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conda-forge / conda-forge.github.io

The conda-forge website.
https://conda-forge.org
BSD 3-Clause "New" or "Revised" License
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Package conflicts within conda-forge? #1154

Open JamesSample opened 4 years ago

JamesSample commented 4 years ago

Hi!

Issue

I'm trying to extend the jupyter/datascience-notebook Docker file. I would like to install a lot of additional packages - maybe more than is sensible within a single environment - but since they're all available on conda-forge I thought it was worth a try. I've been careful to make sure that my starting environment only contains packages from conda-forge (see the output from conda list, below) and I'm installing the new packages using

conda install -c conda-forge --strict-channel-priority --override-channels --file conda_requirements.txt

which I think should make sure all the new packages come only from conda-forge too.

The solver "thinks" for quite a long time (about 40 minutes) and then produces a long list of package conflicts. I'm not sure how to interpret this, however, because in most cases I can't identify the conflicts. For example, here is a small part of the output:

Package cligj conflicts for:
regionmask -> rasterio -> cligj[version='>=0.5']
rasterio -> cligj[version='>=0.5']
fiona -> cligj[version='>=0.5']
earthpy -> rasterio -> cligj[version='>=0.5']
geopandas -> fiona -> cligj[version='>=0.5']

Package six conflicts for:
panel -> bokeh[version='>=1.4.0,<2.0'] -> six[version='>=1.5.2']
pymc3 -> h5py[version='>=2.7.0'] -> six[version='>=1.9.0']
fiona -> six[version='>=1.7']
pysal -> pytest -> six[version='>=1.10.0']
iris -> six
geopandas -> fiona -> six[version='>=1.7']
pdfminer.six -> six
branca -> six
regionmask -> six
scikit-image -> six[version='>=1.4|>=1.7.3']
geoviews -> cartopy[version='>=0.17.0'] -> six[version='>=1.5.2']
rpy2 -> six
altair -> jsonschema -> six[version='>=1.11.0']
fbprophet -> holidays[version='>=0.9.5'] -> six
zarr -> fasteners -> six
plotnine -> six
pyresample -> six
lmfit==0.9.14 -> six
pdfminer.six -> cryptography -> six[version='>=1.4.1']
cartopy -> six
pymc3 -> six[version='>=1.10.0']
holoviews -> bokeh[version='>=1.1.0'] -> six[version='>=1.5.2']
statsmodels -> patsy[version='>=0.5.1'] -> six
folium -> branca[version='>=0.3.0'] -> six
altair -> six
earthpy -> geopandas -> six[version='>=1.4|>=1.7.3']
geopandas -> six
gcsfs -> google-auth -> six[version='>=1.6.1|>=1.9.0|>=1.9.0,<2dev']
ipyparallel -> python-dateutil[version='>=2.1'] -> six
seaborn -> patsy -> six
nc-time-axis -> six
pvlib-python -> six

If I'm interpreting this correctly, wouldn't installing cligj=0.5 and six=1.15 (both of which are on conda-forge) satisfy the above? If not, can someone explain where I'm going wrong, please?

More generally, is it unrealistic to expect version and binary compatibility within conda-forge? (I understand there are incompatibilities between channels, but thought I might be OK using just conda-forge.

As additional background, I do actually have a working environment with all the packages I need that I created just using pip, apt-get and R some time ago. However, for this I have to rebuild the entire Jupyter stack (as far as the datascience-notebook) myself, and then add the extra packages. It would be much simpler and more maintainable if I could derive straight from the datascience-notebook using conda instead. I first tried this a few years ago, but at that time not all the packages I wanted were available on conda-forge and I ran into binary incompatibilities between conda-forge and other channels. It now looks as though everything I need is on conda-forge, so I'm keen to try again :-)

Any suggestions or advice gratefully received!

