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binder fails to build environment #389

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Mikejmnez opened this issue Sep 8, 2023 · 16 comments · Fixed by #400
Closed

binder fails to build environment #389

Mikejmnez opened this issue Sep 8, 2023 · 16 comments · Fixed by #400

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@Mikejmnez
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It has been a couple of weeks now, that I have tried and failed to build the environment. The Traceback is

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/srv/conda/lib/python3.11/site-packages/conda/exception_handler.py", line 16, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/srv/conda/lib/python3.11/site-packages/conda_env/cli/main.py", line 49, in do_call
        exit_code = getattr(module, func_name)(args, parser)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/srv/conda/lib/python3.11/site-packages/conda/notices/core.py", line 123, in wrapper
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "/srv/conda/lib/python3.11/site-packages/conda_env/cli/main_update.py", line 139, in execute
        result[installer_type] = installer.install(prefix, specs, args, env)
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/srv/conda/lib/python3.11/site-packages/mamba/mamba_env.py", line 153, in mamba_install
        transaction.fetch_extract_packages()
    RuntimeError: Could not set URL (code: 14 - url = /wheel-0.40.0-pyhd8ed1ab_0.conda)

`$ /srv/conda/bin/mamba update -p /srv/conda/envs/notebook --file binder/environment.yml`

  environment variables:
                 CIO_TEST=<not set>
  CONDA_AUTO_UPDATE_CONDA=false
        CONDA_DEFAULT_ENV=/srv/conda/envs/notebook
                CONDA_DIR=/srv/conda
           CONDA_PLATFORM=linux-64
               CONDA_ROOT=/srv/conda
           CURL_CA_BUNDLE=<not set>
               LD_PRELOAD=<not set>
                     PATH=/home/jovyan/.local/bin:/home/jovyan/.local/bin:/srv/conda/envs/notebo
                          ok/bin:/srv/conda/bin:/srv/npm/bin:/usr/local/sbin:/usr/local/bin:/usr
                          /sbin:/usr/bin:/sbin:/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : None
       user config file : /home/jovyan/.condarc
 populated config files : /srv/conda/.condarc
          conda version : 23.5.2
    conda-build version : not installed
         python version : 3.11.5.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.27=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /srv/conda  (writable)
      conda av data dir : /srv/conda/etc/conda
  conda av metadata url : None
           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/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /srv/conda/pkgs
                          /home/jovyan/.conda/pkgs
       envs directories : /srv/conda/envs
                          /home/jovyan/.conda/envs
               platform : linux-64
             user-agent : conda/23.5.2 requests/2.31.0 CPython/3.11.5 Linux/5.15.0-72-generic ubuntu/18.04.6 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

time: 62.572
Removing intermediate container a94fd0409760
The command '/bin/sh -c TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "binder/environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '' returned a non-zero code: 1

I have seen on forums that a similar failure occurs when Python is pinned to a version (see https://discourse.jupyter.org/t/mybinder-stopped-working-for-repo/21170, also jupyterhub/repo2docker#1301), but in our case Python is not pinned.

I will try to get this run locally in my machine to get a better sense of what the issue is, and get this resolved soon!
@Mikejmnez Mikejmnez self-assigned this Sep 8, 2023
@pravissw
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If you do not require Python 3.11, can you try mybinder with Python pinned to 3.10? i.e., a line - python=3.10.* under dependencies in environment.yml?

That seems to fix the problem at https://github.com/StephanieWehner/IntroQCryptoBook.

@Mikejmnez
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thanks @pravissw for your input. I also think that is what is going on here... I couldn't build the environment locally via repo2docker when pinning python=3.11 to simulate what binder is doing here (as seen above in the Traceback). I had no such error/trouble when pinning python=3.10.

@Mikejmnez Mikejmnez mentioned this issue Sep 11, 2023
Merged
@Mikejmnez
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I merged the PR, and tried to build the binder with python =3.10 , but the binder still fails to build. It gets really close to building the image but then fails.

Here is the Traceback:

Executing transaction: ...working... done
ERROR conda.core.link:_execute(952): An error occurred while installing package 'conda-forge::rise-5.7.1-py310hff52083_2'.
Rolling back transaction: ...working... done

LinkError: post-link script failed for package conda-forge::rise-5.7.1-py310hff52083_2
location of failed script: /srv/conda/envs/notebook/bin/.rise-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: 
stderr: Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3108, in _dep_map
    return self.__dep_map
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2901, in __getattr__
    raise AttributeError(attr)
AttributeError: _DistInfoDistribution__dep_map

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3099, in _parsed_pkg_info
    return self._pkg_info
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2901, in __getattr__
    raise AttributeError(attr)
AttributeError: _pkg_info. Did you mean: 'egg_info'?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-nbextension", line 10, in <module>
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_core/application.py", line 277, in launch_instance
    return super().launch_instance(argv=argv, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/traitlets/config/application.py", line 1043, in launch_instance
    app.start()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 972, in start
    super().start()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_core/application.py", line 266, in start
    self.subapp.start()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 882, in start
    self.toggle_nbextension_python(self.extra_args[0])
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 855, in toggle_nbextension_python
    return toggle(module,
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 470, in enable_nbextension_python
    return _set_nbextension_state_python(True, module, user, sys_prefix,
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 368, in _set_nbextension_state_python
    m, nbexts = _get_nbextension_metadata(module)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 1107, in _get_nbextension_metadata
    m = import_item(module)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/traitlets/utils/importstring.py", line 38, in import_item
    return __import__(parts[0])
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/rise/__init__.py", line 3, in <module>
    __version__ = pkg_resources.require("rise")[0].version
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 966, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 832, in resolve
    new_requirements = dist.requires(req.extras)[::-1]
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2821, in requires
    dm = self._dep_map
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3110, in _dep_map
    self.__dep_map = self._compute_dependencies()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3119, in _compute_dependencies
    for req in self._parsed_pkg_info.get_all('Requires-Dist') or []:
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3101, in _parsed_pkg_info
    metadata = self.get_metadata(self.PKG_INFO)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1517, in get_metadata
    value = self._get(path)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1726, in _get
    with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: '/srv/conda/envs/notebook/lib/python3.10/site-packages/ipython-8.14.0.dist-info/METADATA'

return code: 1

Issue remains open. I will maybe look at this later in the week. Need to prioritize.

