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vatlab / sos-notebook

Multi-language Jupyter Notebook
http://vatlab.github.io/SoS
BSD 3-Clause "New" or "Revised" License
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cannot import name 'Sequence' from 'collections' (/opt/conda/lib/python3.10/collections/__init__.py) #347

Closed benwilks closed 1 year ago

benwilks commented 1 year ago

Getting import error using python3.10 and the %use R command in an sos notebook. It looks like it needs to be from collections.abc import Sequence for python 3.10. I can still run R: from the cell, just not the %use R command. Are there any plans to update support for python 3.10?

BoPeng commented 1 year ago

It should be supported. Could you update your sos-r?

benwilks commented 1 year ago

Hi,

Thank you for the quick reply! I installed sos-r with conda install -c conda-forge sos-r and it looks like it installs v0.19.6. I'm still getting the "cannot import name 'Sequence' from 'collections' (/opt/conda/lib/python3.10/collections/init.py)" error though.

I'm using the jupyter/datascience docker as the base container and then installed sos packages with conda/mamba.

packages in environment at /opt/conda:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge _sysroot_linux-64_curr_repodata_hack 3 h5bd9786_13 conda-forge aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge alembic 1.10.4 pyhd8ed1ab_0 conda-forge altair 4.2.2 pyhd8ed1ab_0 conda-forge ansi2html 1.8.0 py310hff52083_1 conda-forge ansiwrap 0.8.4 py_0 conda-forge anyio 3.6.2 pyhd8ed1ab_0 conda-forge aom 3.5.0 h27087fc_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge arrow 1.2.3 pyhd8ed1ab_0 conda-forge arrow-cpp 11.0.0 ha770c72_14_cpu conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge async_generator 1.10 py_0 conda-forge atk-1.0 2.38.0 hd4edc92_1 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge autopep8 2.0.2 pyhd8ed1ab_0 conda-forge aws-c-auth 0.6.26 hf365957_1 conda-forge aws-c-cal 0.5.21 h48707d8_2 conda-forge aws-c-common 0.8.14 h0b41bf4_0 conda-forge aws-c-compression 0.2.16 h03acc5a_5 conda-forge aws-c-event-stream 0.2.20 h00877a2_4 conda-forge aws-c-http 0.7.6 hf342b9f_0 conda-forge aws-c-io 0.13.19 h5b20300_3 conda-forge aws-c-mqtt 0.8.6 hc4349f7_12 conda-forge aws-c-s3 0.2.7 h909e904_1 conda-forge aws-c-sdkutils 0.1.8 h03acc5a_0 conda-forge aws-checksums 0.1.14 h03acc5a_5 conda-forge aws-crt-cpp 0.19.8 hf7fbfca_12 conda-forge aws-sdk-cpp 1.10.57 h17c43bd_8 conda-forge babel 2.12.1 pyhd8ed1ab_1 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge bash 5.2.15 hfbf034d_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge black 23.3.0 py310hff52083_0 conda-forge blas 2.116 openblas conda-forge blas-devel 3.9.0 16_linux64_openblas conda-forge bleach 6.0.0 pyhd8ed1ab_0 conda-forge blinker 1.6.2 pyhd8ed1ab_0 conda-forge blosc 1.21.3 hafa529b_0 conda-forge bokeh 3.1.0 pyhd8ed1ab_0 conda-forge boltons 23.0.0 pyhd8ed1ab_0 conda-forge bottleneck 1.3.7 py310h0a54255_0 conda-forge brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge brotli-python 1.0.9 py310hd8f1fbe_8 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge brunsli 0.1 h9c3ff4c_0 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge c-blosc2 2.8.0 hf91038e_1 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge calysto_bash 0.2.2 py310hff52083_2 conda-forge certifi 2022.12.7 pyhd8ed1ab_0 conda-forge certipy 0.1.3 py_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge cfitsio 4.2.0 hd9d235c_0 conda-forge charls 2.4.1 hcb278e6_0 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.3 pyhd8ed1ab_0 conda-forge conda 23.3.1 py310hff52083_0 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge configurable-http-proxy 4.5.4 h3b247e2_2 conda-forge contourpy 1.0.7 py310hdf3cbec_0 conda-forge cryptography 40.0.2 py310h34c0648_0 conda-forge curl 8.0.1 h588be90_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cython 0.29.34 py310heca2aa9_0 conda-forge cytoolz 0.12.0 py310h5764c6d_1 conda-forge dash 2.9.3 pyhd8ed1ab_0 conda-forge dask 2023.4.0 pyhd8ed1ab_0 conda-forge dask-core 2023.4.0 pyhd8ed1ab_0 conda-forge dav1d 1.0.0 h166bdaf_1 conda-forge debugpy 1.6.7 py310heca2aa9_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dill 0.3.6 pyhd8ed1ab_1 conda-forge distributed 2023.4.0 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge et_xmlfile 1.1.0 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fasteners 0.17.3 pyhd8ed1ab_0 conda-forge feather-format 0.4.1 pyh9f0ad1d_0 conda-forge flask 2.2.3 pyhd8ed1ab_0 conda-forge flask-compress 