ChemmineOB install trouble

[kenlo1]

Hi all,

I am having some issues installing ChemmineOB on CentOS 7.

Basically I don't have root access and have installed openbabel in a custom directory using cmake flags -DCMAKE_INSTALL_PREFIX and -DEIGEN3_INCLUDE_DIR

Since I am using custom paths, I used this to install ChemmineOB. R CMD INSTALL --configure-args='--with-openbabel-include=/nfs/peptide/software/openbabel/include/openbabel3 --with-openbabel-lib=/nfs/peptide/software/openbabel/lib' ./ChemmineOB_1.28.4.tar.gz

Here is what the error message says:

• installing to library ‘/nfs/peptide/home/lok2/bin/R-3.6.3/library’
• installing source package ‘ChemmineOB’ ... using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E configure: creating ./config.status config.status: creating src/Makevars libs g++ -std=gnu++11 -I"/home/lok2/bin/R-3.6.3/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I/nfs/peptide/software/openbabel/include/openbabel3 -I"/nfs/peptide/home/lok2/bin/R-3.6.3/library/BH/include" -I"/nfs/peptide/home/lok2/bin/R-3.6.3/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -c ChemmineOB.cpp -o ChemmineOB.o In file included from ChemmineOB.cpp:1624:0: /nfs/peptide/software/openbabel/include/openbabel3/openbabel/math/align.h:26:22: fatal error: Eigen/Core: No such file or directory

  include <Eigen/Core>

                ^

  compilation terminated. make: *** [ChemmineOB.o] Error 1 ERROR: compilation failed for package ‘ChemmineOB’

• removing ‘/nfs/peptide/home/lok2/bin/R-3.6.3/library/ChemmineOB’

It seems like it is not finding Eigen, then I noticed that -I/usr/inlcude/eigen3, which is not where I have eigen3. Is there an install flag that can change this? My eigen3 is in /usr/local/include/eigen3.

Any help would be awesome.

Best,

Ken

[khoran]

You can add additional directories by setting some environment variables for the compiler. One way to do this is by creating the file ~/.R/Makevars and setting CXXFLAGS= -I /usr/local/include/eigen3 . If that doesn't modify the compile command, try using PKG_CXXFLAGS.

[kenlo1]

Thanks! I was able to get past that first error. Now my error message reads as follows:

R CMD INSTALL --configure-args='--with-openbabel-include=/nfs/peptide/software/openbabel/include/openbabel3 --with-openbabel-lib=/nfs/peptide/software/openbabel/lib' ./ChemmineOB_1.28.4.tar.gz

• installing to library ‘/nfs/peptide/home/lok2/bin/R-3.6.3/library’
• installing source package ‘ChemmineOB’ ... using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for gcc... gcc -std=gnu99 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E configure: creating ./config.status config.status: creating src/Makevars libs g++ -std=gnu++11 -I"/home/lok2/bin/R-3.6.3/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I/nfs/peptide/software/openbabel/include/openbabel3 -I"/nfs/peptide/home/lok2/bin/R-3.6.3/library/BH/include" -I"/nfs/peptide/home/lok2/bin/R-3.6.3/library/Rcpp/include" -I/usr/local/include -fpic -I/usr/local/include/eigen-3.2.10 -c ChemmineOB.cpp -o ChemmineOB.o g++ -std=gnu++11 -I"/home/lok2/bin/R-3.6.3/include" -DNDEBUG -I/usr/include/openbabel3 -I/usr/include/eigen3 -DUSE_BOOST -DHAVE_EIGEN -I/usr/local/Cellar/eigen/3.3.8_1/include/eigen3 -I/usr/local/Cellar/open-babel/3.1.1_1/include/openbabel3 -I/nfs/peptide/software/openbabel/include/openbabel3 -I"/nfs/peptide/home/lok2/bin/R-3.6.3/library/BH/include" -I"/nfs/peptide/home/lok2/bin/R-3.6.3/library/Rcpp/include" -I/usr/local/include -fpic -I/usr/local/include/eigen-3.2.10 -c canonical.cpp -o canonical.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o ChemmineOB.so ChemmineOB.o canonical.o -L/usr/local/Cellar/open-babel/3.1.1_1/lib -L/nfs/peptide/software/openbabel/lib -lopenbabel installing to /nfs/peptide/home/lok2/bin/R-3.6.3/library/00LOCK-ChemmineOB/00new/ChemmineOB/libs R inst byte-compile and prepare package for lazy loading in method for ‘copyToR’ with signature ‘"_p_std::char_traits<(char)>"’: no definition for class “_p_std::char_traits<(char)>” in method for ‘copyToR’ with signature ‘"_p_std::pair<(unsigned int,unsigned int)>"’: no definition for class “_p_std::pair<(unsigned int,unsigned int)>” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::CharPtrLess"’: no definition for class “_p_OpenBabel::CharPtrLess” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::FptIndexHeader"’: no definition for class “_p_OpenBabel::FptIndexHeader” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereo"’: no definition for class “_p_OpenBabel::OBStereo” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBStereoUnit"’: no definition for class “_p_OpenBabel::OBStereoUnit” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::LineSearchType"’: no definition for class “_p_OpenBabel::LineSearchType” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBTetrahedralConfig"’: no definition for class “_p_OpenBabel::OBTetrahedralConfig” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBCisTransConfig"’: no definition for class “_p_OpenBabel::OBCisTransConfig” in method for ‘copyToR’ with signature ‘"_p_OpenBabel::OBSquarePlanarConfig"’: no definition for class “_p_OpenBabel::OBSquarePlanarConfig” help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘ChemmineOB’: .onLoad failed in loadNamespace() for 'ChemmineOB', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/nfs/peptide/home/lok2/bin/R-3.6.3/library/00LOCK-ChemmineOB/00new/ChemmineOB/libs/ChemmineOB.so': libopenbabel.so.7: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failed
• removing ‘/nfs/peptide/home/lok2/bin/R-3.6.3/library/ChemmineOB’

[khoran]

Set these two environment variables (see INSTALL file):

OPEN_BABEL_INCDIR = path to header files
OPEN_BABEL_LIBDIR = path to shared (.so) library file

[kenlo1]

Does that mean the --configure-args switch does not achieve the same thing?

[kenlo1]

I noticed this in the error message:

libopenbabel.so.7: cannot open shared object file: No such file or directory

I'm not sure if this is relevant, but in the directory specified with the '--with-openbabel-lib' flag, I am seeing libopenbabel.so.7, so that is a little curious.

[khoran]

--configure-args and --with-openbabel-lib are for compile time. But R still needs to know where the library is at runtime. So anytime you want to use the ChemmineOB package, the OPEN_BABEL_* environment variables need to be defined. This is easily accomplished by putting them in your .bashrc file or whatever config file your shell uses.

[kenlo1]

I added to environment variables as per your suggestion. This is what I see when I check the environment variables.

echo $OPEN_BABEL_INCDIR /nfs/peptide/software/openbabel/include/openbabel3

echo $OPEN_BABEL_LIBDIR /nfs/peptide/software/openbabel/lib

I tried installing again with R CMD INSTALL --configure-args='--with-openbabel-include=/nfs/peptide/software/openbabel/include/openbabel3 --with-openbabel-lib=/nfs/peptide/software/openbabel/lib' ./ChemmineOB_1.28.4.tar.gz

but I still get the same error message.

[kenlo1]

Hi Kevin,

I figured out what was wrong. It turns out that my LD_LIBRARY_PATH environment variable wasn't set correctly. I found some additional information from open-babel (https://open-babel.readthedocs.io/en/latest/Installation/install.html#environment-variables). Once I changed it to the correct location, ChemmineOB installed correctly. Thanks for all your help!

Best,

Ken