Hi Dan
Yes, they are in the $RDBASE/lib directory and LD_LIBRARY_PATH is set to
point to this as well. That was also my first guess that LD_LIBRARY_PATH
was not set correctly.
mkdir -p build && cd build
export RDBASE=/home/termo/HFlabs/rdkit
export
LD_LIBRARY_PATH=$RDBASE/lib:/home/termo/miniconda3/envs/rdkit-dev/include
echo ""
echo "LD_LIBRARY_PATH:" $LD_LIBRARY_PATH
ls $RDBASE/lib/libRDKitmaeparser.so.1
echo ""
cmake -DBOOST_ROOT="/home/termo/miniconda3/envs/rdkit-dev" ..
make VERBOSE=1
cd ..
gives this attached output (the same as before, but now also showing the
file exists and LD_LIBRARY_PATH)
On Fri, Jan 3, 2020 at 12:36 AM Dan Nealschneider <
dan.nealschnei...@schrodinger.com> wrote:
> Looks like you're missing libRDKitmaeparser.so.1,
> libRDKitcoordgen.so.1, libRDKitRingDecomposerLib.so.1,
> and libRDKitDataStructs.so.1. Are they in a directory pointed to by your
> LD_LIBRARY_PATH?
>
> *dan nealschneider* | senior developer
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>
>
> On Thu, Jan 2, 2020 at 1:25 PM Rasmus "Termo" Lundsgaard <
> termope...@gmail.com> wrote:
>
>> I have compiled rdkit as suggested in the docs by using a conda
>> environment for c++ and boost.
>>
>> I would like to move from python to cpp with my RDkit work, and I thought
>> to start with the C++ exaples in the Docs/Book, but I'm having some
>> problems getting the minimal c++ examples to link with the current CMake
>> files there.
>>
>> Attached is the output from the make command where I have only set it to
>> make "example1.cpp" in CMakeLists.txt
>>
>> I guess the problem is the "/bin/ld: warning: libRDKitmaeparser.so.1,
>> needed by /home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so, not found"
>>
>> I have set RDBASE and LD_LIBRARY_PATH, and as far as I can see with the
>> "-Wl,-rpath,/home/termo/HFlabs/rdkit/lib" part in the linking command it
>> should find the needed .so file (that is there).
>>
>> Any idea why it fails to find the .so files?
>>
>> /Rasmus
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
LD_LIBRARY_PATH:
/home/termo/HFlabs/rdkit/lib:/home/termo/miniconda3/envs/rdkit-dev/include
/home/termo/HFlabs/rdkit/lib/libRDKitmaeparser.so.1
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler:
/home/termo/miniconda3/envs/rdkit-dev/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler:
/home/termo/miniconda3/envs/rdkit-dev/bin/x86_64-conda_cos6-linux-gnu-cc --
works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler:
/home/termo/miniconda3/envs/rdkit-dev/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler:
/home/termo/miniconda3/envs/rdkit-dev/bin/x86_64-conda_cos6-linux-gnu-c++ --
works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Boost: /home/termo/miniconda3/envs/rdkit-dev/include (found version
"1.67.0") found components: iostreams filesystem system regex
Looking for RDKit component ChemReactions
MyRDKit_LIBRARY_ChemReactions :
/home/termo/HFlabs/rdkit/lib/libRDKitChemReactions.so
Looking for RDKit component FileParsers
MyRDKit_LIBRARY_FileParsers :
/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so
Looking for RDKit component SmilesParse
MyRDKit_LIBRARY_SmilesParse :
/home/termo/HFlabs/rdkit/lib/libRDKitSmilesParse.so
Looking for RDKit component Depictor
MyRDKit_LIBRARY_Depictor : /home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so
Looking for RDKit component RDGeometryLib
MyRDKit_LIBRARY_RDGeometryLib :
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so
Looking for RDKit component RDGeneral
MyRDKit_LIBRARY_RDGeneral : /home/termo/HFlabs/rdkit/lib/libRDKitRDGeneral.so
Looking for RDKit component SubstructMatch
MyRDKit_LIBRARY_SubstructMatch :
/home/termo/HFlabs/rdkit/lib/libRDKitSubstructMatch.so
Looking for RDKit component Subgraphs
MyRDKit_LIBRARY_Subgraphs : /home/termo/HFlabs/rdkit/lib/libRDKitSubgraphs.so
Looking for RDKit component MolDraw2D
MyRDKit_LIBRARY_MolDraw2D : /home/termo/HFlabs/rdkit/lib/libRDKitMolDraw2D.so
Looking for RDKit component GraphMol
MyRDKit_LIBRARY_GraphMol : /home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so
Looking for RDKit component DistGeometry
MyRDKit_LIBRARY_DistGeometry :
/home/termo/HFlabs/rdkit/lib/libRDKitDistGeometry.so
Looking for RDKit component DistGeomHelpers
MyRDKit_LIBRARY_DistGeomHelpers :
/home/termo/HFlabs/rdkit/lib/libRDKitDistGeomHelpers.so
Looking for RDKit component MolAlign
MyRDKit_LIBRARY_MolAlign : /home/termo/HFlabs/rdkit/lib/libRDKitMolAlign.so
Looking for RDKit component Optimizer
MyRDKit_LIBRARY_Optimizer : /home/termo/HFlabs/rdkit/lib/libRDKitOptimizer.so
Looking for RDKit component ForceField
MyRDKit_LIBRARY_ForceField : /home/termo/HFlabs/rdkit/lib/libRDKitForceField.so
Looking for RDKit component ForceFieldHelpers
MyRDKit_LIBRARY_ForceFieldHelpers :
/home/termo/HFlabs/rdkit/lib/libRDKitForceFieldHelpers.so
Looking for RDKit component Alignment
MyRDKit_LIBRARY_Alignment : /home/termo/HFlabs/rdkit/lib/libRDKitAlignment.so
Looking for RDKit component ForceField
MyRDKit_LIBRARY_ForceField : /home/termo/HFlabs/rdkit/lib/libRDKitForceField.so
Looking for RDKit component MolTransforms
MyRDKit_LIBRARY_MolTransforms :
/home/termo/HFlabs/rdkit/lib/libRDKitMolTransforms.so
Looking for RDKit component EigenSolvers
MyRDKit_LIBRARY_EigenSolvers :
/home/termo/HFlabs/rdkit/lib/libRDKitEigenSolvers.so
RDKIT_INCLUDE_DIR : /home/termo/HFlabs/rdkit/Code
RDKIT_LIBRARIES :
/home/termo/HFlabs/rdkit/lib/libRDKitChemReactions.so;/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so;/home/termo/HFlabs/rdkit/lib/libRDKitSmilesParse.so;/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so;/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so;/home/termo/HFlabs/rdkit/lib/libRDKitRDGeneral.so;/home/termo/HFlabs/rdkit/lib/libRDKitSubstructMatch.so;/home/termo/HFlabs/rdkit/lib/libRDKitSubgraphs.so;/home/termo/HFlabs/rdkit/lib/libRDKitMolDraw2D.so;/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so;/home/termo/HFlabs/rdkit/lib/libRDKitDistGeometry.so;/home/termo/HFlabs/rdkit/lib/libRDKitDistGeomHelpers.so;/home/termo/HFlabs/rdkit/lib/libRDKitMolAlign.so;/home/termo/HFlabs/rdkit/lib/libRDKitOptimizer.so;/home/termo/HFlabs/rdkit/lib/libRDKitForceField.so;/home/termo/HFlabs/rdkit/lib/libRDKitForceFieldHelpers.so;/home/termo/HFlabs/rdkit/lib/libRDKitAlignment.so;/home/termo/HFlabs/rdkit/lib/libRDKitForceField.so;/home/termo/HFlabs/rdkit/lib/libRDKitMolTransforms.so;/home/termo/HFlabs/rdkit/lib/libRDKitEigenSolvers.so
RDKIT_FOUND : MyRDKit_FOUND
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to:
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build
/home/termo/miniconda3/envs/rdkit-dev/bin/cmake
-S/home/termo/HFlabs/rdkit/Docs/Book/C++Examples
-B/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build --check-build-system
CMakeFiles/Makefile.cmake 0
/home/termo/miniconda3/envs/rdkit-dev/bin/cmake -E cmake_progress_start
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
'/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build'
make -f CMakeFiles/test.dir/build.make CMakeFiles/test.dir/depend
make[2]: Entering directory
'/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build'
cd /home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build &&
/home/termo/miniconda3/envs/rdkit-dev/bin/cmake -E cmake_depends "Unix
Makefiles" /home/termo/HFlabs/rdkit/Docs/Book/C++Examples
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles/test.dir/DependInfo.cmake
--color=
Dependee
"/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles/test.dir/DependInfo.cmake"
is newer than depender
"/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles/test.dir/depend.internal".
