Hello,
I tried to install openbabel-2.3.1 and got problem when I was compiling it. The
cmake process went out successfully but there was problem after "make"
installation.
Please see attached two files "cmake.out" and "make.out".
If you need any more information, please let me know. Thank you! I look forward
to hearing from you.
Best,
Hongshan
-- The C compiler identification is GNU 4.1.0
-- The CXX compiler identification is GNU 4.1.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Using included inchi library.
-- Could NOT find LibXml2 (missing: LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
CMake Warning at CMakeLists.txt:152 (message):
libxml2 not found - disabling CML support!
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Could NOT find wxWidgets (missing: wxWidgets_FOUND)
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Could NOT find Eigen2 (missing: EIGEN2_INCLUDE_DIR EIGEN2_VERSION_OK)
(Required is at least version "2.0.0")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.20")
-- checking for module 'cairo'
-- package 'cairo' not found
-- Could NOT find Cairo. PNG output will NOT be supported.
-- Looking for getopt
-- Looking for getopt - found
-- Attempting to build the GUI
-- wxWidgets not found => GUI will not be built
-- Found PythonInterp: /usr/bin/python (found version "2.4.2")
-- Configuring done
-- Generating done
-- Build files have been written to: /exports2/lai/Tools/ob-build
Scanning dependencies of target openbabel
[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
[ 0%] Building CXX object src/CMakeFiles/openbabel.dir/atom.o
[ 1%] Building CXX object src/CMakeFiles/openbabel.dir/base.o
[ 1%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.o
[ 1%] Building CXX object src/CMakeFiles/openbabel.dir/bond.o
[ 2%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.o
[ 2%] Building CXX object src/CMakeFiles/openbabel.dir/builder.o
[ 2%] Building CXX object src/CMakeFiles/openbabel.dir/canon.o
[ 3%] Building CXX object src/CMakeFiles/openbabel.dir/chains.o
[ 3%] Building CXX object src/CMakeFiles/openbabel.dir/chargemodel.o
[ 3%] Building CXX object src/CMakeFiles/openbabel.dir/chiral.o
[ 4%] Building CXX object src/CMakeFiles/openbabel.dir/data.o
[ 4%] Building CXX object src/CMakeFiles/openbabel.dir/descriptor.o
[ 4%] Building CXX object src/CMakeFiles/openbabel.dir/fingerprint.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/forcefield.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/format.o
[ 5%] Building CXX object src/CMakeFiles/openbabel.dir/generic.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/graphsym.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/grid.o
[ 6%] Building CXX object src/CMakeFiles/openbabel.dir/griddata.o
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/isomorphism.o
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/kekulize.o
[ 7%] Building CXX object src/CMakeFiles/openbabel.dir/locale.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/matrix.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/mcdlutil.o
[ 8%] Building CXX object src/CMakeFiles/openbabel.dir/molchrg.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/mol.o
[ 9%] Building CXX object src/CMakeFiles/openbabel.dir/obconversion.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/oberror.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obiter.o
[ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obutil.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/op.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/parsmart.o
[ 11%] Building CXX object src/CMakeFiles/openbabel.dir/patty.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/plugin.o
[ 12%] Building CXX object src/CMakeFiles/openbabel.dir/pointgroup.o
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/query.o
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/rand.o
[ 13%] Building CXX object src/CMakeFiles/openbabel.dir/residue.o
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/ring.o
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/rotamer.o
[ 14%] Building CXX object src/CMakeFiles/openbabel.dir/rotor.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/spectrophore.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/tokenst.o
[ 15%] Building CXX object src/CMakeFiles/openbabel.dir/transform.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/typer.o
[ 16%] Building CXX object src/CMakeFiles/openbabel.dir/obmolecformat.o
/exports2/lai/Tools/openbabel-2.3.1/src/obmolecformat.cpp: In static member function âstatic bool OpenBabel::OBMoleculeFormat::ReadNameIndex(std::tr1::unordered_map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int, std::tr1::hash<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int> >, false>&, const std::string&, OpenBabel::OBFormat*)â:
/exports2/lai/Tools/openbabel-2.3.1/src/obmolecformat.cpp:516: error: no matching function for call to âInternal::hashtable_iterator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int>, false, false>::hashtable_iterator()â
/usr/include/c++/4.1.0/tr1/hashtable:309: note: candidates are: Internal::hashtable_iterator<Value, constant_iterators, cache>::hashtable_iterator(Internal::hash_node<Value, cache>**) [with Value = std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int>, bool constant_iterators = false, bool cache = false]
/usr/include/c++/4.1.0/tr1/hashtable:305: note: Internal::hashtable_iterator<Value, constant_iterators, cache>::hashtable_iterator(Internal::hash_node<Value, cache>*, Internal::hash_node<Value, cache>**) [with Value = std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int>, bool constant_iterators = false, bool cache = false]
/usr/include/c++/4.1.0/tr1/hashtable:295: note: Internal::hashtable_iterator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int>, false, false>::hashtable_iterator(const Internal::hashtable_iterator<std::pair<const std::basic_string<char, std::char_traits<char>, std::allocator<char> >, unsigned int>, false, false>&)
make[2]: *** [src/CMakeFiles/openbabel.dir/obmolecformat.o] Error 1
make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
make: *** [all] Error 2
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