Thank you :-)


Environment (conda list):

``` # packages in environment at /opt/conda: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge aiohttp 3.6.2 py38h516909a_0 conda-forge alembic 1.4.2 pyh9f0ad1d_0 conda-forge appdirs 1.4.3 py_1 conda-forge argon2-cffi 20.1.0 py38h1e0a361_1 conda-forge astroid 2.4.2 py38h32f6830_0 conda-forge async-timeout 3.0.1 py_1000 conda-forge async_generator 1.10 py_0 conda-forge attrs 20.1.0 pyh9f0ad1d_0 conda-forge autopep8 1.5.4 pyh9f0ad1d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge beautifulsoup4 4.9.1 py_1 conda-forge binutils_impl_linux-64 2.34 h2122c62_9 conda-forge binutils_linux-64 2.34 h47ac705_27 conda-forge black 19.10b0 py_4 conda-forge blas 2.14 openblas conda-forge bleach 3.1.5 pyh9f0ad1d_0 conda-forge blinker 1.4 py_1 conda-forge blosc 1.20.0 he1b5a44_0 conda-forge bokeh 2.1.1 py38h32f6830_0 conda-forge bottleneck 1.3.2 py38h8790de6_1 conda-forge branca 0.3.1 py_0 conda-forge brotli 1.0.7 he1b5a44_1004 conda-forge brotlipy 0.7.0 py38h1e0a361_1000 conda-forge brunsli 0.1 he1b5a44_0 conda-forge bwidget 1.9.14 0 conda-forge bzip2 1.0.8 h516909a_3 conda-forge c-ares 1.16.1 h516909a_3 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge certifi 2020.6.20 py38h32f6830_0 conda-forge certipy 0.1.3 py_0 conda-forge cffi 1.14.1 py38h5bae8af_0 conda-forge chardet 3.0.4 py38h32f6830_1006 conda-forge charls 2.1.0 he1b5a44_2 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge cloudpickle 1.5.0 py_0 conda-forge colorama 0.4.3 py_0 conda-forge conda 4.8.3 py38h32f6830_2 conda-forge conda-package-handling 1.7.0 py38h1e0a361_4 conda-forge configurable-http-proxy 4.2.1 node13_he01fd0c_0 conda-forge cryptography 3.0 py38h766eaa4_0 conda-forge curl 7.71.1 he644dc0_5 conda-forge cycler 0.10.0 py_2 conda-forge cython 0.29.21 py38h950e882_0 conda-forge cytoolz 0.10.1 py38h516909a_0 conda-forge dask 2.20.0 py_0 conda-forge dask-core 2.20.0 py_0 conda-forge dask-labextension 3.0.0 py_0 conda-forge dask_labextension 3.0.0 0 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge dill 0.3.2 pyh9f0ad1d_0 conda-forge distributed 2.24.0 py38h32f6830_0 conda-forge entrypoints 0.3 py38h32f6830_1001 conda-forge fastcache 1.1.0 py38h1e0a361_1 conda-forge flake8 3.8.3 py_1 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge freetype 2.10.2 he06d7ca_0 conda-forge fribidi 1.0.10 h516909a_0 conda-forge fsspec 0.8.0 py_0 conda-forge future 0.18.2 py38h32f6830_1 conda-forge gcc_impl_linux-64 7.5.0 hdb87b24_16 conda-forge gcc_linux-64 7.5.0 hf34d7eb_27 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge gfortran_impl_linux-64 7.5.0 h1104b78_16 conda-forge gfortran_linux-64 7.5.0 ha781d05_27 conda-forge giflib 5.2.1 h516909a_2 conda-forge gitdb 4.0.5 py_0 conda-forge gitpython 3.1.7 py_0 conda-forge glib 2.65.0 h6f030ca_0 conda-forge gmp 6.2.0 he1b5a44_2 conda-forge gmpy2 2.1.0b1 py38h04dde30_0 conda-forge graphite2 1.3.13 he1b5a44_1001 conda-forge gsl 2.6 h294904e_0 conda-forge gxx_impl_linux-64 7.5.0 h1104b78_16 conda-forge gxx_linux-64 7.5.0 ha781d05_27 conda-forge h5py 2.10.0 nompi_py38hfb01d0b_104 conda-forge harfbuzz 2.4.0 h9f30f68_3 conda-forge hdf5 1.10.6 nompi_h3c11f04_101 conda-forge heapdict 1.0.1 py_0 conda-forge icu 64.2 he1b5a44_1 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge imagecodecs 2020.5.30 py38h36e1e94_2 conda-forge imageio 2.9.0 py_0 conda-forge importlib-metadata 1.7.0 py38h32f6830_0 conda-forge importlib_metadata 1.7.0 0 conda-forge ipykernel 5.3.4 py38h23f93f0_0 conda-forge ipyleaflet 0.13.3 pyh9f0ad1d_0 conda-forge ipympl 0.5.7 pyh9f0ad1d_1 conda-forge ipython 7.17.0 py38h1cdfbd6_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.5.1 py_0 conda-forge isort 5.4.2 py38h32f6830_0 conda-forge