@Mikejmnez
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FYI I was able to build the binder environment using repo2docker with python=3.10, and successfully runs the notebook locally. The environment is:

$ conda env list
# 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                   1.8.1              pyhd8ed1ab_0    conda-forge
anyio                     3.6.1              pyhd8ed1ab_1    conda-forge
aom                       3.5.0                h27087fc_0    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_2    conda-forge
asciitree                 0.3.3                      py_2    conda-forge
asttokens                 2.0.8              pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
aws-c-auth                0.7.0                hf8751d9_2    conda-forge
aws-c-cal                 0.6.0                h93469e0_0    conda-forge
aws-c-common              0.8.23               hd590300_0    conda-forge
aws-c-compression         0.2.17               h862ab75_1    conda-forge
aws-c-event-stream        0.3.1                h9599702_1    conda-forge
aws-c-http                0.7.11               hbe98c3e_0    conda-forge
aws-c-io                  0.13.28              h3870b5a_0    conda-forge
aws-c-mqtt                0.8.14               h2e270ba_2    conda-forge
aws-c-s3                  0.3.13               heb0bb06_2    conda-forge
aws-c-sdkutils            0.1.11               h862ab75_1    conda-forge
aws-checksums             0.1.16               h862ab75_1    conda-forge
aws-crt-cpp               0.20.3               he9c0e7f_4    conda-forge
aws-sdk-cpp               1.10.57             hbc2ea52_17    conda-forge
babel                     2.10.3             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
blinker                   1.5                pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
bokeh                     3.2.2              pyhd8ed1ab_0    conda-forge
bottleneck                1.3.7           py310h0a54255_0    conda-forge
brotli                    1.0.9                h166bdaf_9    conda-forge
brotli-bin                1.0.9                h166bdaf_9    conda-forge
brotlipy                  0.7.0           py310h5764c6d_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.9.24            ha878542_0    conda-forge
cachetools                5.3.1              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h0c91306_1017    conda-forge
cartopy                   0.22.0          py310h7cbd5c2_0    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cf_xarray                 0.8.4              pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_0    conda-forge
cftime                    1.6.2           py310hde88566_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.0           py310hd41b1e2_0    conda-forge
cryptography              41.0.3          py310h75e40e8_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.2          py310h2372a71_0    conda-forge
dask                      2023.9.1           pyhd8ed1ab_0    conda-forge
dask-core                 2023.9.1           pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hd590300_0    conda-forge
dbus                      1.13.18              hb2f20db_0    defaults
debugpy                   1.6.3           py310hd8f1fbe_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distributed               2023.9.1           pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
esmf                      8.4.2           mpi_mpich_h2a0de38_103    conda-forge
esmpy                     8.4.2              pyhc1e730c_4    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 1.1.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
ffmpeg                    6.0.0           gpl_h14e97fc_104    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.42.1          py310h2372a71_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
fsspec                    2023.9.0           pyh1a96a4e_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
geographiclib             1.52               pyhd8ed1ab_0    conda-forge
geopy                     2.4.0              pyhd8ed1ab_0    conda-forge
geos                      3.12.0               h59595ed_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
glib                      2.78.0               hfc55251_0    conda-forge
glib-tools                2.78.0               hfc55251_0    conda-forge
glog                      0.6.0                h6f12383_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gnutls                    3.7.8                hf3e180e_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
greenlet                  1.1.3           py310hd8f1fbe_0    conda-forge
gst-plugins-base          1.14.1               h6a678d5_1    defaults
gstreamer                 1.14.1               h5eee18b_1    defaults
harfbuzz                  8.2.0                h3d44ed6_0    conda-forge
hdf4                      4.2.15               h9772cbc_5    conda-forge
hdf5                      1.14.2          mpi_mpich_ha2c2bf8_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       5.10.0             pyhd8ed1ab_0    conda-forge
intake                    0.7.0              pyhd8ed1ab_0    conda-forge
intake-xarray             0.7.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.16.0             pyh210e3f2_0    conda-forge
ipython                   8.15.0             pyh0d859eb_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.16.0             pyhd8ed1ab_0    conda-forge
jupyter-contrib-core      0.4.2                    pypi_0    pypi
jupyter-contrib-nbextensions 0.7.0                    pypi_0    pypi
jupyter-highlight-selected-word 0.2.0                    pypi_0    pypi
jupyter-nbextensions-configurator 0.6.3                    pypi_0    pypi
jupyter-offlinenotebook   0.2.2              pyh1d7be83_0    conda-forge
jupyter-resource-usage    0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_client            7.4.2              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.1          py310hff52083_0    conda-forge
jupyter_server            1.21.0             pyhd8ed1ab_0    conda-forge
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub-base           1.5.0           py310hff52083_1    conda-forge
jupyterhub-singleuser     1.5.0           py310hff52083_1    conda-forge
jupyterlab                3.4.8              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.15.2             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.3              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py310hd41b1e2_0    conda-forge
krb5                      1.20.1               h81ceb04_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libabseil                 20230125.3      cxx17_h59595ed_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libarrow                  12.0.1           hd2d78f0_7_cpu    conda-forge
libass                    0.17.1               h8fe9dca_1    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_9    conda-forge
libbrotlidec              1.0.9                h166bdaf_9    conda-forge
libbrotlienc              1.0.9                h166bdaf_9    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libclang                  14.0.6          default_h7634d5b_1    conda-forge
libclang13                14.0.6          default_h9986a30_1    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcups                   2.3.3                h36d4200_3    conda-forge
libcurl                   8.2.1                h251f7ec_0    defaults
libdeflate                1.10                 h7f98852_0    conda-forge
libdrm                    2.4.114              h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            13.2.0               h69a702a_0    conda-forge
libgfortran5              13.2.0               ha4646dd_0    conda-forge
libglib                   2.78.0               hebfc3b9_0    conda-forge
libgomp                   12.1.0              h8d9b700_16    conda-forge
libgoogle-cloud           2.12.0               hac9eb74_1    conda-forge
libgrpc                   1.54.2               hb20ce57_2    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libnetcdf                 4.9.2           mpi_mpich_hef9003c_12    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libnuma                   2.0.16               h0b41bf4_1    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpciaccess              0.17                 h166bdaf_0    conda-forge
libpnetcdf                1.12.3          mpi_mpich_h4ac58e2_101    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     12.15                hdbd6064_1    defaults
libprotobuf               3.21.12              hfc55251_2    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.43.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libtasn1                  4.19.0               h166bdaf_0    conda-forge
libthrift                 0.18.1               h8fd135c_2    conda-forge
libtiff                   4.3.0                h0fcbabc_4    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libutf8proc               2.8.0                h166bdaf_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.44.2               h166bdaf_0    conda-forge
libva                     2.19.0               hd590300_0    conda-forge
libvpx                    1.13.0               hcb278e6_0    conda-forge
libwebp-base              1.3.1                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxkbcommon              1.5.0                h5d7e998_3    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libzip                    1.10.1               h2629f0a_3    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.40.1          py310h1b8f574_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lxml                      4.9.3                    pypi_0    pypi
lz4                       4.3.2           py310h0cfdcf0_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
mako                      1.2.3              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1           py310h5764c6d_1    conda-forge
matplotlib                3.7.2           py310hff52083_0    conda-forge
matplotlib-base           3.7.2           py310hf38f957_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpich                     4.1.2              h846660c_100    conda-forge
msgpack-python            1.0.5           py310hdf3cbec_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql                     5.7.20            hf484d3e_1001    conda-forge
nbclassic                 0.4.6              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.1              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.1              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           mpi_mpich_hdf31df6_2    conda-forge
netcdf4                   1.6.4           nompi_py310hba70d50_102    conda-forge
nettle                    3.8.1                hc379101_1    conda-forge
nodejs                    20.5.1               hb753e55_1    conda-forge
notebook                  6.4.12             pyha770c72_0    conda-forge
notebook-shim             0.1.0              pyhd8ed1ab_0    conda-forge
nteract_on_jupyter        2.1.3                      py_0    conda-forge
numba                     0.57.1          py310h0f6aa51_0    conda-forge
numcodecs                 0.11.0          py310heca2aa9_1    conda-forge
numpy                     1.24.4          py310ha4c1d20_0    conda-forge
oauthlib                  3.2.1              pyhd8ed1ab_0    conda-forge
oceanspy                  0.3.5.dev21+g497bd23          pypi_0    pypi
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openh264                  2.3.1                hcb278e6_2    conda-forge
openjpeg                  2.5.0                h7d73246_0    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
orc                       1.9.0                h2f23424_1    conda-forge
p11-kit                   0.24.1               hc5aa10d_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    2.1.0           py310hcc13569_0    conda-forge
pandoc                    2.19.2               ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parallelio                2.6.2           mpi_mpich_h79a22d0_100    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.4.0              pyhd8ed1ab_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    8.4.0           py310h07f4688_0    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.1.1              pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyha770c72_3    conda-forge
proj                      8.0.1                h277dcde_0    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    conda-forge
prompt_toolkit            3.0.31               hd8ed1ab_0    conda-forge
psutil                    5.9.2           py310h5764c6d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pyarrow                   12.0.1          py310h0576679_7_cpu    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pycurl                    7.45.1          py310h60f9ec7_3    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.5.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyproj                    3.3.1           py310h6d1f8f5_1    conda-forge
pyqt                      5.15.4          py310hd8f1fbe_0    conda-forge
pyqt5-sip                 12.9.0          py310hd8f1fbe_0    conda-forge
pyrsistent                0.18.1          py310h5764c6d_1    conda-forge
pyshp                     2.3.1              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.1              pyh9f0ad1d_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytz                      2022.4             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_0    conda-forge
pyzmq                     24.0.1          py310h330234f_0    conda-forge
qt-main                   5.15.2              h53bd1ea_10    defaults
rdma-core                 28.9                 h59595ed_1    conda-forge
re2                       2023.03.02           h8c504da_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
rise                      5.7.1           py310hff52083_2    conda-forge
ruamel.yaml               0.17.21         py310h5764c6d_1    conda-forge
ruamel.yaml.clib          0.2.6           py310h5764c6d_1    conda-forge
s2n                       1.3.46               h06160fa_0    conda-forge
scipy                     1.11.2          py310ha4c1d20_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.4.1             pyhd8ed1ab_0    conda-forge
shapely                   2.0.1           py310h7dcad9a_2    conda-forge
sip                       6.5.1           py310h122e73d_2    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sparse                    0.14.0             pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.41          py310h5764c6d_0    conda-forge
sqlite                    3.43.0               h2c6b66d_0    conda-forge
stack_data                0.5.1              pyhd8ed1ab_0    conda-forge
svt-av1                   1.7.0                h59595ed_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
terminado                 0.16.0             pyh41d4057_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310h5764c6d_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.4.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022e                h191b570_0    conda-forge
ucx                       1.14.1               h64cca9d_4    conda-forge
unicodedata2              15.0.0          py310h5764c6d_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.1              pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.3              pyhd8ed1ab_0    conda-forge
x264                      1!164.3095           h166bdaf_2    conda-forge
x265                      3.5                  h924138e_3    conda-forge
xarray                    2023.8.0           pyhd8ed1ab_0    conda-forge
xesmf                     0.8.1              pyhd8ed1ab_0    conda-forge
xgcm                      0.8.1              pyhd8ed1ab_0    conda-forge
xkeyboard-config          2.39                 hd590300_0    conda-forge
xmitgcm                   0.5.2              pyhd8ed1ab_0    conda-forge
xoak                      0.1.1              pyhd8ed1ab_0    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xyzservices               2023.7.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zarr                      2.16.1             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zict                      3.0.0              pyhd8ed1ab_0    conda-forge
zipp                      3.9.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

@ThomasHaine
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@Mikejmnez how do you reproduce the error? On SciServer the notebooks in the binder folder run fine for me.

