Closed Mikejmnez closed 11 months ago
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.
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
.
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.
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
@Mikejmnez how do you reproduce the error? On SciServer the notebooks in the binder
folder run fine for me.
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.
@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
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).
Hmmm. It looks like I'm using python 3.10.12
as well, but it fails.
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?
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:
──────────────────────────────────────────────────────────────────────────────────────────────────────
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+ 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 ${NB_PYTHON_PREFIX} '' returned a non-zero code: 1%
I was able to successfully build the oceanspy binder, with the current binder environment pinned to python= 3.10
.
The steps that I followed are:
Fresh installed mamba forge. For my personal mac computer I used the following snippet (as is).
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(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
On the new (base) environment, I installed repo2docker
python3 -m pip install jupyter-repo2docker
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...
Hmmm. It fails for me in the same way as before on my MacBook.
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.
Just to confirm that with this merge, I was able to build the binder
It has been a couple of weeks now, that I have tried and failed to build the environment. The Traceback is
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 https://github.com/jupyterhub/repo2docker/issues/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!