1.13 pyhd8ed1ab_0 conda-forge flit-core 3.8.0 pyhd8ed1ab_0 conda-forge fmt 9.1.0 h924138e_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 4.39.3 py310h1fa729e_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge fsspec 2023.4.0 pyh1a96a4e_0 conda-forge gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge gdk-pixbuf 2.42.10 h05c8ddd_0 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge gh 2.25.1 ha8f183a_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge git 2.40.0 pl5321h3ca6407_1 conda-forge gitdb 4.0.10 pyhd8ed1ab_0 conda-forge gitpython 3.1.31 pyhd8ed1ab_0 conda-forge glog 0.6.0 h6f12383_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gmpy2 2.1.2 py310h3ec546c_1 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge graphviz 2.50.0 h5abf519_3 conda-forge greenlet 2.0.2 py310heca2aa9_0 conda-forge gsl 2.7 he838d99_0 conda-forge gtk2 2.24.33 h90689f9_2 conda-forge gts 0.7.6 h64030ff_2 conda-forge gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge h5py 3.8.0 nompi_py310ha66b2ad_101 conda-forge harfbuzz 6.0.0 h8e241bc_0 conda-forge hdf5 1.14.0 nompi_hb72d44e_103 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imagecodecs 2023.1.23 py310ha3ed6a1_0 conda-forge imageio 2.28.0 pyh24c5eb1_0 conda-forge importlib-metadata 6.6.0 pyha770c72_0 conda-forge importlib_metadata 6.6.0 hd8ed1ab_0 conda-forge importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge ipykernel 6.22.0 pyh210e3f2_0 conda-forge ipympl 0.9.3 pyhd8ed1ab_0 conda-forge ipyparallel 8.6.1 pyhd8ed1ab_0 conda-forge ipython 8.12.0 pyh41d4057_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 8.0.6 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge isort 5.12.0 pyhd8ed1ab_1 conda-forge itsdangerous 2.1.2 pyhd8ed1ab_0 conda-forge jedi 0.18.2 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge joblib 1.2.0 pyhd8ed1ab_0 conda-forge jpeg 9e h166bdaf_2 conda-forge json5 0.9.5 pyh9f0ad1d_0 conda-forge jsonpatch 1.32 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.17.3 pyhd8ed1ab_0 conda-forge jupyter-dash 0.4.2 pyhd8ed1ab_1 conda-forge jupyter-server-mathjax 0.2.6 pyh5bfe37b_1 conda-forge jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.0 py310hff52083_0 conda-forge jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge jupyter_server 2.5.0 pyhd8ed1ab_0 conda-forge jupyter_server_fileid 0.9.0 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge jupyter_server_ydoc 0.8.0 pyhd8ed1ab_0 conda-forge jupyter_telemetry 0.1.0 pyhd8ed1ab_1 conda-forge jupyter_ydoc 0.2.3 pyhd8ed1ab_0 conda-forge jupyterhub 4.0.0 pyh2a2186d_0 conda-forge jupyterhub-base 4.0.0 pyh2a2186d_0 conda-forge jupyterlab 3.6.3 pyhd8ed1ab_0 conda-forge jupyterlab-git 0.41.0 pyhd8ed1ab_1 conda-forge jupyterlab-sos 0.8.8 ha770c72_0 conda-forge jupyterlab-transient-display-data 0.4.3 pyhc268e32_0 conda-forge jupyterlab_code_formatter 1.6.0 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge jupyterlab_sos 0.8.8 pyh76afe40_0 conda-forge jupyterlab_widgets 3.0.7 pyhd8ed1ab_0 conda-forge jxrlib 1.1 h7f98852_2 conda-forge kernel-headers_linux-64 3.10.0 h4a8ded7_13 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py310hbf28c38_1 conda-forge krb5 1.20.1 h81ceb04_0 conda-forge lazy_loader 0.2 pyhd8ed1ab_0 conda-forge lcms2 2.15 hfd0df8a_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230125.0 cxx17_hcb278e6_1 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libarchive 3.6.2 h3d51595_0 conda-forge libarrow 11.0.0 h93537a5_14_cpu conda-forge libavif 0.11.1 h5cdd6b5_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_8 conda-forge libbrotlidec 1.0.9 h166bdaf_8 conda-forge libbrotlienc 1.0.9 h166bdaf_8 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.0.1 h588be90_0 conda-forge libdeflate 1.17 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 h28343ad_4 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgd 2.3.3 h695aa2c_1 defaults libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgit2 1.6.4 h747ad27_0 conda-forge libglib 2.76.2 hebfc3b9_0 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libgoogle-cloud 2.8.0 h0bc5f78_1 conda-forge libgrpc 1.52.1 hcf146ea_1 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libjpeg-turbo 2.1.4 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge liblapacke 3.9.0 16_linux64_openblas conda-forge libllvm11 11.1.0 he0ac6c6_5 conda-forge libmamba 1.4.2 hcea66bb_0 conda-forge libmambapy 1.4.2 py310h1428755_0 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 0.3.21 pthreads_h78a6416_3 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 3.21.12 h3eb15da_0 