@Mikejmnez
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The issue is not on Sciserver, where the notebooks have already a built compute environment (Sciserver's that is). The issue is when trying to build the interactive (browser) binder environment. This is accessible either as a blue icon on the main github repo that says binder, or on the website (https://oceanspy.readthedocs.io/en/latest/) inside the blue box that says: Interactive Demo.

In addition, the url is: www.bndr.it/gfvgd.

I tried again, and it yields the same error.

@ThomasHaine
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@Mikejmnez Is it correct that you can build the binder environment locally with repo2docker and python=3.10, but not without the 3.10 pin? It fails for me with python=3.10

@Mikejmnez
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Something like that.... I first tried to build the binder env through repo2docker by pinning python=3.11 which was unsuccessful. Then tried again but now with python=3.10, which was successful (once). I copied+pasted the environment that repo2docker built above in a separate comment last week, and there you can find python 3.10.12 was build with conda-forge. I was even able to open a jupyter notebook on the browser and run the LiveDemo notebook.

I remember I had to try a couple of timesto build the env , and it took a very long time. In fact, I kind of forgot about it since I was doing some other testing/coding that was more pressing. Later that day I saw the terminal had build the env and it provided even a url http to run interactively the environment (notebooks and local terminal).

@ThomasHaine
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Hmmm. It looks like I'm using python 3.10.12 as well, but it fails.

@Mikejmnez
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from the new Traceback, it looks like binder also tries to install 3.10.12 but fails at the last minute. Can you please share your Traceback/ error?

@ThomasHaine
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Here's the repo2binder output+ traceback:

Step 39/52 : RUN TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "binder/environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '
 ---> Running in ecabe60672fa


Looking for: ['numpy', 'matplotlib', 'pandas', 'bokeh', 'rise', 'dask', 'distributed', 'bottleneck', 'netcdf4', 'xarray', 'xoak', 'cartopy', 'esmpy', 'intake-xarray', 'geopy', "xesmf[version='>0.6.3']", 'esmf', 'xgcm', 'ipython', 'xmitgcm', 'ffmpeg', 'tqdm', 'pip']


Transaction

  Prefix: /srv/conda/envs/notebook

  Updating specs:

   - numpy
   - matplotlib
   - pandas
   - bokeh
   - rise
   - dask
   - distributed
   - bottleneck
   - netcdf4
   - xarray
   - xoak
   - cartopy
   - esmpy
   - intake-xarray
   - geopy
   - xesmf[version='>0.6.3']
   - esmf
   - xgcm
   - xmitgcm
   - ffmpeg
   - tqdm
   - ipython
   - pip


  Package                           Version  Build                    Channel                   Size
──────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────────────