jedi 0.17.2 py38h32f6830_0 conda-forge jinja2 2.11.2 pyh9f0ad1d_0 conda-forge joblib 0.16.0 py_0 conda-forge jpeg 9d h516909a_0 conda-forge json5 0.9.4 pyh9f0ad1d_0 conda-forge jsonschema 3.2.0 py38h32f6830_1 conda-forge jupyter-archive 0.7.0 py_0 conda-forge jupyter-rsession-proxy 1.0b6 py_0 conda-forge jupyter-server-proxy 1.5.0 py_0 conda-forge jupyter_client 6.1.6 py_0 conda-forge jupyter_core 4.6.3 py38h32f6830_1 conda-forge jupyter_server 0.1.1 py38_0 conda-forge jupyter_telemetry 0.0.5 py_0 conda-forge jupyterhub 1.1.0 py38h32f6830_4 conda-forge jupyterhub-base 1.1.0 py38h32f6830_4 conda-forge jupyterlab 2.2.5 py_0 conda-forge jupyterlab-git 0.21.0 py_0 conda-forge jupyterlab_code_formatter 1.3.6 py_0 conda-forge jupyterlab_pygments 0.1.1 pyh9f0ad1d_0 conda-forge jupyterlab_server 1.2.0 py_0 conda-forge jxrlib 1.1 h516909a_2 conda-forge kernel-headers_linux-64 2.6.32 h77966d4_13 conda-forge kiwisolver 1.2.0 py38hbf85e49_0 conda-forge krb5 1.17.1 hfafb76e_2 conda-forge lazy-object-proxy 1.4.3 py38h1e0a361_2 conda-forge lcms2 2.11 hbd6801e_0 conda-forge ld_impl_linux-64 2.34 hc38a660_9 conda-forge lerc 2.2 he1b5a44_0 conda-forge libaec 1.0.4 he1b5a44_1 conda-forge libblas 3.8.0 14_openblas conda-forge libcblas 3.8.0 14_openblas conda-forge libcurl 7.71.1 hcdd3856_5 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_0 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-devel_linux-64 7.5.0 h42c25f5_16 conda-forge libgcc-ng 9.3.0 h24d8f2e_16 conda-forge libgfortran-ng 7.5.0 hdf63c60_16 conda-forge libgomp 9.3.0 h24d8f2e_16 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.8.0 14_openblas conda-forge liblapacke 3.8.0 14_openblas conda-forge libllvm8 8.0.1 hc9558a2_0 conda-forge libnghttp2 1.41.0 h8cfc5f6_2 conda-forge libopenblas 0.3.7 h5ec1e0e_6 conda-forge libpng 1.6.37 hed695b0_2 conda-forge libprotobuf 3.12.4 h8b12597_0 conda-forge libsodium 1.0.18 h516909a_0 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-devel_linux-64 7.5.0 h4084dd6_16 conda-forge libstdcxx-ng 9.3.0 hdf63c60_16 conda-forge libtiff 4.1.0 hc7e4089_6 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libuv 1.34.0 h516909a_0 conda-forge libwebp-base 1.1.0 h516909a_3 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.10 hee79883_0 conda-forge libzopfli 1.0.3 he1b5a44_0 conda-forge llvmlite 0.31.0 py38h4f45e52_1 conda-forge locket 0.2.0 py_2 conda-forge lz4-c 1.9.2 he1b5a44_3 conda-forge lzo 2.10 h516909a_1000 conda-forge make 4.3 h516909a_0 conda-forge mako 1.1.3 pyh9f0ad1d_0 conda-forge markupsafe 1.1.1 py38h1e0a361_1 conda-forge matplotlib-base 3.2.2 py38h2af1d28_0 conda-forge mccabe 0.6.1 py_1 conda-forge mistune 0.8.4 py38h1e0a361_1001 conda-forge mock 4.0.2 py38h32f6830_0 conda-forge mpc 1.1.0 h04dde30_1009 conda-forge mpfr 4.0.2 he80fd80_1 conda-forge mpmath 1.1.0 py_0 conda-forge msgpack-python 1.0.0 py38hbf85e49_1 conda-forge multidict 4.7.5 py38h1e0a361_1 conda-forge nbconvert 5.6.1 py38h32f6830_1 conda-forge nbdime 2.0.0 py_1 conda-forge nbformat 5.0.7 py_0 conda-forge ncurses 6.2 he1b5a44_1 conda-forge networkx 2.5 py_0 conda-forge nodejs 13.13.0 hf5d1a2b_0 conda-forge notebook 6.1.3 py38h32f6830_0 conda-forge numba 0.48.0 py38hb3f55d8_0 conda-forge numexpr 2.7.1 py38hcb8c335_1 conda-forge numpy 1.19.1 py38hbc27379_2 conda-forge oauthlib 3.0.1 py_0 conda-forge olefile 0.46 py_0 conda-forge openjpeg 2.3.1 h981e76c_3 conda-forge openssl 1.1.1g h516909a_1 conda-forge packaging 20.4 pyh9f0ad1d_0 conda-forge pamela 1.0.0 py_0 conda-forge pandas 1.1.1 py38h950e882_0 conda-forge pandoc 2.10.1 h516909a_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge pango 1.42.4 h7062337_4 conda-forge parso 0.7.1 pyh9f0ad1d_0 conda-forge partd 1.1.0 py_0 conda-forge pathspec 0.8.0 