You can install the Python packages anywhere. The "best" place is not
to define the PYTHON_PREFIX at all (-DPYTHON_PREFIX=), and just use
the one that your version of Python defines. You shouldn't be using
this mechanism to place the files in a particular site-packages folder
(rather it is for a local install).

If you don't use the default location, then you need to tell Python
where you installed the bindings, using the Python environment
variable PYTHON_PATH=wherever.

If "babel --version" isn't right, then you need to prepend your
install directory to your PATH, just like any software. "which babel"
tells you the location of the babel executable on the PATH.

BTW, rather than using "unix find", try running "sudo updatedb" and
then "locate obabel" or so.

- Noel

On 12 October 2011 04:09, Chris Mayne <cgma...@gmail.com> wrote:
> OK, I scrapped my Fink install and reinstalled a number of dependencies.
> "Cmake" and "make" operations seem to go well.  "sudo make install" appears
> to go well until it tries to write the python bindings.  "make tests" passes
> all but 58, 59, 60 -- the python bindings tests.
>
> I ran a unix find to look for directories named "site-packages" for python.
> Some of them probably came from my trials at setting -DPYTHON_PREFIX
> incorrectly.
>
> /Applications/Komodo
> Edit.app/Contents/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages
> /Applications/MacPyMOL.app/pymol/ext/lib/python2.5/site-packages
> /Library/Python/2.3/site-packages
> /Library/Python/2.5/site-packages
> /Library/Python/2.6/site-packages
> /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages
> /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python2.6/site-packages
> /System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib/python2.6/site-packages
> /usr/local/bin/lib/python2.6/site-packages
>
> remaining questions
> 1) from the various "site-packages" directories that exist, is there any way
> to know which one is the "best" one?
>
> 2) how do i correctly use the -DPYTHON_PREFIX flag to tell openbabel which
> one is the correct one?  (for instance, if i give it
> /Library/Python/2.6/site-packages, it appears to make subdirectories
> /lib/python2.6/site-packages instead of just copying to the given path)
>
> 3) after intalling, if i type "babel --version" it's still showing the
> version information from my previous install.  How do I know if this new
> install has replaced it properly?
>
>
> Thanks,
> Chris
>
>
>
>
>
> On Tue, Oct 11, 2011 at 2:36 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> Your command-line would have worked perfectly on a Linux system.
>>
>> After googling, it seems that you are using Fink, and and for some
>> reason you have the 32-bit version. Since the compiler is compiling in
>> 64-bit this does not make your Mac happy. I don't use a Mac, but you
>> could (a) install Fink 64-bit (this may require some care), or (b)
>> just remove the Fink folders from all environment variables (I don't
>> know which have been affected by Fink), delete CMakeCache.txt and
>> rerun the build.
>>
>> - Noel
>>
>> On 11 October 2011 20:21, Chris Mayne <cgma...@gmail.com> wrote:
>> > My initial aim was to install the dev code in the hopes of fixing the
>> > aforementioned smiles -> fs problems, but also to build the python
>> > bindings
>> > so that I could use Dalke's chemfp code.
>> >
>> > I found various pages with directions for compiling, but those of the
>> > Cmake
>> > page (http://openbabel.org/wiki/CMake) seemed the most straight forward,
>> > and
>> > abridge instructions in other places.  After wrestling with some
>> > dependencies (SWIG and Eigen2), I was finally able to get cmake to
>> > finish
>> > successfully.  The make step, however, gets to about %50 where it starts
>> > complaining.  The initial problems seem to be that the build is for i386
>> > but
>> > my OS is x86_64, but something regarding parsing XML format is what
>> > kills it
>> > with this error:
>> >
>> > ld: symbol(s) not found
>> > collect2: ld returned 1 exit status
>> > make[2]: *** [lib/cdxmlformat.so] Error 1
>> > make[1]: *** [src/formats/CMakeFiles/cdxmlformat.dir/all] Error 2
>> > make: *** [all] Error 2
>> >
>> > As you may or may not be able to tell, I am not particularly well versed
>> > at
>> > compiling from source.  Very specifically, the steps that i have done
>> > are
>> > given below, along with the resulting output.  My system is a Mac 2.66
>> > GHz
>> > Intel Core i7, running 10.6.8.