  + alsa-lib                          1.2.9  hd590300_0               conda-forge/linux-64     547kB
  + aom                               3.5.0  h27087fc_0               conda-forge/linux-64       3MB
  + appdirs                           1.4.4  pyh9f0ad1d_0             conda-forge/noarch        13kB
  + asciitree                         0.3.3  py_2                     conda-forge/noarch         6kB
  + attr                              2.5.1  h166bdaf_1               conda-forge/linux-64      71kB
  + aws-c-auth                        0.7.3  he2921ad_3               conda-forge/linux-64     102kB
  + aws-c-cal                         0.6.2  hc309b26_1               conda-forge/linux-64      51kB
  + aws-c-common                      0.9.0  hd590300_0               conda-forge/linux-64     198kB
  + aws-c-compression                0.2.17  h4d4d85c_2               conda-forge/linux-64      19kB
  + aws-c-event-stream                0.3.2  h2e3709c_0               conda-forge/linux-64      54kB
  + aws-c-http                       0.7.12  hc865f51_1               conda-forge/linux-64     194kB
  + aws-c-io                        0.13.32  h1a03231_3               conda-forge/linux-64     154kB
  + aws-c-mqtt                        0.9.5  h3a0376c_1               conda-forge/linux-64     164kB
  + aws-c-s3                         0.3.14  h1678ad6_3               conda-forge/linux-64      86kB
  + aws-c-sdkutils                   0.1.12  h4d4d85c_1               conda-forge/linux-64      53kB
  + aws-checksums                    0.1.17  h4d4d85c_1               conda-forge/linux-64      50kB
  + aws-crt-cpp                      0.23.0  h40cdbb9_5               conda-forge/linux-64     323kB
  + aws-sdk-cpp                     1.10.57  h6f6b8fa_21              conda-forge/linux-64       4MB
  + blosc                            1.21.5  h0f2a231_0               conda-forge/linux-64      49kB
  + bokeh                             3.2.2  pyhd8ed1ab_0             conda-forge/noarch         5MB
  + bottleneck                        1.3.7  py310h0a54255_0          conda-forge/linux-64     123kB
  + c-ares                           1.19.1  hd590300_0               conda-forge/linux-64     113kB
  + cachetools                        5.3.1  pyhd8ed1ab_0             conda-forge/noarch        15kB
  + cairo                            1.16.0  hbbf8b49_1016            conda-forge/linux-64       1MB
  + cartopy                          0.22.0  py310h7cbd5c2_0          conda-forge/linux-64       2MB
  + cf_xarray                         0.8.4  pyhd8ed1ab_0             conda-forge/noarch        53kB
  + cftime                            1.6.2  py310hde88566_1          conda-forge/linux-64     246kB
  + click                             8.1.7  unix_pyh707e725_0        conda-forge/noarch        84kB
  + cloudpickle                       2.2.1  pyhd8ed1ab_0             conda-forge/noarch        28kB
  + colorama                          0.4.6  pyhd8ed1ab_0             conda-forge/noarch        25kB
  + contourpy                         1.1.1  py310hd41b1e2_0          conda-forge/linux-64     224kB
  + cycler                           0.11.0  pyhd8ed1ab_0             conda-forge/noarch        10kB
  + cytoolz                          0.12.2  py310h2372a71_0          conda-forge/linux-64     367kB
  + dask                           2023.9.2  pyhd8ed1ab_0             conda-forge/noarch         7kB
  + dask-core                      2023.9.2  pyhd8ed1ab_0             conda-forge/noarch       859kB
  + dav1d                             1.2.1  hd590300_0               conda-forge/linux-64     760kB
  + dbus                             1.13.6  h5008d03_3               conda-forge/linux-64     619kB
  + distributed                    2023.9.2  pyhd8ed1ab_0             conda-forge/noarch       785kB
  + esmf                              8.4.2  mpi_mpich_h2a0de38_103   conda-forge/linux-64      24MB
  + esmpy                             8.4.2  pyhc1e730c_4             conda-forge/noarch         2MB
  + expat                             2.5.0  hcb278e6_1               conda-forge/linux-64     137kB
  + fasteners                        0.17.3  pyhd8ed1ab_0             conda-forge/noarch        20kB
  + ffmpeg                            6.0.0  gpl_h14e97fc_104         conda-forge/linux-64      10MB
  + font-ttf-dejavu-sans-mono          2.37  hab24e00_0               conda-forge/noarch       397kB
  + font-ttf-inconsolata              3.000  h77eed37_0               conda-forge/noarch        97kB
  + font-ttf-source-code-pro          2.038  h77eed37_0               conda-forge/noarch       701kB
  + font-ttf-ubuntu                    0.83  hab24e00_0               conda-forge/noarch         2MB
  + fontconfig                       2.14.2  h14ed4e7_0               conda-forge/linux-64     272kB
  + fonts-conda-ecosystem                 1  0                        conda-forge/noarch         4kB
  + fonts-conda-forge                     1  0                        conda-forge/noarch         4kB
  + fonttools                        4.42.1  py310h2372a71_0          conda-forge/linux-64       2MB
  + freetype                         2.12.1  h267a509_2               conda-forge/linux-64     635kB
  + fribidi                          1.0.10  h36c2ea0_0               conda-forge/linux-64     114kB
  + fsspec                         2023.9.1  pyh1a96a4e_0             conda-forge/noarch       124kB
  + future                           0.18.3  pyhd8ed1ab_0             conda-forge/noarch       366kB
  + geographiclib                      1.52  pyhd8ed1ab_0             conda-forge/noarch        36kB
  + geopy                             2.4.0  pyhd8ed1ab_0             conda-forge/noarch        73kB
  + geos                             3.12.0  h59595ed_0               conda-forge/linux-64       2MB
  + gettext                          0.21.1  h27087fc_0               conda-forge/linux-64       4MB
  + gflags                            2.2.2  he1b5a44_1004            conda-forge/linux-64     117kB
  + glib                             2.78.0  hfc55251_0               conda-forge/linux-64     491kB
  + glib-tools                       2.78.0  hfc55251_0               conda-forge/linux-64     112kB
  + glog                              0.6.0  h6f12383_0               conda-forge/linux-64     114kB
  + gmp                               6.2.1  h58526e2_0               conda-forge/linux-64     826kB
  + gnutls                            3.7.8  hf3e180e_0               conda-forge/linux-64       2MB
  + graphite2                        1.3.13  h58526e2_1001            conda-forge/linux-64     105kB
  + gst-plugins-base                 1.22.5  hf7dbed1_0               conda-forge/linux-64       3MB
  + gstreamer                        1.22.5  h98fc4e7_0               conda-forge/linux-64       2MB
  + harfbuzz                          7.3.0  hdb3a94d_0               conda-forge/linux-64       1MB
  + hdf4                             4.2.15  h501b40f_6               conda-forge/linux-64     758kB
  + hdf5                             1.14.2  mpi_mpich_ha2c2bf8_0     conda-forge/linux-64       4MB
  + intake                            0.7.0  pyhd8ed1ab_0             conda-forge/noarch       193kB
  + intake-xarray                     0.7.0  pyhd8ed1ab_0             conda-forge/noarch        28kB
  + keyutils                          1.6.1  h166bdaf_0               conda-forge/linux-64     118kB
  + kiwisolver                        1.4.5  py310hd41b1e2_0          conda-forge/linux-64      73kB
  + krb5                             1.21.2  h659d440_0               conda-forge/linux-64       1MB
  + lame                              3.100  h166bdaf_1003            conda-forge/linux-64     508kB