pyh9f0ad1d_0 conda-forge patsy 0.5.1 py_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge pexpect 4.8.0 py38h32f6830_1 conda-forge pickleshare 0.7.5 py38h32f6830_1001 conda-forge pillow 7.2.0 py38h9776b28_1 conda-forge pip 20.2.2 py_0 conda-forge pixman 0.38.0 h516909a_1003 conda-forge pluggy 0.13.1 py38h32f6830_2 conda-forge prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge prompt-toolkit 3.0.6 py_0 conda-forge protobuf 3.12.4 py38h950e882_0 conda-forge psutil 5.7.2 py38h1e0a361_0 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge ptyprocess 0.6.0 py_1001 conda-forge pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge pycosat 0.6.3 py38h1e0a361_1004 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pycurl 7.43.0.5 py38h4400d41_2 conda-forge pydocstyle 5.1.1 py_0 conda-forge pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge pygments 2.6.1 py_0 conda-forge pyjwt 1.7.1 py_0 conda-forge pylint 2.6.0 py38h32f6830_0 conda-forge pyopenssl 19.1.0 py_1 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.16.0 py38h1e0a361_0 conda-forge pysocks 1.7.1 py38h32f6830_1 conda-forge pytables 3.6.1 py38h1b207d3_2 conda-forge python 3.8.5 h1103e12_5_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-editor 1.0.4 py_0 conda-forge python-json-logger 0.1.11 py_0 conda-forge python-jsonrpc-server 0.3.4 pyh9f0ad1d_1 conda-forge python-language-server 0.34.1 py38h32f6830_0 conda-forge python_abi 3.8 1_cp38 conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge pywavelets 1.1.1 py38h8790de6_1 conda-forge pyyaml 5.3.1 py38h1e0a361_0 conda-forge pyzmq 19.0.2 py38ha71036d_0 conda-forge r-askpass 1.1 r36hcdcec82_2 conda-forge r-assertthat 0.2.1 r36h6115d3f_2 conda-forge r-backports 1.1.9 r36hcdcec82_0 conda-forge r-base 3.6.3 h316533a_2 conda-forge r-base64enc 0.1_3 r36hcdcec82_1004 conda-forge r-bit 4.0.4 r36hcdcec82_0 conda-forge r-bit64 4.0.2 r36hcdcec82_0 conda-forge r-bitops 1.0_6 r36hcdcec82_1004 conda-forge r-blob 1.2.1 r36h6115d3f_1 conda-forge r-brew 1.0_6 r36h6115d3f_1003 conda-forge r-broom 0.7.0 r36h6115d3f_0 conda-forge r-callr 3.4.3 r36h6115d3f_1 conda-forge r-caret 6.0_86 r36hcdcec82_2 conda-forge r-cellranger 1.1.0 r36h6115d3f_1003 conda-forge r-class 7.3_17 r36hcdcec82_1 conda-forge r-cli 2.0.2 r36h6115d3f_1 conda-forge r-clipr 0.7.0 r36h6115d3f_1 conda-forge r-codetools 0.2_16 r36h6115d3f_1002 conda-forge r-colorspace 1.4_1 r36hcdcec82_2 conda-forge r-commonmark 1.7 r36hcdcec82_1002 conda-forge r-covr 3.5.0 r36h0357c0b_1 conda-forge r-crayon 1.3.4 r36h6115d3f_1003 conda-forge r-crosstalk 1.1.0.1 r36h6115d3f_1 conda-forge r-curl 4.3 r36hcdcec82_1 conda-forge r-data.table 1.12.8 r36hcdcec82_1 conda-forge r-dbi 1.1.0 r36h6115d3f_1 conda-forge r-dbplyr 1.4.4 r36h6115d3f_0 conda-forge r-desc 1.2.0 r36h6115d3f_1003 conda-forge r-devtools 2.3.1 r36h6115d3f_0 conda-forge r-digest 0.6.25 r36h0357c0b_2 conda-forge r-dplyr 1.0.2 r36h0357c0b_0 conda-forge r-dt 0.15 r36h6115d3f_0 conda-forge r-ellipsis 0.3.1 r36hcdcec82_0 conda-forge r-evaluate 0.14 r36h6115d3f_2 conda-forge r-fansi 0.4.1 r36hcdcec82_1 conda-forge r-farver 2.0.3 r36h0357c0b_1 conda-forge r-fastmap 1.0.1 r36h0357c0b_1 conda-forge r-forcats 0.5.0 r36h6115d3f_1 conda-forge r-foreach 1.5.0 r36h6115d3f_1 conda-forge r-forecast 8.12 r36hc8faad4_1 conda-forge 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xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge yapf 0.30.0 pyh9f0ad1d_0 conda-forge yarl 1.4.2 py38h516909a_0 conda-forge zeromq 4.3.2 he1b5a44_3 conda-forge zfp 0.5.5 he1b5a44_1 conda-forge zict 2.0.0 py_0 conda-forge zipp 3.1.0 py_0 conda-forge zlib 1.2.11 h516909a_1007 conda-forge zstd 1.4.5 h6597ccf_2 conda-forge ```


Details about conda and system ( conda info ):