>> >
>> > Thanks,
>> > Chris
>> >
>> > cd ~
>> > mkdir openbabel; cd openbabel; mkdir src; cd src
>> > svn co
>> > https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk
>> > openbabel
>> > cd ~/openbabel; mkdir build; cd build; mkdir openbabel
>> > $ cmake -DCMAKE_INSTALL_PREFIX=/usr/local/bin ../../src/openbabel
>> > -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON
>> >
>> > -DPYTHON_PREFIX=/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6
>> >
>> > the output was this:
>> > -- The C compiler identification is GNU
>> > -- The CXX compiler identification is GNU
>> > -- Checking whether C compiler has -isysroot
>> > -- Checking whether C compiler has -isysroot - yes
>> > -- Checking whether C compiler supports OSX deployment target flag
>> > -- Checking whether C compiler supports OSX deployment target flag - yes
>> > -- Check for working C compiler: /usr/bin/gcc
>> > -- Check for working C compiler: /usr/bin/gcc -- works
>> > -- Detecting C compiler ABI info
>> > -- Detecting C compiler ABI info - done
>> > -- Checking whether CXX compiler has -isysroot
>> > -- Checking whether CXX compiler has -isysroot - yes
>> > -- Checking whether CXX compiler supports OSX deployment target flag
>> > -- Checking whether CXX compiler supports OSX deployment target flag -
>> > yes
>> > -- 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.
>> > -- Found LibXml2: /sw/lib/libxml2.dylib
>> > -- Found ZLIB: /usr/include (found version "1.2.3")
>> > -- Found wxWidgets: TRUE
>> > -- 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 - not 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 - found
>> > -- Looking for snprintf
>> > -- Looking for snprintf - found
>> > -- Looking for sranddev
>> > -- Looking for sranddev - 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
>> > -- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR
>> > EIGEN3_VERSION_OK)
>> > (Required is at least version "2.91.0")
>> > -- Found Eigen2: /sw/include/eigen2 (Required is at least version
>> > "2.0.0")
>> > -- checking for module 'cairo'
>> > --   found cairo, version 1.8.10
>> > -- Found Cairo: /sw/lib/libcairo.dylib
>> > -- Cairo found. PNG output will be supported.
>> > -- Looking for getopt
>> > -- Looking for getopt - found
>> > -- GUI will not be built
>> > -- Found PythonInterp: /sw/bin/python2.6
>> > -- Found SWIG: /sw/bin/swig (found version "2.0.1")
>> > -- Found SWIG: /sw/bin/swig (found suitable version "2.0.1", required is
>> > "2.0")
>> > -- Found PythonLibs: /usr/lib/libpython2.6.dylib
>> > -- Python bindings will be compiled
>> > -- Configuring done
>> > -- Generating done
>> > -- Build files have been written to:
>> > /Users/cmayne/openbabel/build/openbabel
>> >
>> > $ make
>> > the output was this:
>> > Scanning dependencies of target openbabel
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>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 44%] Built target CSRformat
>> > Scanning dependencies of target MCDLformat
>> > [ 44%] Building CXX object
>> > src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.o
>> > Linking CXX shared module ../../lib/MCDLformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 44%] Built target MCDLformat
>> > Scanning dependencies of target MNAformat
>> > [ 45%] Building CXX object
>> > src/formats/CMakeFiles/MNAformat.dir/MNAformat.o
>> > Linking CXX shared module ../../lib/MNAformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 45%] Built target MNAformat
>> > Scanning dependencies of target PQSformat
>> > [ 45%] Building CXX object
>> > src/formats/CMakeFiles/PQSformat.dir/PQSformat.o
>> > Linking CXX shared module ../../lib/PQSformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 45%] Built target PQSformat
>> > Scanning dependencies of target abinitformat
>> > [ 46%] Building CXX object
>> > src/formats/CMakeFiles/abinitformat.dir/abinitformat.o
>> > Linking CXX shared module ../../lib/abinitformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 46%] Built target abinitformat
>> > Scanning dependencies of target acesformat
>> > [ 46%] Building CXX object
>> > src/formats/CMakeFiles/acesformat.dir/acesformat.o