Dependee
"/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles/CMakeDirectoryInformation.cmake"
is newer than depender
"/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build/CMakeFiles/test.dir/depend.internal".
Scanning dependencies of target test
make[2]: Leaving directory
'/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build'
make -f CMakeFiles/test.dir/build.make CMakeFiles/test.dir/build
make[2]: Entering directory
'/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build'
[ 50%] Building CXX object CMakeFiles/test.dir/example1.cpp.o
/home/termo/miniconda3/envs/rdkit-dev/bin/x86_64-conda_cos6-linux-gnu-c++
-I/home/termo/HFlabs/rdkit/Code -fvisibility-inlines-hidden -std=c++17
-fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC
-fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem
/home/termo/miniconda3/envs/rdkit-dev/include -Wall -o
CMakeFiles/test.dir/example1.cpp.o -c
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/example1.cpp
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/example1.cpp: In function 'int
main(int, char**)':
/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/example1.cpp:11:17: warning:
unused variable 'mol1' [-Wunused-variable]
RDKit::ROMol *mol1 = RDKit::SmilesToMol( "Cc1ccccc1" );
^~~~
[100%] Linking CXX executable ../test
/home/termo/miniconda3/envs/rdkit-dev/bin/cmake -E cmake_link_script
CMakeFiles/test.dir/link.txt --verbose=1
/home/termo/miniconda3/envs/rdkit-dev/bin/x86_64-conda_cos6-linux-gnu-c++
-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona
-mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
-ffunction-sections -pipe -isystem
/home/termo/miniconda3/envs/rdkit-dev/include -Wall -Wl,-O2 -Wl,--sort-common
-Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags
-Wl,--gc-sections -Wl,-rpath,/home/termo/miniconda3/envs/rdkit-dev/lib
-Wl,-rpath-link,/home/termo/miniconda3/envs/rdkit-dev/lib
-L/home/termo/miniconda3/envs/rdkit-dev/lib -rdynamic
CMakeFiles/test.dir/example1.cpp.o -o ../test
-Wl,-rpath,/home/termo/HFlabs/rdkit/lib
/home/termo/HFlabs/rdkit/lib/libRDKitChemReactions.so
/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so
/home/termo/HFlabs/rdkit/lib/libRDKitSmilesParse.so
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeneral.so
/home/termo/HFlabs/rdkit/lib/libRDKitSubstructMatch.so
/home/termo/HFlabs/rdkit/lib/libRDKitSubgraphs.so
/home/termo/HFlabs/rdkit/lib/libRDKitMolDraw2D.so
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so
/home/termo/HFlabs/rdkit/lib/libRDKitDistGeometry.so
/home/termo/HFlabs/rdkit/lib/libRDKitDistGeomHelpers.so
/home/termo/HFlabs/rdkit/lib/libRDKitMolAlign.so
/home/termo/HFlabs/rdkit/lib/libRDKitOptimizer.so
/home/termo/HFlabs/rdkit/lib/libRDKitForceField.so
/home/termo/HFlabs/rdkit/lib/libRDKitForceFieldHelpers.so
/home/termo/HFlabs/rdkit/lib/libRDKitAlignment.so
/home/termo/HFlabs/rdkit/lib/libRDKitForceField.so
/home/termo/HFlabs/rdkit/lib/libRDKitMolTransforms.so
/home/termo/HFlabs/rdkit/lib/libRDKitEigenSolvers.so
/home/termo/miniconda3/envs/rdkit-dev/lib/libboost_iostreams.a -lz
/home/termo/HFlabs/rdkit/lib/libRDKitForceFieldHelpers.so
/home/termo/HFlabs/rdkit/lib/libRDKitAlignment.so
/home/termo/HFlabs/rdkit/lib/libRDKitMolTransforms.so
/home/termo/HFlabs/rdkit/lib/libRDKitEigenSolvers.so -lz
/home/termo/miniconda3/envs/rdkit-dev/lib/libboost_regex.a -lpthread
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
warning: libRDKitmaeparser.so.1, needed by
/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so, not found (try using
-rpath or -rpath-link)
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
warning: libRDKitcoordgen.so.1, needed by
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so, not found (try using -rpath
or -rpath-link)
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
warning: libRDKitRingDecomposerLib.so.1, needed by
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so, not found (try using -rpath
or -rpath-link)
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
warning: libRDKitDataStructs.so.1, needed by
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so, not found (try using -rpath
or -rpath-link)
