Rdkit: custom installation prefix

Created on 14 Dec 2015 · 5Comments · Source: rdkit/rdkit

I'm trying to install rdkit into non default prefix, but i can't figure how. i have my custom prefix in /s/ls2/users/npryanichnikov/opt/ (this is centos 5 cluster).

Here is my ENV variables:

echo $RDBASE
/s/ls2/users/npryanichnikov/opt/
echo $PATH
/s/ls2/users/npryanichnikov/opt/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin
echo $LD_LIBRARY_PATH
/s/ls2/users/npryanichnikov/opt//lib:/s/ls2/users/npryanichnikov/opt/lib:/s/ls2/users/npryanichnikov/opt/lib64/R/lib:
echo $PYTHONPATH
/s/ls2/users/npryanichnikov/opt/:/s/ls2/users/npryanichnikov/opt/lib/python3.4/site-packages

Here is my cmake options:

cmake .. -DBOOST_ROOT=/s/ls2/users/npryanichnikov/opt/ \
-DPYTHON_LIBRARY=/s/ls2/users/npryanichnikov/opt/lib/python3.4/config-3.4m/libpython3.4m.a \ 
-DPYTHON_INCLUDE_PATH=/s/ls2/users/npryanichnikov/opt/include/python3.4m/ \ 
-DPYTHON_INCLUDE_DIR=/s/ls2/users/npryanichnikov/opt/include/python3.4m/ \ 
-DPYTHON_EXECUTABLE=/s/ls2/users/npryanichnikov/opt/bin/python3.4

I also tried to set CMAKE_INSTALL_PREFIX:PATH option:

cmake .. 
-DCMAKE_INSTALL_PREFIX:PATH=/s/ls2/users/npryanichnikov/opt/ \
-DBOOST_ROOT=/s/ls2/users/npryanichnikov/opt/ \
-DPYTHON_LIBRARY=/s/ls2/users/npryanichnikov/opt/lib/python3.4/config-3.4m/libpython3.4m.a \ 
-DPYTHON_INCLUDE_PATH=/s/ls2/users/npryanichnikov/opt/include/python3.4m/ \ 
-DPYTHON_INCLUDE_DIR=/s/ls2/users/npryanichnikov/opt/include/python3.4m/ \ 
-DPYTHON_EXECUTABLE=/s/ls2/users/npryanichnikov/opt/bin/python3.4

make && make install is ok

But when i do find /s/ls2/users/npryanichnikov/opt/ -name 'rdBase.so' it returns nothing.
What i'm doing wrong?

Source

lpenguin

Most helpful comment

Here is a concrete example that may help:

#PATH TO RDKIT
RDKIT=/Users/brian/devel/rdkit
#install location
INSTALL=`pwd`/rdkit_build

cmake -DRDK_INSTALL_INTREE=OFF \
           -DCMAKE_INSTALL_PREFIX=$INSTALL \
            $RDKIT

bp-kelley on 1 Feb 2016

👍3

All 5 comments

When you do the make install it normally tells you where it's installing the libraries to. Do those end up going to the appropriate place?

Regardless you might try: DESTDIR=/s/ls2/users/npryanichnikov/opt make install

greglandrum on 14 Dec 2015

In addition, please also try using both -DRDK_INSTALL_INTREE=OFF and -DCMAKE_INSTALL_PREFIX=...

rvianello on 14 Dec 2015

👍1

Here is a concrete example that may help:

#PATH TO RDKIT
RDKIT=/Users/brian/devel/rdkit
#install location
INSTALL=`pwd`/rdkit_build

cmake -DRDK_INSTALL_INTREE=OFF \
           -DCMAKE_INSTALL_PREFIX=$INSTALL \
            $RDKIT

bp-kelley on 1 Feb 2016

👍3

@lpenguin did any of these suggestions help?

bp-kelley on 14 Feb 2016

This would be helpful in the docs.