Error compiling trunk

Daniel_Asarnow · March 30, 2010, 9:26pm

I just cloned the github repository and generated the Makefile using

cmake -DOPENBABEL2_INCLUDE_DIR=$HOME/local/src/openbabel-2.2/include
-DOPENBABEL2_LIBRARIES=$HOME/local/src/openbabel-2.2/src/.libs/libopenbabel.so
-DOPENBABEL2_VERSION_MET=true -DOPENBABEL_IS_NEWER_THAN_2_2_99=1
$HOME/local/src/avogadro

which proceeded successfully.
make then exits with a bunch of errors for molecule.cpp:

[ 16%] Building CXX object
libavogadro/src/CMakeFiles/avogadro.dir/molecule.cpp.o
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:101: warning: ISO
C++ forbids declaration of ‘OBDOSData’ with no type
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:101: error: invalid
use of ‘::’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:101: error:
expected ‘;’ before ‘’ token
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:102: warning: ISO
C++ forbids declaration of ‘OBElectronicTransitionData’ with no type
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:102: error: invalid
use of ‘::’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:102: error:
expected ‘;’ before ‘’ token
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp: In constructor
‘Avogadro::MoleculePrivate::MoleculePrivate()’:
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:64: error: class
‘Avogadro::MoleculePrivate’ does not have any field named ‘obdosdata’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:64: error: class
‘Avogadro::MoleculePrivate’ does not have any field named
‘obelectronictransitiondata’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp: In member function
‘void Avogadro::Molecule::calculateGroupIndices() const’:
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:796: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:797: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:812: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:813: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp: In member function
‘double Avogadro::Molecule::energy(int) const’:
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1049: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp: In member function
‘void Avogadro::Molecule::setEnergy(int, double)’:
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1067: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp: In member function
‘OpenBabel::OBMol Avogadro::Molecule::OBMol() const’:
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1224: error: ‘const
class Avogadro::MoleculePrivate’ has no member named ‘obdosdata’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1225: error: ‘const
class Avogadro::MoleculePrivate’ has no member named ‘obdosdata’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1229: error: ‘const
class Avogadro::MoleculePrivate’ has no member named
‘obelectronictransitiondata’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1230: error: ‘const
class Avogadro::MoleculePrivate’ has no member named
‘obelectronictransitiondata’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp: In member function
‘bool Avogadro::Molecule::setOBMol(OpenBabel::OBMol*)’:
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1321: warning:
comparison between signed and unsigned integer expressions
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1371: error:
‘DOSData’ is not a member of ‘OpenBabel::OBGenericDataType’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
‘OBDOSData’ is not a member of ‘OpenBabel’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
‘dosData’ was not declared in this scope
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
expected type-specifier
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
expected >' /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error: expected(’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
‘OBDOSData’ is not a member of ‘OpenBabel’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
expected primary-expression before ‘>’ token
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
‘DOSData’ is not a member of ‘OpenBabel::OBGenericDataType’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1372: error:
expected )' before ‘;’ token /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1373: error: ‘class Avogadro::MoleculePrivate’ has no member named ‘obdosdata’ /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1377: error: ‘ElectronicTransitionData’ is not a member of ‘OpenBabel::OBGenericDataType’ /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1378: error: ‘OBElectronicTransitionData’ is not a member of ‘OpenBabel’ /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1378: error: ‘etd’ was not declared in this scope /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1379: error: expected type-specifier /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1379: error: expected>’
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1379: error:
expected (' /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1379: error: ‘OBElectronicTransitionData’ is not a member of ‘OpenBabel’ /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1379: error: expected primary-expression before ‘>’ token /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1380: error: ‘ElectronicTransitionData’ is not a member of ‘OpenBabel::OBGenericDataType’ /home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1380: error: expected)’ before ‘;’ token
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1381: error: ‘class
Avogadro::MoleculePrivate’ has no member named ‘obelectronictransitiondata’
In file included from
/home/da/local/src/avogadro/libavogadro/src/molecule.cpp:1681:
/home/da/local/build/avogadro/libavogadro/include/avogadro/primitive.h: At
global scope:
/home/da/local/build/avogadro/libavogadro/include/avogadro/primitive.h:40:
warning: ‘Avogadro::FALSE_ID’ defined but not used
make[2]: *** [libavogadro/src/CMakeFiles/avogadro.dir/molecule.cpp.o] Error
1
make[2]: *** Waiting for unfinished jobs…
make[1]: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
make: *** [all] Error 2

My bad at configuration or mistake in source? Thanks for any help.

-da

ghutchis · March 30, 2010, 9:31pm

I just cloned the github repository and generated the Makefile using

cmake -DOPENBABEL2_INCLUDE_DIR=$HOME/local/src/openbabel-2.2/include -DOPENBABEL2_LIBRARIES=$HOME/local/src/openbabel-2.2/src/.libs/libopenbabel.so -DOPENBABEL2_VERSION_MET=true -DOPENBABEL_IS_NEWER_THAN_2_2_99=1 $HOME/local/src/avogadro

Then I can guarantee you are not using the latest SVN trunk of Open Babel.

ghlaptop % openbabel: grep DOS include/openbabel/generic.h

//! \class OBDOSData generic.h <openbabel/generic.h>
class OBAPI OBDOSData: public OBGenericData
//! Integrated DOS vector
…

Hope that helps,
-Geoff

allison.vacanti · March 30, 2010, 9:52pm

On Tue, Mar 30, 2010 at 5:31 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

I just cloned the github repository and generated the Makefile using

cmake -DOPENBABEL2_INCLUDE_DIR=$HOME/local/src/openbabel-2.2/include
-DOPENBABEL2_LIBRARIES=$HOME/local/src/openbabel-2.2/src/.libs/libopenbabel.so
-DOPENBABEL2_VERSION_MET=true -DOPENBABEL_IS_NEWER_THAN_2_2_99=1
$HOME/local/src/avogadro

Then I can guarantee you are not using the latest SVN trunk of Open Babel.

Yes, if you tell Avogadro you are using trunk OpenBabel the
compilation will fail spectacularly Try the second suggestion in
my earlier email (the lines that you should remove are the last block
of cmake/modules/FindOpenBabel2.cmake). Remove them, delete
CMakeCache.txt, and re-run cmake and avogadro should compile.

Dave

Daniel_Asarnow · March 30, 2010, 10:49pm

Aha. After your message I did try the latest OpenBabel trunk, but I ran
into some errors and just compiled using my distribution’s openbabel
(2.2.3).

Thanks again.

-da

On Tue, Mar 30, 2010 at 14:52, David Lonie loniedavid@gmail.com wrote:

On Tue, Mar 30, 2010 at 5:31 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

I just cloned the github repository and generated the Makefile using

cmake -DOPENBABEL2_INCLUDE_DIR=$HOME/local/src/openbabel-2.2/include

-DOPENBABEL2_LIBRARIES=$HOME/local/src/openbabel-2.2/src/.libs/libopenbabel.so

-DOPENBABEL2_VERSION_MET=true -DOPENBABEL_IS_NEWER_THAN_2_2_99=1
$HOME/local/src/avogadro

Then I can guarantee you are not using the latest SVN trunk of Open
Babel.

Yes, if you tell Avogadro you are using trunk OpenBabel the
compilation will fail spectacularly Try the second suggestion in
my earlier email (the lines that you should remove are the last block
of cmake/modules/FindOpenBabel2.cmake). Remove them, delete
CMakeCache.txt, and re-run cmake and avogadro should compile.

Dave