``` active environment : None user config file : /home/jovyan/.condarc populated config files : /opt/conda/.condarc conda version : 4.8.3 conda-build version : not installed python version : 3.8.5.final.0 virtual packages : __glibc=2.31 base environment : /opt/conda (writable) 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 : /opt/conda/pkgs /home/jovyan/.conda/pkgs envs directories : /opt/conda/envs /home/jovyan/.conda/envs platform : linux-64 user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.5 Linux/4.19.76-linuxkit ubuntu/20.04 glibc/2.31 UID:GID : 1000:100 netrc file : None offline mode : False ```
scopatz commented 4 years ago

Thanks for opening this, @JamesSample. This is really more of a conda question than a conda-forge question. But yes, the purpose of conda-forge is to produce binary-compatible environments. So the error message you are seeing is say that this is not possible for the packages listed. In this situation, you have a couple of options:

JamesSample commented 4 years ago

Thanks for the reply, @scopatz!

When you say "loosening the pins", do you mean the pinned package versions in my requirements.txt, or is there some other setting in conda I'm not aware of? At present, I have no version pinning at all in requirements.txt in order to give the solver maximum flexibility in finding a solution (I did have the versions pinned initially, but have progressively removed them). Right now, conda is saying my selected conda-forge packages are just fundamentally incompatible, regardless of versions.

Do you have any advice for interpreting the output from the solver regarding version conflicts, please? conda thinks there are problems, but I can't see them in the output above. Am I reading it wrongly?

Thanks for suggesting mamba - I hadn't heard of it before but it sounds great! I'll definitely give it a go :-)

scopatz commented 4 years ago

Ahh yeah, then maybe you should try adding version pins in the requirement.txt to restrict the search space.

Do you have any advice for interpreting the output from the solver regarding version conflicts, please? conda thinks there are problems, but I can't see them in the output above. Am I reading it wrongly?

I wish I did! I often have problems reading them myself, and sometimes they report incorrect conflicts (that are a result of higher-level problems). This is an NP-hard problem, so it has been tricky for the conda team to figure out how to report meaningful info here. What I do in these situations is to try to remove/comment-out packages until I get to an environment that is installable, then add packages back in to find what fails. It is a binary search method basically. Even then it doesn't always work

JamesSample commented 4 years ago

Thanks @scopatz ! The workflow you've described is basically my current approach, so I'll keep iterating to see if I can find a workable solution. Good to know it's not just me, anyway!

I've also just had a go using mamba, and although it still isn't working it is much faster, and so far the error messages seem more helpful. Thanks for the tip :-)

scopatz commented 4 years ago

Great! Glad I could help!