  + lcms2                              2.15  h7f713cb_2               conda-forge/linux-64     241kB
  + lerc                              4.0.0  h27087fc_0               conda-forge/linux-64     282kB
  + libabseil                    20230125.3  cxx17_h59595ed_0         conda-forge/linux-64       1MB
  + libaec                            1.0.6  hcb278e6_1               conda-forge/linux-64      34kB
  + libarrow                         13.0.0  hb9dc469_0_cpu           conda-forge/linux-64      28MB
  + libass                           0.17.1  hc9aadba_0               conda-forge/linux-64     126kB
  + libblas                           3.9.0  18_linux64_openblas      conda-forge/linux-64      15kB
  + libcap                             2.69  h0f662aa_0               conda-forge/linux-64     101kB
  + libcblas                          3.9.0  18_linux64_openblas      conda-forge/linux-64      14kB
  + libclang                         15.0.7  default_h7634d5b_3       conda-forge/linux-64     133kB
  + libclang13                       15.0.7  default_h9986a30_3       conda-forge/linux-64      10MB
  + libcrc32c                         1.1.2  h9c3ff4c_0               conda-forge/linux-64      20kB
  + libcups                           2.3.3  h4637d8d_4               conda-forge/linux-64       5MB
  + libcurl                           8.3.0  hca28451_0               conda-forge/linux-64     388kB
  + libdeflate                         1.19  hd590300_0               conda-forge/linux-64      67kB
  + libdrm                          2.4.114  h166bdaf_0               conda-forge/linux-64     305kB
  + libedit                    3.1.20191231  he28a2e2_2               conda-forge/linux-64     124kB
  + libev                              4.33  h516909a_1               conda-forge/linux-64     106kB
  + libevent                         2.1.12  hf998b51_1               conda-forge/linux-64     427kB
  + libexpat                          2.5.0  hcb278e6_1               conda-forge/linux-64      78kB
  + libflac                           1.4.3  h59595ed_0               conda-forge/linux-64     394kB
  + libgcrypt                        1.10.1  h166bdaf_0               conda-forge/linux-64     720kB
  + libgfortran-ng                   13.2.0  h69a702a_0               conda-forge/linux-64      23kB
  + libgfortran5                     13.2.0  ha4646dd_0               conda-forge/linux-64       1MB
  + libglib                          2.78.0  hebfc3b9_0               conda-forge/linux-64       3MB
  + libgoogle-cloud                  2.12.0  h840a212_1               conda-forge/linux-64      46MB
  + libgpg-error                       1.47  h71f35ed_0               conda-forge/linux-64     261kB
  + libgrpc                          1.56.2  h3905398_1               conda-forge/linux-64       6MB
  + libiconv                           1.17  h166bdaf_0               conda-forge/linux-64       1MB
  + libidn2                           2.3.4  h166bdaf_0               conda-forge/linux-64     160kB
  + libjpeg-turbo                   2.1.5.1  hd590300_1               conda-forge/linux-64     496kB
  + liblapack                         3.9.0  18_linux64_openblas      conda-forge/linux-64      14kB
  + libllvm14                        14.0.6  hcd5def8_4               conda-forge/linux-64      31MB
  + libllvm15                        15.0.7  h5cf9203_3               conda-forge/linux-64      33MB
  + libnetcdf                         4.9.2  mpi_mpich_hef9003c_12    conda-forge/linux-64     865kB
  + libnghttp2                       1.52.0  h61bc06f_0               conda-forge/linux-64     622kB
  + libnuma                          2.0.16  h0b41bf4_1               conda-forge/linux-64      41kB
  + libogg                            1.3.4  h7f98852_1               conda-forge/linux-64     211kB
  + libopenblas                      0.3.24  pthreads_h413a1c8_0      conda-forge/linux-64       5MB
  + libopus                           1.3.1  h7f98852_1               conda-forge/linux-64     261kB
  + libpciaccess                       0.17  h166bdaf_0               conda-forge/linux-64      40kB
  + libpnetcdf                       1.12.3  mpi_mpich_h4ac58e2_101   conda-forge/linux-64       2MB
  + libpng                           1.6.39  h753d276_0               conda-forge/linux-64     283kB
  + libpq                              15.4  hfc447b1_0               conda-forge/linux-64       2MB
  + libprotobuf                      4.23.3  hd1fb520_1               conda-forge/linux-64       2MB
  + libsndfile                        1.2.2  hbc2eb40_0               conda-forge/linux-64     355kB
  + libssh2                          1.11.0  h0841786_0               conda-forge/linux-64     271kB
  + libsystemd0                         254  h3516f8a_0               conda-forge/linux-64     400kB
  + libtasn1                         4.19.0  h166bdaf_0               conda-forge/linux-64     117kB
  + libthrift                        0.18.1  h8fd135c_2               conda-forge/linux-64       4MB
  + libtiff                           4.6.0  h29866fb_1               conda-forge/linux-64     277kB
  + libunistring                     0.9.10  h7f98852_0               conda-forge/linux-64       1MB
  + libutf8proc                       2.8.0  h166bdaf_0               conda-forge/linux-64     101kB
  + libva                            2.20.0  hd590300_0               conda-forge/linux-64     188kB
  + libvorbis                         1.3.7  h9c3ff4c_0               conda-forge/linux-64     286kB
  + libvpx                           1.13.0  hcb278e6_0               conda-forge/linux-64     987kB
  + libwebp-base                      1.3.2  hd590300_0               conda-forge/linux-64     402kB
  + libxcb                             1.15  h0b41bf4_0               conda-forge/linux-64     384kB
  + libxkbcommon                      1.5.0  h5d7e998_3               conda-forge/linux-64     561kB
  + libxml2                          2.11.5  h0d562d8_0               conda-forge/linux-64     705kB
  + libzip                           1.10.1  h2629f0a_3               conda-forge/linux-64     107kB
  + llvmlite                         0.40.1  py310h1b8f574_0          conda-forge/linux-64       3MB
  + locket                            1.0.0  pyhd8ed1ab_0             conda-forge/noarch         8kB
  + lz4                               4.3.2  py310h0cfdcf0_0          conda-forge/linux-64      37kB
  + lz4-c                             1.9.4  hcb278e6_0               conda-forge/linux-64     143kB
  + matplotlib                        3.8.0  py310hff52083_0          conda-forge/linux-64       8kB
  + matplotlib-base                   3.8.0  py310h62c0568_0          conda-forge/linux-64       7MB
  + mpg123                           1.31.3  hcb278e6_0               conda-forge/linux-64     485kB
  + mpi                                 1.0  mpich                    conda-forge/linux-64       4kB
  + mpich                             4.1.2  h846660c_100             conda-forge/linux-64      26MB
  + msgpack-python                    1.0.5  py310hdf3cbec_0          conda-forge/linux-64      85kB
  + munkres                           1.1.4  pyh9f0ad1d_0             conda-forge/noarch        12kB
  + mysql-common                     8.0.33  hf1915f5_4               conda-forge/linux-64     767kB
  + mysql-libs                       8.0.33  hca2cd23_4               conda-forge/linux-64       2MB
  + netcdf-fortran                    4.6.1  mpi_mpich_hdf31df6_2     conda-forge/linux-64     433kB
  + netcdf4                           1.6.4  nompi_py310hba70d50_102  conda-forge/linux-64     529kB
