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
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