1:15.0.7-0ubuntu0.22.04.3 [25.4 MB]
Get:10 http://archive.ubuntu.com/ubuntu jammy/main amd64 libsensors-config all 1:3.6.0-7ubuntu1 [5,274 B]
Get:11 http://archive.ubuntu.com/ubuntu jammy/main amd64 libsensors5 amd64 1:3.6.0-7ubuntu1 [26.3 kB]
Get:12 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-dri3-0 amd64 1.14-3ubuntu3 [6,968 B]
Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libgl1-mesa-dri amd64 23.2.1-1ubuntu3.1~22.04.2 [8,860 kB]
Get:14 http://archive.ubuntu.com/ubuntu jammy/main amd64 libglvnd0 amd64 1.4.0-1 [73.6 kB]
Get:15 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libx11-xcb1 amd64 2:1.7.5-1ubuntu0.3 [7,802 B]
Get:16 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-dri2-0 amd64 1.14-3ubuntu3 [7,206 B]
Get:17 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-glx0 amd64 1.14-3ubuntu3 [25.9 kB]
Get:18 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-present0 amd64 1.14-3ubuntu3 [5,734 B]
Get:19 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-randr0 amd64 1.14-3ubuntu3 [18.3 kB]
Get:20 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-sync1 amd64 1.14-3ubuntu3 [9,416 B]
Get:21 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxcb-xfixes0 amd64 1.14-3ubuntu3 [9,996 B]
Get:22 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxfixes3 amd64 1:6.0.0-1 [11.7 kB]
Get:23 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxshmfence1 amd64 1.3-1build4 [5,394 B]
Get:24 http://archive.ubuntu.com/ubuntu jammy/main amd64 libxxf86vm1 amd64 1:1.1.4-1build3 [10.4 kB]
Get:25 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libglx-mesa0 amd64 23.2.1-1ubuntu3.1~22.04.2 [158 kB]
Get:26 http://archive.ubuntu.com/ubuntu jammy/main amd64 libglx0 amd64 1.4.0-1 [41.0 kB]
Get:27 http://archive.ubuntu.com/ubuntu jammy/main amd64 libgl1 amd64 1.4.0-1 [110 kB]
Get:28 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 libgl1-mesa-glx amd64 23.0.4-0ubuntu1~22.04.1 [5,584 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 35.0 MB in 1s (56.8 MB/s)
Selecting previously unselected package libdrm-common.
(Reading database ... 22499 files and directories currently installed.)
Preparing to unpack .../00-libdrm-common_2.4.113-2~ubuntu0.22.04.1_all.deb ...
Unpacking libdrm-common (2.4.113-2~ubuntu0.22.04.1) ...
Selecting previously unselected package libdrm2:amd64.
Preparing to unpack .../01-libdrm2_2.4.113-2~ubuntu0.22.04.1_amd64.deb ...
Unpacking libdrm2:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Selecting previously unselected package libdrm-amdgpu1:amd64.
Preparing to unpack .../02-libdrm-amdgpu1_2.4.113-2~ubuntu0.22.04.1_amd64.deb ...
Unpacking libdrm-amdgpu1:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Selecting previously unselected package libpciaccess0:amd64.
Preparing to unpack .../03-libpciaccess0_0.16-3_amd64.deb ...
Unpacking libpciaccess0:amd64 (0.16-3) ...
Selecting previously unselected package libdrm-intel1:amd64.
Preparing to unpack .../04-libdrm-intel1_2.4.113-2~ubuntu0.22.04.1_amd64.deb ...
Unpacking libdrm-intel1:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Selecting previously unselected package libdrm-nouveau2:amd64.
Preparing to unpack .../05-libdrm-nouveau2_2.4.113-2~ubuntu0.22.04.1_amd64.deb ...
Unpacking libdrm-nouveau2:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Selecting previously unselected package libdrm-radeon1:amd64.
Preparing to unpack .../06-libdrm-radeon1_2.4.113-2~ubuntu0.22.04.1_amd64.deb ...
Unpacking libdrm-radeon1:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Selecting previously unselected package libglapi-mesa:amd64.
Preparing to unpack .../07-libglapi-mesa_23.2.1-1ubuntu3.1~22.04.2_amd64.deb ...
Unpacking libglapi-mesa:amd64 (23.2.1-1ubuntu3.1~22.04.2) ...
Selecting previously unselected package libllvm15:amd64.
Preparing to unpack .../08-libllvm15_1%3a15.0.7-0ubuntu0.22.04.3_amd64.deb ...
Unpacking libllvm15:amd64 (1:15.0.7-0ubuntu0.22.04.3) ...
Selecting previously unselected package libsensors-config.