  + nettle                            3.8.1  hc379101_1               conda-forge/linux-64       1MB
  + nspr                               4.35  h27087fc_0               conda-forge/linux-64     227kB
  + nss                                3.92  h1d7d5a4_0               conda-forge/linux-64       2MB
  + numba                            0.57.1  py310h0f6aa51_0          conda-forge/linux-64       4MB
  + numcodecs                        0.11.0  py310heca2aa9_1          conda-forge/linux-64     671kB
  + numpy                            1.24.4  py310ha4c1d20_0          conda-forge/linux-64       7MB
  + openh264                          2.3.1  hcb278e6_2               conda-forge/linux-64     719kB
  + openjpeg                          2.5.0  h488ebb8_3               conda-forge/linux-64     357kB
  + orc                               1.9.0  h385abfd_1               conda-forge/linux-64       1MB
  + p11-kit                          0.24.1  hc5aa10d_0               conda-forge/linux-64       5MB
  + pandas                            2.1.1  py310hcc13569_0          conda-forge/linux-64      12MB
  + parallelio                        2.6.2  mpi_mpich_h79a22d0_100   conda-forge/linux-64     347kB
  + partd                             1.4.0  pyhd8ed1ab_1             conda-forge/noarch        21kB
  + pcre2                             10.40  hc3806b6_0               conda-forge/linux-64       2MB
  + pillow                           10.0.1  py310h29da1c1_1          conda-forge/linux-64      46MB
  + pixman                           0.40.0  h36c2ea0_0               conda-forge/linux-64     643kB
  + ply                                3.11  py_1                     conda-forge/noarch        45kB
  + proj                              8.0.1  h1217e81_0               pkgs/main/linux-64         3MB
  + pthread-stubs                       0.4  h36c2ea0_1001            conda-forge/linux-64       6kB
  + pulseaudio-client                  16.1  hb77b528_5               conda-forge/linux-64     755kB
  + pyarrow                          13.0.0  py310hf9e7431_0_cpu      conda-forge/linux-64       4MB
  + pyparsing                         3.1.1  pyhd8ed1ab_0             conda-forge/noarch        90kB
  + pyproj                            3.3.1  py310h6d1f8f5_1          conda-forge/linux-64     497kB
  + pyqt                             5.15.9  py310h04931ad_4          conda-forge/linux-64       5MB
  + pyqt5-sip                       12.12.2  py310hc6cd4ac_4          conda-forge/linux-64      85kB
  + pyshp                             2.3.1  pyhd8ed1ab_0             conda-forge/noarch       964kB
  + python-tzdata                    2023.3  pyhd8ed1ab_0             conda-forge/noarch       143kB
  + qt-main                          5.15.8  h7fe3ca9_15              conda-forge/linux-64      61MB
  + rdma-core                          28.9  h59595ed_1               conda-forge/linux-64       4MB
  + re2                          2023.03.02  h8c504da_0               conda-forge/linux-64     201kB
  + rise                              5.7.1  py310hff52083_2          conda-forge/linux-64       3MB
  + s2n                              1.3.51  h06160fa_0               conda-forge/linux-64     375kB
  + scipy                            1.11.2  py310hb13e2d6_1          conda-forge/linux-64      16MB
  + shapely                           2.0.1  py310h7dcad9a_2          conda-forge/linux-64     422kB
  + sip                              6.7.11  py310hc6cd4ac_0          conda-forge/linux-64     494kB
  + snappy                           1.1.10  h9fff704_0               conda-forge/linux-64      39kB
  + sortedcontainers                  2.4.0  pyhd8ed1ab_0             conda-forge/noarch        26kB
  + sparse                           0.14.0  pyhd8ed1ab_0             conda-forge/noarch        66kB
  + sqlite                           3.42.0  h2c6b66d_0               conda-forge/linux-64     818kB
  + svt-av1                           1.7.0  h59595ed_0               conda-forge/linux-64       3MB
  + tblib                             2.0.0  pyhd8ed1ab_0             conda-forge/noarch        17kB
  + toml                             0.10.2  pyhd8ed1ab_0             conda-forge/noarch        18kB
  + toolz                            0.12.0  pyhd8ed1ab_0             conda-forge/noarch        49kB
  + tqdm                             4.66.1  pyhd8ed1ab_0             conda-forge/noarch        89kB
  + ucx                              1.14.1  h64cca9d_5               conda-forge/linux-64      15MB
  + unicodedata2                     15.0.0  py310h5764c6d_0          conda-forge/linux-64     512kB
  + x264                         1!164.3095  h166bdaf_2               conda-forge/linux-64     898kB
  + x265                                3.5  h924138e_3               conda-forge/linux-64       3MB
  + xarray                         2023.8.0  pyhd8ed1ab_0             conda-forge/noarch       690kB
  + xcb-util                          0.4.0  hd590300_1               conda-forge/linux-64      20kB
  + xcb-util-image                    0.4.0  h8ee46fc_1               conda-forge/linux-64      24kB
  + xcb-util-keysyms                  0.4.0  h8ee46fc_1               conda-forge/linux-64      14kB
  + xcb-util-renderutil               0.3.9  hd590300_1               conda-forge/linux-64      17kB
  + xcb-util-wm                       0.4.1  h8ee46fc_1               conda-forge/linux-64      52kB
  + xesmf                             0.8.2  pyhd8ed1ab_0             conda-forge/noarch        44kB
  + xgcm                              0.8.1  pyhd8ed1ab_0             conda-forge/noarch        80kB
  + xkeyboard-config                   2.39  hd590300_0               conda-forge/linux-64     881kB
  + xmitgcm                           0.5.2  pyhd8ed1ab_0             conda-forge/noarch        89kB
  + xoak                              0.1.1  pyhd8ed1ab_0             conda-forge/noarch        16kB
  + xorg-fixesproto                     5.0  h7f98852_1002            conda-forge/linux-64       9kB
  + xorg-kbproto                      1.0.7  h7f98852_1002            conda-forge/linux-64      27kB
  + xorg-libice                       1.1.1  hd590300_0               conda-forge/linux-64      58kB
  + xorg-libsm                        1.2.4  h7391055_0               conda-forge/linux-64      27kB
  + xorg-libx11                       1.8.6  h8ee46fc_0               conda-forge/linux-64     829kB
  + xorg-libxau                      1.0.11  hd590300_0               conda-forge/linux-64      14kB
  + xorg-libxdmcp                     1.1.3  h7f98852_0               conda-forge/linux-64      19kB
  + xorg-libxext                      1.3.4  h0b41bf4_2               conda-forge/linux-64      50kB
  + xorg-libxfixes                    5.0.3  h7f98852_1004            conda-forge/linux-64      18kB
  + xorg-libxrender                  0.9.11  hd590300_0               conda-forge/linux-64      38kB
  + xorg-renderproto                 0.11.1  h7f98852_1002            conda-forge/linux-64      10kB
  + xorg-xextproto                    7.3.0  h0b41bf4_1003            conda-forge/linux-64      30kB
  + xorg-xf86vidmodeproto             2.3.1  h7f98852_1002            conda-forge/linux-64      24kB
  + xorg-xproto                      7.0.31  h7f98852_1007            conda-forge/linux-64      75kB
  + xyzservices                    2023.7.0  pyhd8ed1ab_0             conda-forge/noarch        36kB
  + zarr                             2.16.1  pyhd8ed1ab_0             conda-forge/noarch       158kB
  + zict                              3.0.0  pyhd8ed1ab_0             conda-forge/noarch        36kB
  + zstd                              1.5.5  hfc55251_0               conda-forge/linux-64     545kB

