Unable to build from source on debian 11

[someonetookmyname]

Hi,

I'm having trouble building rdkit on debian 11.

I performed the steps at https://www.rdkit.org/docs/Install.html#building-from-source.
I see the same problems whether I use Release_2021_09_5.tar.gz or download the zip from https://github.com/rdkit/rdkit. My complete steps are shown at the bottom.

I see trouble with ctest:

andrew@debian11d:~/zip/rdkit-master/build$ ctest
Test project /home/andrew/zip/rdkit-master/build
        Start   1: testInchi
  1/205 Test   #1: testInchi ..............................   Passed   23.47 sec
        Start   2: testAvalonLib1
  2/205 Test   #2: testAvalonLib1 .........................   Passed   11.04 sec
        Start   3: pyAvalonTools
  3/205 Test   #3: pyAvalonTools ..........................***Failed    0.03 sec
Traceback (most recent call last):
  File "/home/andrew/zip/rdkit-master/External/AvalonTools/Wrap/testAvalonTools.py", line 6, in <module>
    from rdkit import RDConfig
  File "/home/andrew/zip/rdkit-master/rdkit/__init__.py", line 6, in <module>
    from . import rdBase
ImportError: cannot import name 'rdBase' from partially initialized module 'rdkit' (most likely due to a circular import) (/home/andrew/zip/rdkit-master/rdkit/__init__.py)

I also see trouble after make install (hoping the ctest errors were an artifact):

andrew@debian11d:~$ export RDBASE=/home/andrew/zip/rdkit-master
andrew@debian11d:~$ export PYTHONPATH=$RDBASE
andrew@debian11d:~$ python3
Python 3.9.2 (default, Feb 28 2021, 17:03:44) 
[GCC 10.2.1 20210110] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import Chem
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/andrew/zip/rdkit-master/rdkit/__init__.py", line 6, in <module>
    from . import rdBase
ImportError: libRDKitRDBoost.so.1: cannot open shared object file: No such file or directory
>>> 

No other errors were observed during build.
My build steps (above error grabs came from trying to build with the current zip, while the below steps show use of Release_2021_09_5.tar.gz .. results were the same):

Starting with fresh debian 11 install using debian-live-11.2.0-amd64-gnome.iso

sudo apt update
sudo apt upgrade
sudo apt install cmake
sudo apt install libboost-all-dev
sudo apt install clang
sudo apt install python3-dev
sudo apt install python3-pip
sudo apt install libsqlite3-dev
sudo apt install libcairo2-dev
sudo apt install wget
sudo apt install libeigen3-dev
pip install numpy
(restart to have /home/andrew/.local/bin added to PATH)
cd ~/
wget https://github.com/rdkit/rdkit/archive/Release_2021_09_5.tar.gz
gunzip Release_2021_09_5.tar.gz
tar -xvf Release_2021_09_5.tar
export RDBASE=/home/andrew/rdkit-Release_2021_09_5
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
cd $RDBASE
mkdir build
cd build
cmake -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_CAIRO_SUPPORT=ON ..
make
export CTEST_OUTPUT_ON_FAILURE=1
ctest
sudo make install

Any guidance would be greatly appreciated. Please let me know if any other information would be useful.

Thank you.

Andrew

[greglandrum]

You either have to do make install before you run the tests (so that the DLLs are copied to the appropriate place) or include $RDBASE/build/lib in LD_LIBRARY_PATH

[someonetookmyname]

Thanks for the quick response, Greg. pythonTestDirChem had a few problems, but otherwise all tests passed using your suggestions.

Just for completeness, the (unrelated) error I saw/mentioned after "make install" in my original post was from a reboot where I had lost my LD_LIBRARY_PATH setting .. once I re-set it, that error went away.

Thanks again!