>> > Linking CXX shared module ../../lib/acesformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 46%] Built target acesformat
>> > Scanning dependencies of target acrformat
>> > [ 46%] Building CXX object
>> > src/formats/CMakeFiles/acrformat.dir/acrformat.o
>> > Linking CXX shared module ../../lib/acrformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 46%] Built target acrformat
>> > Scanning dependencies of target adfformat
>> > [ 47%] Building CXX object
>> > src/formats/CMakeFiles/adfformat.dir/adfformat.o
>> > Linking CXX shared module ../../lib/adfformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 47%] Built target adfformat
>> > Scanning dependencies of target alchemyformat
>> > [ 47%] Building CXX object
>> > src/formats/CMakeFiles/alchemyformat.dir/alchemyformat.o
>> > Linking CXX shared module ../../lib/alchemyformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 47%] Built target alchemyformat
>> > Scanning dependencies of target amberformat
>> > [ 47%] Building CXX object
>> > src/formats/CMakeFiles/amberformat.dir/amberformat.o
>> > Linking CXX shared module ../../lib/amberformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 47%] Built target amberformat
>> > Scanning dependencies of target balstformat
>> > [ 47%] Building CXX object
>> > src/formats/CMakeFiles/balstformat.dir/balstformat.o
>> > Linking CXX shared module ../../lib/balstformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 47%] Built target balstformat
>> > Scanning dependencies of target bgfformat
>> > [ 47%] Building CXX object
>> > src/formats/CMakeFiles/bgfformat.dir/bgfformat.o
>> > Linking CXX shared module ../../lib/bgfformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 47%] Built target bgfformat
>> > Scanning dependencies of target boxformat
>> > [ 48%] Building CXX object
>> > src/formats/CMakeFiles/boxformat.dir/boxformat.o
>> > Linking CXX shared module ../../lib/boxformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 48%] Built target boxformat
>> > Scanning dependencies of target cacaoformat
>> > [ 48%] Building CXX object
>> > src/formats/CMakeFiles/cacaoformat.dir/cacaoformat.o
>> > Linking CXX shared module ../../lib/cacaoformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 48%] Built target cacaoformat
>> > Scanning dependencies of target cacheformat
>> > [ 48%] Building CXX object
>> > src/formats/CMakeFiles/cacheformat.dir/cacheformat.o
>> > Linking CXX shared module ../../lib/cacheformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 48%] Built target cacheformat
>> > Scanning dependencies of target carformat
>> > [ 48%] Building CXX object
>> > src/formats/CMakeFiles/carformat.dir/carformat.o
>> > Linking CXX shared module ../../lib/carformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 48%] Built target carformat
>> > Scanning dependencies of target castepformat
>> > [ 49%] Building CXX object
>> > src/formats/CMakeFiles/castepformat.dir/castepformat.o
>> > Linking CXX shared module ../../lib/castepformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 49%] Built target castepformat
>> > Scanning dependencies of target cccformat
>> > [ 49%] Building CXX object
>> > src/formats/CMakeFiles/cccformat.dir/cccformat.o
>> > Linking CXX shared module ../../lib/cccformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > [ 49%] Built target cccformat
>> > Scanning dependencies of target cdxmlformat
>> > [ 49%] Building CXX object
>> > src/formats/CMakeFiles/cdxmlformat.dir/xml/cdxmlformat.o
>> > [ 50%] Building CXX object
>> > src/formats/CMakeFiles/cdxmlformat.dir/xml/xml.o
>> > Linking CXX shared module ../../lib/cdxmlformat.so
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libxml2.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > ld: warning: in /sw/lib/libcairo.dylib, file was built for i386 which is
>> > not
>> > the architecture being linked (x86_64)
>> > Undefined symbols:
>> >   "_xmlTextReaderGetAttribute", referenced from:
>> >       OpenBabel::XMLConversion::GetAttribute(char const*)in xml.o
>> >   "_xmlTextReaderRead", referenced from:
>> >       OpenBabel::XMLConversion::GetContentDouble(double&)in xml.o
