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I am trying to install RDKit on an Ubuntu 16.04.6 LTS Virtual Machine.

Reading the installation guide, I used the following commands:

sudo apt-get -y install python-rdkit librdkit1 rdkit-data

sudo wget https://github.com/rdkit/rdkit/archive/Release_2019_09_3.tar.gz

tar xvzf Release_2019_09_3.tar.gz
rm -f xvzf Release_2019_09_3.tar.gz


cd  rdkit-Release_2019_09_3
mkdir build
cd build
sudo cmake .. -DPYTHON_EXECUTABLE=python3

But I am getting the message

-- Configuring incomplete, errors occurred!
See also "/home/vagrant/rdkit-Release_2019_09_3/build/CMakeFiles/CMakeOutput.log".
See also "/home/vagrant/rdkit-Release_2019_09_3/build/CMakeFiles/CMakeError.log".

checking the CMakeError.log file, I see:

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/vagrant/rdkit-Release_2019_09_3/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_7b6d6/fast"
/usr/bin/make -f CMakeFiles/cmTC_7b6d6.dir/build.make CMakeFiles/cmTC_7b6d6.dir/build
make[1]: Entering directory '/home/vagrant/rdkit-Release_2019_09_3/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_7b6d6.dir/CheckFunctionExists.c.o
/usr/bin/cc    -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_7b6d6.dir/CheckFunctionExists.c.o   -c /usr/share/cmake-3.5/Modules/CheckFunctionExists.c
Linking C executable cmTC_7b6d6
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_7b6d6.dir/link.txt --verbose=1
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTC_7b6d6.dir/CheckFunctionExists.c.o  -o cmTC_7b6d6 -rdynamic -lpthreads 
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_7b6d6.dir/build.make:97: recipe for target 'cmTC_7b6d6' failed
make[1]: *** [cmTC_7b6d6] Error 1
make[1]: Leaving directory '/home/vagrant/rdkit-Release_2019_09_3/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_7b6d6/fast' failed
make: *** [cmTC_7b6d6/fast] Error 2

What should I do to correctly install RDKit on python3? I do not use conda on this VM.

user2182857
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    Impossible to reproduce your errors. "Any Linux OS" can build rdkit https://www.dropbox.com/s/ys4ovl2xz1wieg3/RDKIT_cmake-configuration.txt?dl=0 ... Note 1: Some applications will fail in a virtual machine. ( My tests were done with four different OS : All installed to hard disk.) .. .... Note 2: Do not use sudo for the commands wget, cmake. 'sudo' is for administrative tasks only ! – Knud Larsen Mar 07 '20 at 11:20
  • Thank you very much for taking the time to try. Do you have any ideas on how I should proceed? – user2182857 Mar 07 '20 at 18:30
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    If not caused by the "Virtual Machine", it just looks like a corrupt OS. I tested with PCLinuxOS-2020, Ubuntu 18.04.4 and two different Ubuntu 16.04.6 : No errors. – Knud Larsen Mar 07 '20 at 22:14

0 Answers0