Deprecated Dependency Versions in Environment.yml

[ropuia22]

Hi Team,

I need a little help. I am trying to create an environment using the defult environent.yml in a ubuntu 18.04.6 ARM machine.
But I am facing issues with the following packages-

• freetype==2.9.1=h8a8886c_1
• libxslt==1.1.33=h7d1a2b0_0
• setuptools==46.4.0=py37_0
• yaml==0.1.7=had09818_2
• intel-openmp==2020.1=217
• mkl==2020.1=217
• tensorflow==1.13.1=gpu_py37hc158e3b_0
• itsdangerous==1.1.0=py37_0
• scikit-learn==0.22.1=py37hd81dba3_0
• libstdcxx-ng==9.1.0=hdf63c60_0
• pyzmq==18.1.1=py37he6710b0_0
• lxml==4.5.0=py37hefd8a0e_0
• beautifulsoup4==4.9.1=py37_0
• icu==58.2=he6710b0_3
• lz4-c==1.9.2=he6710b0_0
• webencodings==0.5.1=py37_1
• ipykernel==5.1.4=py37h39e3cac_0
• mkl-service==2.3.0=py37he904b0f_0
• libtiff==4.1.0=h2733197_1
• docopt==0.6.2=py37_0
• libboost==1.67.0=h46d08c1_4
• sip==4.19.8=py37hf484d3e_0
• blas==1.0=mkl
• libffi==3.3=he6710b0_1
• openssl==1.1.1g=h7b6447c_0
• cffi==1.14.0=py37he30daa8_1
• send2trash==1.5.0=py37_0
• astor==0.8.0=py37_0
• zeromq==4.3.1=he6710b0_3
• _tflow_select==2.1.0=gpu
• dbus==1.13.14=hb2f20db_0
• gst-plugins-base==1.14.0=hbbd80ab_1
• ld_impl_linux-64==2.33.1=h53a641e_7
• tensorboard==1.13.1=py37hf484d3e_0
• sqlite==3.31.1=h62c20be_1
• pyqt==5.9.2=py37h05f1152_2
• hdf5==1.10.4=hb1b8bf9_0
• py4j==0.10.8.1=py37_0
• cycler==0.10.0=py37_0
• cudnn==7.6.5=cuda10.0_0
• cudatoolkit==10.0.130=0
• libgfortran-ng==7.3.0=hdf63c60_0
• qt==5.9.7=h5867ecd_1
• c-ares==1.15.0=h7b6447c_1001
• numpy-base==1.18.1=py37hde5b4d6_1
• glib==2.63.1=h3eb4bd4_1
• libedit==3.1.20181209=hc058e9b_0
• kiwisolver==1.2.0=py37hfd86e86_0
• libgcc-ng==9.1.0=hdf63c60_0
• ncurses==6.2=he6710b0_1
• pyyaml==5.3.1=py37h7b6447c_0
• matplotlib-base==3.1.3=py37hef1b27d_0
• expat==2.2.6=he6710b0_0
• pickleshare==0.7.5=py37_0
• libxml2==2.9.9=hea5a465_1
• cairo==1.14.12=h8948797_3
• markdown==3.1.1=py37_0
• entrypoints==0.3=py37_0
• numpy==1.18.1=py37h4f9e942_0
• libuuid==1.0.3=h1bed415_2
• mistune==0.8.4=py37h7b6447c_0
• ipython==7.13.0=py37h5ca1d4c_0
• pyrsistent==0.16.0=py37h7b6447c_0
• zstd==1.4.4=h0b5b093_3
• pandas==1.0.3=py37h0573a6f_0
• tensorflow-base==1.13.1=gpu_py37h8d69cac_0
• libpng==1.6.37=hbc83047_0
• importlib-metadata==1.6.0=py37_0
• markupsafe==1.1.1=py37h7b6447c_0
• py-boost==1.67.0=py37h04863e7_4
• ipython_genutils==0.2.0=py37_0
• tensorflow-gpu==1.13.1=h0d30ee6_0
• absl-py==0.9.0=py37_0
• urllib3==1.25.8=py37_0
• python==3.7.7=hcff3b4d_5
• gmp==6.1.2=h6c8ec71_1
• cupti==10.0.130=0
• jpeg==9b=h024ee3a_2
• readline==8.0=h7b6447c_0
• pcre==8.43=he6710b0_0
• h5py==2.10.0=py37h7918eee_0
• mkl_random==1.1.1=py37h0573a6f_0
• pillow==7.1.2=py37hb39fc2d_0
• jedi==0.17.0=py37_0
• ca-certificates==2020.1.1=0
• keras-base==2.3.1=py37_0
• pandocfilters==1.4.2=py37_1
• pixman==0.38.0=h7b6447c_0
• gstreamer==1.14.0=hb31296c_0
• xz==5.2.5=h7b6447c_0
• tk==8.6.8=hbc83047_0
• fontconfig==2.13.0=h9420a91_0
• bzip2==1.0.8=h7b6447c_0
• pandoc==2.2.3.2=0
• pip==20.0.2=py37_3
• libsodium==1.0.16=h1bed415_0
• jupyter==1.0.0=py37_7
• scipy==1.4.1=py37h0b6359f_0
• certifi==2020.4.5.1=py37_0
• libprotobuf==3.11.4=hd408876_0
• sqlalchemy==1.3.17=py37h7b6447c_0
• tornado==6.0.4=py37h7b6447c_1
• ptyprocess==0.6.0=py37_0
• libxcb==1.13=h1bed415_1
• grpcio==1.27.2=py37hf8bcb03_0
• protobuf==3.11.4=py37he6710b0_0
• backcall==0.1.0=py37_0
• rdkit==2020.03.2.0=py37hc20afe1_1
• zlib==1.2.11=h7b6447c_3
• keras-gpu==2.3.1=0
• mkl_fft==1.0.15=py37ha843d7b_0
• termcolor==1.1.0=py37_1
• cryptography==2.9.2=py37h1ba5d50_0

While checking conda channels, I found that the versions and build mentioned above are not available.
I have not worked with conda before.
Kindly let me know if there is an easy way to replace them with an existing version/build wihtout having to perform conda search for each packages and updating the info individually/manually.

If you can update the environment.yml file from your side, that would be much appreciated.

[sishida21]

@ropuia22
Thank you for letting us know about the issue. Please check the setup instruction (https://github.com/clinfo/ReTReK/blob/master/doc/setup.md) and try to set up your environment following the Install the dependency libraries section instead of using the environment.yml.

Below is the excerpt:

# Install the dependency libraries.
conda install py4j=10.8.1 tqdm oddt mendeleev
conda install -c rdkit rdkit=2020.03.2.0
conda install keras-gpu=2.3.1 tensorflow-gpu=1.13.1 cudatoolkit=10.0
pip install --upgrade git+https://github.com/clinfo/kGCN.git

I hope the answer will helpful for you.