>> >       OpenBabel::XMLConversion::GetContentInt(int&)   in xml.o
>> >       OpenBabel::XMLConversion::GetContent()      in xml.o
>> >       OpenBabel::XMLConversion::SkipXML(char const*)in xml.o
>> >       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
>> > OpenBabel::OBBase*)in xml.o
>> >   "_xmlTextWriterSetIndentString", referenced from:
>> >       OpenBabel::XMLConversion::SetupWriter()      in xml.o
>> >   "_xmlTextReaderConstValue", referenced from:
>> >       OpenBabel::XMLConversion::GetContentDouble(double&)in xml.o
>> >       OpenBabel::XMLConversion::GetContentInt(int&)   in xml.o
>> >       OpenBabel::XMLConversion::GetContent()      in xml.o
>> >   "_xmlResetError", referenced from:
>> >       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
>> > OpenBabel::OBBase*)in xml.o
>> >   "_xmlOutputBufferCreateIO", referenced from:
>> >       OpenBabel::XMLConversion::SetupWriter()      in xml.o
>> >   "_xmlFreeTextReader", referenced from:
>> >       OpenBabel::XMLConversion::~XMLConversion()in xml.o
>> >       OpenBabel::XMLConversion::~XMLConversion()in xml.o
>> >       OpenBabel::XMLConversion::GetDerived(OpenBabel::OBConversion*,
>> > bool)in
>> > xml.o
>> >   "_xmlTextWriterEndElement", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextWriterStartElement", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextWriterWriteDTD", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextReaderNodeType", referenced from:
>> >       OpenBabel::XMLConversion::SkipXML(char const*)in xml.o
>> >       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
>> > OpenBabel::OBBase*)in xml.o
>> >   "_xmlNewTextWriter", referenced from:
>> >       OpenBabel::XMLConversion::SetupWriter()      in xml.o
>> >   "_xmlStrcmp", referenced from:
>> >       OpenBabel::XMLConversion::SkipXML(char const*)in xml.o
>> >   "_xmlGetLastError", referenced from:
>> >       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
>> > OpenBabel::OBBase*)in xml.o
>> >   "_xmlInitParser", referenced from:
>> >       OpenBabel::XMLConversion::SetupReader()      in xml.o
>> >   "_xmlTextWriterWriteFormatAttribute", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextWriterSetIndent", referenced from:
>> >       OpenBabel::XMLConversion::SetupWriter()      in xml.o
>> >       OpenBabel::XMLConversion::SetupWriter()      in xml.o
>> >   "_xmlTextWriterEndDocument", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextReaderConstLocalName", referenced from:
>> >       OpenBabel::XMLConversion::SkipXML(char const*)in xml.o
>> >       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
>> > OpenBabel::OBBase*)in xml.o
>> >   "_xmlReaderForIO", referenced from:
>> >       OpenBabel::XMLConversion::SetupReader()      in xml.o
>> >   "_xmlOutputBufferFlush", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextWriterStartDocument", referenced from:
>> >       OpenBabel::ChemDrawXMLFormat::WriteMolecule(OpenBabel::OBBase*,
>> > OpenBabel::OBConversion*)in cdxmlformat.o
>> >   "_xmlTextReaderConstNamespaceUri", referenced from:
>> >       OpenBabel::XMLConversion::ReadXML(OpenBabel::XMLBaseFormat*,
>> > OpenBabel::OBBase*)in xml.o
>> >   "_xmlFreeTextWriter", referenced from:
>> >       OpenBabel::XMLConversion::~XMLConversion()in xml.o
>> >       OpenBabel::XMLConversion::~XMLConversion()in xml.o
>> >   "_xmlFree", referenced from:
>> >       OpenBabel::XMLConversion::GetAttribute(char const*)in xml.o
>> > ld: symbol(s) not found
>> > collect2: ld returned 1 exit status
>> > make[2]: *** [lib/cdxmlformat.so] Error 1
>> > make[1]: *** [src/formats/CMakeFiles/cdxmlformat.dir/all] Error 2
>> > make: *** [all] Error 2
>> >
>> >
>> > On Tue, Oct 11, 2011 at 12:58 PM, Noel O'Boyle <baoille...@gmail.com>
>> > wrote:
>> >>
>> >> On 10 October 2011 18:23, Chris Mayne <cgma...@gmail.com> wrote:
>> >> > however, I have not yet been successful in compiling from source
>> >> > (which
>> >> > is a
>> >> > nightmare, btw).
>> >>
>> >> Well, regarding compilation problems, you're going to have to give us
>> >> a bit more to work with here. What exactly is the problem?
>> >>
>> >> - Noel
>> >
>> >
>
>

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