Hi Jasmin,
after you have activated your environment it should be sufficient to run
the command
conda install boost
and then build the RDKit as you were doing previously. cmake should now
pick the conda Boost instead of system Boost.
Cheers,
p.
On 07/09/19 12:14, Jasmin wrote:
Hi Paolo,
yes, you're right. This is probably a stupid question but how do I
built within the anaconda environment?
Given that 'my_env' is a environment I built with "conda create --name
my_env", I thought I can just run "conda activate my_env" but this
does not seem to change anything.
Best,
Jasmin
Am 09.07.2019 10:03 schrieb Paolo Tosco:
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 <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 [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
Rdkit-discuss@lists.sourceforge.net
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
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