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_getNofURF'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_getNofRC'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_getNodesForURF'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_calculate'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so: undefined reference to
`schrodinger::mae::Block::getIndexedBlock(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::getLength() const'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::getTotalVal() const'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_addUEdge'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_getEdgesForURF'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::getVal(unsigned int) const'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizer::runGenerateCoordinates()'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::operator+=(RDKit::DiscreteValueVect const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizerMolecule::addNewAtom()'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::operator&(RDKit::DiscreteValueVect const&) const'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::operator|(RDKit::DiscreteValueVect const&) const'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`ExplicitBitVect::ExplicitBitVect(ExplicitBitVect const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::initFromText(char const*, unsigned int)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::setVal(unsigned int, unsigned int)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::toString[abi:cxx11]() const'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`ExplicitBitVect::ExplicitBitVect(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizer::initialize(sketcherMinimizerMolecule*)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizer::sketcherMinimizer(float)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizer::~sketcherMinimizer()'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::DiscreteValueVect(RDKit::DiscreteValueVect const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizerMolecule::assignBondsAndNeighbors(std::vector<sketcherMinimizerAtom*,
std::allocator<sketcherMinimizerAtom*> >&, std::vector<sketcherMinimizerBond*,
std::allocator<sketcherMinimizerBond*> >&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_deleteGraph'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizer::setTemplateFileDir(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so: undefined reference to
`schrodinger::mae::Reader::next(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitFileParsers.so: undefined reference to
`schrodinger::mae::Reader::Reader(std::shared_ptr<std::istream>, unsigned long)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`typeinfo for ExplicitBitVect'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`ExplicitBitVect::~ExplicitBitVect()'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_initNewGraph'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::DiscreteValueVect::operator-=(RDKit::DiscreteValueVect const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizerBond::setAbsoluteStereoFromStereoInfo()'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitRDGeometryLib.so: undefined reference to
`RDKit::computeL1Norm(RDKit::DiscreteValueVect const&, RDKit::DiscreteValueVect
const&)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizerMolecule::addNewBond(sketcherMinimizerAtom*,
sketcherMinimizerAtom*)'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitDepictor.so: undefined reference to
`sketcherMinimizerMolecule::sketcherMinimizerMolecule()'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_deleteData'
/home/termo/miniconda3/envs/rdkit-dev/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld:
/home/termo/HFlabs/rdkit/lib/libRDKitGraphMol.so: undefined reference to
`RDL_INVALID_RESULT'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/test.dir/build.make:110: ../test] Error 1
make[2]: Leaving directory
'/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build'
make[1]: *** [CMakeFiles/Makefile2:76: CMakeFiles/test.dir/all] Error 2
make[1]: Leaving directory
'/home/termo/HFlabs/rdkit/Docs/Book/C++Examples/build'
make: *** [Makefile:84: all] Error 2
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