martin-g
commented
1 year ago I am facing a similar error on Linux ARM64:
wget https://github.com/openbabel/openbabel/releases/download/openbabel-3-1-1/openbabel-3.1.1-source.tar.bz2
tar jxvf openbabel-3.1.1-source.tar.bz2
cd openbabel-3.1.1-source
mkdir build && cd build
cmake ..
make -j
export OPEN_BABEL_HOME="/home/biocbuild/openbabel-3.1.1"
cmake --install . --prefix $OPEN_BABEL_HOME
export OPENBABEL_LIBS="$OPEN_BABEL_HOME/lib"
export OPENBABEL_CFLAGS="-I$OPEN_BABEL_HOME/include/openbabel3 -L$OPENBABEL_LIBS"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OPENBABEL_LIBS
R CMD INSTALL ChemmineOBError:
* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 OPENBABEL... yes
checking for OPENBABEL... yes
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
make: Nothing to be done for 'all'.
installing to /home/biocbuild/R/R-4.3.0/site-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 '/home/biocbuild/R/R-4.3.0/site-library/00LOCK-ChemmineOB/00new/ChemmineOB/libs/ChemmineOB.so':
/home/biocbuild/R/R-4.3.0/site-library/00LOCK-ChemmineOB/00new/ChemmineOB/libs/ChemmineOB.so: undefined symbol: _ZTIN9OpenBabel6OBBaseE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/R/R-4.3.0/site-library/ChemmineOB’
khoran
Hi:
When I tried to install ChemmineOB on my institutional Mac (no root access), I find I am unable to properly install Here is the code i used in R to install, I use brew-installed openbabel 3.1.1 located at a custom location.
BiocManager::install(pkgs = "ChemmineOB",INSTALL_opts = '--no-lock', configure.args = '--with-openbabel-include=/Users/xx/anaconda3/pkgs/openbabel-3.1.1-py310he467037_4/include/openbabel3 --with-openbabel-lib=/Users/xx/anaconda3/pkgs/openbabel-3.1.1-py310he467037_4/lib/openbabel/3.1.0')Here is the error codeI don't know what does it means to say the symbol not found in flat namespace. And here is the R version I used: