Hi Jasmin, I would definitely expect the conda installation to work. The paths that your output shows are a bit strange: it looks like your username on the Azure machine is "<Username>". If that is the case, it could be that this is causing a problem (I've not seen user names with "<>" characters before.
Could you please execute the following 4 commands and send the entire output that you get? cd pwd which conda conda install -c rdkit rdkit Best, -greg On Wed, Jul 3, 2019 at 8:19 AM Jasmin <zweitm...@posteo.de> wrote: > Hello! > > I am experiencing problems with installing rdkit by conda in a > Miniconda-environment on a Azure Ubuntu machine using "conda install -c > rdkit rdkit". > The error message I'm getting is: > ''' > environment variables: > CIO_TEST=<not set> > CONDA_DEFAULT_ENV=base > CONDA_EXE=/home/<username>/programs/Miniconda3/bin/conda > CONDA_PREFIX=/home/<username>/programs/Miniconda3 > CONDA_PROMPT_MODIFIER= > > CONDA_PYTHON_EXE=/home/<username>/programs/Miniconda3/bin/python > CONDA_ROOT=/home/<username>/programs/Miniconda3 > CONDA_SHLVL=1 > > > PATH=/home/<username>/programs/Miniconda3/bin:/home/<username>/programs/Miniconda > > 3/bin:/home/<username>/programs/Miniconda3/condabin:/usr/local/sbin:/usr/ > > local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/s > nap/bin > REQUESTS_CA_BUNDLE=<not set> > SSL_CERT_FILE=<not set> > ftp_proxy=<set> > http_proxy=<set> > https_proxy=<set> > > active environment : base > active env location : /home/<username>/programs/Miniconda3 > shell level : 1 > user config file : /home/<username>/.condarc > populated config files : /home/<username>/.condarc > conda version : 4.7.5 > conda-build version : not installed > python version : 3.7.3.final.0 > virtual packages : > base environment : /home/<username>/programs/Miniconda3 > (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 : /home/<username>/programs/Miniconda3/pkgs > /home/<username>/.conda/pkgs > envs directories : /home/<username>/programs/Miniconda3/envs > /home/<username>/.conda/envs > platform : linux-64 > user-agent : conda/4.7.5 requests/2.21.0 CPython/3.7.3 > Linux/4.18.0-1018-azure ubuntu/18.04.2 glibc/2.27 > UID:GID : 1002:1003 > netrc file : None > offline mode : False > > An unexpected error has occurred. Conda has prepared the above report. > ''' > > I also tried to install from repositories: sudo apt-get install > python-rdkit librdkit1 rdkit-data > There is no error message but trying to import rdkit in a python3 > console gives me a "module not found". > > The third thing I tried is to build from source in conda > (https://www.rdkit.org/docs/Install.html). But when running: > cmake .. -DPy_ENABLE_SHARED=1 \ > -DRDK_INSTALL_INTREE=ON \ > -DRDK_INSTALL_STATIC_LIBS=OFF \ > -DRDK_BUILD_CPP_TESTS=ON \ > > -DPYTHON_NUMPY_INCLUDE_PATH="$CONDA_PREFIX/lib/python3.7/site-packages/numpy/core/include" > > \ > -DBOOST_ROOT="$CONDA_PREFIX" > I'm getting: > ''' > -- Catch not found in > /home/<Username>/programs/rdkit-master/External/catch/catch > Downloading https://github.com/catchorg/Catch2/archive/v2.1.2.tar.gz... > % Total % Received % Xferd Average Speed Time Time Time > Current > Dload Upload Total Spent Left > Speed > 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- > 0 > curl: (35) error:1408F10B:SSL routines:ssl3_get_record:wrong version > number > CMake Error at Code/cmake/Modules/RDKitUtils.cmake:218 (MESSAGE): > The md5 checksum for > /home/<Username>/programs/rdkit-master/External/catch/master.tar.gz is > incorrect; expected: 4c5740d7446d9b4e3735dcff0951aaca, found: > d41d8cd98f00b204e9800998ecf8427e > Call Stack (most recent call first): > External/catch/CMakeLists.txt:16 (downloadAndCheckMD5) > > > -- Configuring incomplete, errors occurred! > ''' > I thought maybe the script could not access github, but dowloading the > tar.gz and putting it in /rdkit-master/External/catch/catch did not > help. Also, a curl on github shows no problems. > > Has anyone experienced these problems before? > Is there any workaround? > > Thanks a lot, > Jasmin > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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