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Re: [Rdkit-discuss] Problem with Installation Conda Miniconda Azure Linux
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From: Paolo T. <pao...@gm...> - 2019-07-09 08:04:02
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Hi Jasmin, as it looks like you are attempting to build RDKit in a conda environment, you should be building against the Boost version supplied by conda, while this line Boost include path: /usr/include shows that cmake has picked up the system-installed Boost from libboost-all-dev.This Boost is most likely built against the system Python, which is probably different and incompatible with python3.6 as supplied from conda. If you do a conda install boost in the conda environment where you are building the RDKit you should see that cmake picks up the conda Boost, and the problem should then disappear. Cheers, p. On 07/09/19 08:37, Jasmin wrote: > Hello! > > My Problem still persists. > > I am trying to build from source right now. Now I am having problems > with the boost-libraries. > The output says: > " > CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 > (message): > No header defined for python3; skipping header check > " > and later: > " > CMake Error at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1947 > (message): > Unable to find the requested Boost libraries. > > Boost version: 1.62.0 > > Boost include path: /usr/include > > Could not find the following Boost libraries: > > boost_python > > No Boost libraries were found. You may need to set BOOST_LIBRARYDIR > to the > directory containing Boost libraries or BOOST_ROOT to the location of > Boost. > " > and the same thing for boost_system. > I installed libboost-all-dev. I think I found the boost-libraries in > /usr/lib/x86_64-linux-gnu/ . Does > " > cmake .. -DPy_ENABLE_SHARED=1 -DRDK_INSTALL_INTREE=ON > -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_CPP_TESTS=ON > -DPYTHON_NUMPY_INCLUDE_PATH="$CONDA_PREFIX/lib/python3.6/site-packages/numpy/core/include" > -DBOOST_ROOT="$CONDA_PREFIX" > " > assume the libraries are in $CONDA_PREFIX? Doe I need move/ copy > something here? > > Thank you for your time. Any help is appreciated! > Best, > Jasmin > > > Am 03.07.2019 10:38 schrieb Jasmin: >> Hi Greg, >> >> no, I just replaced my real username. >> >> Best, >> Jasmin >> >> Am 03.07.2019 08:55 schrieb Greg Landrum: >>> 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 <zwe...@po...> 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 [1] >>>> >>>> https://conda.anaconda.org/conda-forge/noarch [2] >>>> >>>> https://repo.anaconda.com/pkgs/main/linux-64 [3] >>>> >>>> https://repo.anaconda.com/pkgs/main/noarch [4] >>>> >>>> https://repo.anaconda.com/pkgs/r/linux-64 [5] >>>> https://repo.anaconda.com/pkgs/r/noarch >>>> [6] >>>> 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 [7]). 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. [8].. >>>> % 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 >>>> Rdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss [9] >>> >>> >>> Links: >>> ------ >>> [1] https://conda.anaconda.org/conda-forge/linux-64 >>> [2] https://conda.anaconda.org/conda-forge/noarch >>> [3] https://repo.anaconda.com/pkgs/main/linux-64 >>> [4] https://repo.anaconda.com/pkgs/main/noarch >>> [5] https://repo.anaconda.com/pkgs/r/linux-64 >>> [6] https://repo.anaconda.com/pkgs/r/noarch >>> [7] https://www.rdkit.org/docs/Install.html >>> [8] https://github.com/catchorg/Catch2/archive/v2.1.2.tar.gz. >>> [9] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdk...@li... >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss |