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Setting up libxfixes3:amd64 (1:6.0.0-1) ...
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Setting up libsensors5:amd64 (1:3.6.0-7ubuntu1) ...
Setting up libglapi-mesa:amd64 (23.2.1-1ubuntu3.1~22.04.2) ...
Setting up libxcb-dri2-0:amd64 (1.14-3ubuntu3) ...
Setting up libxshmfence1:amd64 (1.3-1build4) ...
Setting up libxcb-randr0:amd64 (1.14-3ubuntu3) ...
Setting up libllvm15:amd64 (1:15.0.7-0ubuntu0.22.04.3) ...
Setting up libdrm-common (2.4.113-2~ubuntu0.22.04.1) ...
Setting up libdrm2:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Setting up libdrm-nouveau2:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Setting up libdrm-radeon1:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Setting up libdrm-intel1:amd64 (2.4.113-2~ubuntu0.22.04.1) ...
Setting up libgl1-mesa-dri:amd64 (23.2.1-1ubuntu3.1~22.04.2) ...
Setting up libglx-mesa0:amd64 (23.2.1-1ubuntu3.1~22.04.2) ...
Setting up libglx0:amd64 (1.4.0-1) ...
Setting up libgl1:amd64 (1.4.0-1) ...
Setting up libgl1-mesa-glx:amd64 (23.0.4-0ubuntu1~22.04.1) ...
Processing triggers for libc-bin (2.35-0ubuntu3.8) ...
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 ---> ba593cfbf5ca
Step 39/54 : USER root
 ---> Running in c08643c524ca
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 ---> 475c62ba94a5
Step 40/54 : COPY --chown=1000:1000 src/ ${REPO_DIR}/
 ---> d384033f4bd8
Step 41/54 : USER ${NB_USER}
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Step 42/54 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"
 ---> Running in 5708ea498336
Collecting ophys-nway-matching@ git+https://github.com/AllenInstitute/ophys_nway_matching@545504ab55922717ab623f8ede2c521a60aa1458 (from -r requirements.txt (line 16))
  Cloning https://github.com/AllenInstitute/ophys_nway_matching (to revision 545504ab55922717ab623f8ede2c521a60aa1458) to /tmp/pip-install-coj5b77j/ophys-nway-matching_404a4598b0c24f3b9a3f739f6215577e
  Running command git clone --filter=blob:none --quiet https://github.com/AllenInstitute/ophys_nway_matching /tmp/pip-install-coj5b77j/ophys-nway-matching_404a4598b0c24f3b9a3f739f6215577e
  Running command git rev-parse -q --verify 'sha^545504ab55922717ab623f8ede2c521a60aa1458'
  Running command git fetch -q https://github.com/AllenInstitute/ophys_nway_matching 545504ab55922717ab623f8ede2c521a60aa1458
  Running command git checkout -q 545504ab55922717ab623f8ede2c521a60aa1458
  Resolved https://github.com/AllenInstitute/ophys_nway_matching to commit 545504ab55922717ab623f8ede2c521a60aa1458
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting ssm@ git+https://github.com/lindermanlab/ssm (from -r requirements.txt (line 24))
  Cloning https://github.com/lindermanlab/ssm to /tmp/pip-install-coj5b77j/ssm_10f050f090fd40caa3ba048557d57ad5
  Running command git clone --filter=blob:none --quiet https://github.com/lindermanlab/ssm /tmp/pip-install-coj5b77j/ssm_10f050f090fd40caa3ba048557d57ad5
  Resolved https://github.com/lindermanlab/ssm to commit 6c856ad3967941d176eb348bcd490cfaaa08ba60
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-coj5b77j/ssm_10f050f090fd40caa3ba048557d57ad5/setup.py", line 3, in <module>
          import numpy as np
      ModuleNotFoundError: No module named 'numpy'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
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The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"' returned a non-zero code: 1
@rcpeene
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rcpeene commented Sep 9, 2024

This looks similar to a suspicious issue we had with trying to install the databook on our test ubuntu runners in github workflows. We have less control over binder though so it might be more challenging to patch.

It might be worth officially deprecating binder as one of our platforms; it seems to have problems and isn't frequently maintained.

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