  Upgrade:
──────────────────────────────────────────────────────────────────────────────────────────────────────

  - ipython                          8.14.0  pyh41d4057_0             conda-forge
  + ipython                          8.15.0  pyh0d859eb_0             conda-forge/noarch       588kB
  - openssl                           3.1.1  hd590300_1               conda-forge
  + openssl                           3.1.3  hd590300_0               conda-forge/linux-64       3MB
  - pip                              23.1.2  pyhd8ed1ab_0             conda-forge
  + pip                              23.2.1  pyhd8ed1ab_0             conda-forge/noarch         1MB

  Summary:

  Install: 230 packages
  Upgrade: 3 packages

  Total download: 539MB

──────────────────────────────────────────────────────────────────────────────────────────────────────



Downloading and Extracting Packages

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Rolling back transaction: ...working... ERROR conda.core.link:_execute(745): An error occurred while installing package 'conda-forge::rise-5.7.1-py310hff52083_2'.
done

LinkError: post-link script failed for package conda-forge::rise-5.7.1-py310hff52083_2
location of failed script: /srv/conda/envs/notebook/bin/.rise-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3108, in _dep_map
    return self.__dep_map
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2901, in __getattr__
    raise AttributeError(attr)
AttributeError: _DistInfoDistribution__dep_map

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3099, in _parsed_pkg_info
    return self._pkg_info
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2901, in __getattr__
    raise AttributeError(attr)
AttributeError: _pkg_info. Did you mean: 'egg_info'?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/bin/jupyter-nbextension", line 10, in <module>
    sys.exit(main())
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_core/application.py", line 277, in launch_instance
    return super().launch_instance(argv=argv, **kwargs)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/traitlets/config/application.py", line 1043, in launch_instance
    app.start()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 972, in start
    super().start()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/jupyter_core/application.py", line 266, in start
    self.subapp.start()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 882, in start
    self.toggle_nbextension_python(self.extra_args[0])
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 855, in toggle_nbextension_python
    return toggle(module,
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 470, in enable_nbextension_python
    return _set_nbextension_state_python(True, module, user, sys_prefix,
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 368, in _set_nbextension_state_python
    m, nbexts = _get_nbextension_metadata(module)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/notebook/nbextensions.py", line 1107, in _get_nbextension_metadata
    m = import_item(module)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/traitlets/utils/importstring.py", line 38, in import_item
    return __import__(parts[0])
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/rise/__init__.py", line 3, in <module>
    __version__ = pkg_resources.require("rise")[0].version
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 966, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 832, in resolve
    new_requirements = dist.requires(req.extras)[::-1]
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 2821, in requires
    dm = self._dep_map
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3110, in _dep_map
    self.__dep_map = self._compute_dependencies()
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3119, in _compute_dependencies
    for req in self._parsed_pkg_info.get_all('Requires-Dist') or []:
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 3101, in _parsed_pkg_info
    metadata = self.get_metadata(self.PKG_INFO)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1517, in get_metadata
    value = self._get(path)
  File "/srv/conda/envs/notebook/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1726, in _get
    with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: '/srv/conda/envs/notebook/lib/python3.10/site-packages/ipython-8.14.0.dist-info/METADATA'

return code: 1

()

time: 102.076
Removing intermediate container ecabe60672fa
The command '/bin/sh -c TIMEFORMAT='time: %3R' bash -c 'time ${MAMBA_EXE} env update -p ${NB_PYTHON_PREFIX} --file "binder/environment.yml" && time ${MAMBA_EXE} clean --all -f -y && ${MAMBA_EXE} list -p ${NB_PYTHON_PREFIX} '' returned a non-zero code: 1%

@Mikejmnez
Copy link
Collaborator Author

Mikejmnez commented Sep 25, 2023 •
edited
Loading

I was able to successfully build the oceanspy binder, with the current binder environment pinned to python= 3.10.

The steps that I followed are:

  1. Fresh installed mamba forge. For my personal mac computer I used the following snippet (as is).
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh

For more details on the installation (and other plataform options), see https://github.com/conda-forge/miniforge#mambaforge

  1. On the new (base) environment, I installed repo2docker
python3 -m pip install jupyter-repo2docker
  1. Build the binder env from hainegroup repo source using the following:
jupyter-repo2docker https://github.com/Hainegroup/oceanspy.git

I forgot to mentioned that I also have a pretty fresh installation of Docker...

@ThomasHaine
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Collaborator

Hmmm. It fails for me in the same way as before on my MacBook.

@Mikejmnez
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Collaborator Author

Mikejmnez commented Sep 26, 2023 •
edited
Loading

Ok. I restated Docker and tried again, and now I am getting the same errors and no image built. I wonder if my system was perhaps using an old build that I had done (speculation..). Well, at least we are getting consistent errors.

Sorry I couldn't be of more help.

TomWinder added a commit to TomWinder/QuakeMigrate that referenced this issue Sep 27, 2023
@TomWinder
fix(binder): Seems to currently be a bug with at least 3.11, try 3.10..
8bf5773 
As per: hainegroup/oceanspy#389
@Mikejmnez Mikejmnez removed their assignment Oct 9, 2023
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see damianavila/RISE#644

@Mikejmnez Mikejmnez mentioned this issue Nov 9, 2023
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Mikejmnez commented Nov 11, 2023 •
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Just to confirm that with this merge, I was able to build the binder

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replacing rise with jupyterlab-rise allows binder to get build Mikejmnez/oceanspy
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@Mikejmnez @pravissw @ThomasHaine