conda-forge librsvg 2.54.4 h7abd40a_0 conda-forge libsanitizer 12.2.0 h46fd767_19 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsolv 0.7.23 h3eb15da_0 conda-forge libsqlite 3.40.0 h753d276_1 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libthrift 0.18.1 h5e4af38_0 conda-forge libtiff 4.5.0 h6adf6a1_2 conda-forge libtool 2.4.7 h27087fc_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 libwebp-base 1.3.0 h0b41bf4_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge libzopfli 1.0.3 h9c3ff4c_0 conda-forge llvm-openmp 16.0.2 h4dfa4b3_0 conda-forge llvmlite 0.39.1 py310h58363a5_1 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lz4 4.3.2 py310h0cfdcf0_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge make 4.3 hd18ef5c_1 conda-forge mako 1.2.4 pyhd8ed1ab_0 conda-forge mamba 1.4.2 py310h51d5547_0 conda-forge markdown 3.4.3 pyhd8ed1ab_0 conda-forge markupsafe 2.1.2 py310h1fa729e_0 conda-forge matplotlib-base 3.7.1 py310he60537e_0 conda-forge matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge metakernel 0.29.4 pyhd8ed1ab_0 conda-forge mistune 2.0.5 pyhd8ed1ab_0 conda-forge mpc 1.3.1 hfe3b2da_0 conda-forge mpfr 4.2.0 hb012696_0 conda-forge mpmath 1.3.0 pyhd8ed1ab_0 conda-forge msgpack-python 1.0.5 py310hdf3cbec_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mypy_extensions 1.0.0 pyha770c72_0 conda-forge nb_conda 2.2.1 unix_6 conda-forge nb_conda_kernels 2.3.1 py310hff52083_2 conda-forge nbclassic 0.5.5 pyhb4ecaf3_1 conda-forge nbclient 0.7.3 pyhd8ed1ab_0 conda-forge nbconvert 7.3.1 pyhd8ed1ab_0 conda-forge nbconvert-core 7.3.1 pyhd8ed1ab_0 conda-forge nbconvert-pandoc 7.3.1 pyhd8ed1ab_0 conda-forge nbdime 3.2.0 pyhd8ed1ab_0 conda-forge nbformat 5.8.0 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge nodejs 16.19.0 h8d033a5_0 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge notebook 6.5.4 pyha770c72_0 conda-forge notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge numba 0.56.4 py310h0e39c9b_1 conda-forge numexpr 2.8.4 py310h690d005_100 conda-forge numpy 1.23.5 py310h53a5b5f_0 conda-forge oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge openblas 0.3.21 pthreads_h320a7e8_3 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openpyxl 3.1.1 py310h1fa729e_0 conda-forge openssl 3.1.0 hd590300_2 conda-forge orc 1.8.3 hfdbbad2_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pamela 1.0.0 py_0 conda-forge pandas 2.0.1 py310h7cbd5c2_0 conda-forge pandoc 2.19.2 h32600fe_2 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge pango 1.50.14 hd33c08f_0 conda-forge papermill 2.3.4 pyhd8ed1ab_0 conda-forge parquet-cpp 1.5.1 2 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge partd 1.4.0 pyhd8ed1ab_0 conda-forge pathspec 0.11.1 pyhd8ed1ab_0 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pexpect 4.8.0 pyh1a96a4e_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 9.4.0 py310h023d228_1 conda-forge pip 23.1.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge platformdirs 3.2.0 pyhd8ed1ab_0 conda-forge plotly 5.14.1 pyhd8ed1ab_0 conda-forge pluggy 1.0.0 pyhd8ed1ab_5 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge portalocker 2.7.0 py310hff52083_0 conda-forge prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.38 pyha770c72_0 conda-forge prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge protobuf 4.21.12 py310heca2aa9_0 conda-forge psutil 5.9.5 py310h1fa729e_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 py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge pyarrow 11.0.0 py310h633f555_14_cpu conda-forge 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py310hff52083_0 conda-forge ucx 1.14.0 h8c404fb_1 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge unixodbc 2.3.10 h583eb01_0 conda-forge uri-template 1.2.0 pyhd8ed1ab_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge webcolors 1.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge werkzeug 2.2.3 pyhd8ed1ab_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.7 pyhd8ed1ab_0 conda-forge xlrd 2.0.1 pyhd8ed1ab_3 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 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 xxhash 0.8.1 h0b41bf4_0 conda-forge xyzservices 2023.2.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge y-py 0.5.9 py310h4426083_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zfp 1.0.0 h27087fc_3 conda-forge zict 3.0.0 pyhd8ed1ab_0 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zlib-ng 2.0.7 h0b41bf4_0 conda-forge zstandard 0.19.0 py310hdeb6495_1 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge

Available kernels:

calysto_bash /opt/conda/share/jupyter/kernels/calysto_bash ir /opt/conda/share/jupyter/kernels/ir julia-1.8 /opt/conda/share/jupyter/kernels/julia-1.8 python3 /opt/conda/share/jupyter/kernels/python3 sos /opt/conda/share/jupyter/kernels/sos

BoPeng commented 1 year ago

https://github.com/conda-forge/sos-r-feedstock/pulls?q=is%3Apr+is%3Aclosed

It looks like sos-r 0.20.0 failed to build so it is not available on conda-forge. This has been going on for a while. :-(

If you already have sos-r installed through conda-forge, I think, pip install sos-r -U should update it. The same applies to other packages that might also be outdated. (e.g. sos-notebook is now at 0.24.1).

benwilks commented 1 year ago

@BoPeng That did the trick! Thank you!

gaow commented 1 year ago

Here is the list of outdated packages on conda-forge that we would need to fix (based on _version.py so some of them may be up to date eg 0.20.8 on conda-forge -> 0.20.9 in _version.py. But recording them anyways):

(I ordered them by what I think the priority to fix)

gaow commented 1 year ago

Also for SoS notebook the noarch version is only 0.20. not 0.24.. That is what got installed on my Mac desktop with M2 chip. ...

gaow commented 1 year ago

There's also this warning message python3.10/site-packages/sos_notebook/kernel.py:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html

BoPeng commented 1 year ago

I will fix this later today.

gaow commented 1 year ago

@BoPeng thank you! Here is another summary of issues related to M2 chip:

├─ jupyterlab-sos 0.9.0**  does not exist (perhaps a typo or a missing channel);
    ├─ sos-bash 0.20.0**  is not installable because it requires
    │  └─ calysto_bash, which does not exist (perhaps a missing channel);
    ├─ sos-notebook 0.24.0**  does not exist (perhaps a typo or a missing channel);
    └─ sos-r 0.19.6**  is not installable because it requires
       └─ r-feather, which does not exist (perhaps a missing channel).

We cannot fix the last one i suppose because r-feather does not have arm64 release. For the others we might want to catch-up on conda-forge to also have support for noarch for the latest version.

gaow commented 9 months ago

@BoPeng to touch base on this ticket, we are still having various issues with using new versions of SoS suite on M2 because many of the conda packages are still not noarch, see a list here: https://github.com/vatlab/sos-notebook/issues/347#issuecomment-1699025485. Not sure what it is involved to fix these releases. I can start a new ticket to keep track if it would take longer than simple fixes.