Compiling Avogadro on MacOS X 10.5

Development
1

Dear all
I am about to start working with Avogadro and will possibly be involved
in modifying it to the needs of our groups (QM of proteins). I am very
much looking forward to be able to contribute to the Avogadro community
as well as benefiting from it.
As obvious from the subject title, I was trying to compile Avogadro on
my MacBook Pro running MacOS 10.5 (Leopard). I would like to install it
as a developer version (so that it is possible to script it via python,
I’m not exactly sure yet how this looks like).
Anyway, my problem at the moment is that I get the following message
when compiling:

mzh @ ~/build/avogadro $ cmake ~/avogadro
– The C compiler identification is GNU
– The CXX compiler identification is GNU
– 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
– 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
– The build type is RelWithDebInfo
– Performing Test HAVE_GCC_VISIBILITY
– Performing Test HAVE_GCC_VISIBILITY - Success
– Performing Test COMPILES_WITHOUT_FPERMISSIVE
– Performing Test COMPILES_WITHOUT_FPERMISSIVE - Success
CMake Error at /Applications/CMake
2.6-4.app/Contents/share/cmake-2.6/Modules/FindQt4.cmake:640 (MESSAGE):
Could NOT find QtCore header
Call Stack (most recent call first):
CMakeLists.txt:125 (find_package)

– Configuring incomplete, errors occurred!

I experienced some difficulties in properly installing the Qt framework.
I would very much appreciate it, if somebody could give me some
instructions on how to install the Qt framework so the compilation of
Avogadro works.

If I finally succed in compling a working version, I would happily be
willing to provide support for people who wish to do the same or to
contribute to some further documentation on this subject.

2

As obvious from the subject title, I was trying to compile Avogadro on
my MacBook Pro running MacOS 10.5 (Leopard). I would like to install
it
as a developer version (so that it is possible to script it via
python,
I’m not exactly sure yet how this looks like).
…
I experienced some difficulties in properly installing the Qt
framework.
I would very much appreciate it,

Here’s what you should do:

  1. Download the latest version of Qt for Mac:
    http://get.qt.nokia.com/qt/source/qt-mac-cocoa-opensource-4.5.3.dmg

  2. Do a default installation of everything – click on the installer
    package and go through the prompts.

  3. That’s it. If you have difficulties, please post any error messages
    you see or problems you have.

Cheers,
-Geoff

3

I run the following cmake command as shown below. its looking good until
this normalize-makro starts making trouble. My idea is that perhaps the
openbabel directory is misnamed? notice also the following output to
prove my openbabel version.

mzh @ ~/build/openbabel $ babel -V
Open Babel 2.2.3 – Nov 26 2009 – 17:19:43

the openbabel source directory is called:
mzh @ ~ $ ls src/
avogadro eigen2 openbabel-2.2

mzh @ ~/build/avogadro $ cmake
-DOPENBABEL2_INCLUDE_DIR=~/src/openbabel-2.2/include
-DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.3.dylib
-DOPENBABEL2_VERSION_MET=true -DEIGEN_INCLUDE_DIR=~/src/eigen2
~/src/avogadro
– The build type is RelWithDebInfo
– Found lupdate: /usr/bin/lupdate
– Found lrelease: /usr/bin/lrelease
– Found lconvert: /usr/bin/lconvert
CMake Error at cmake/modules/MacroEnsureVersion.cmake:95
(NORMALIZE_VERSION):
NORMALIZE_VERSION Macro invoked with incorrect arguments for macro named:
NORMALIZE_VERSION
Call Stack (most recent call first):
cmake/modules/FindOpenBabel2.cmake:108 (macro_ensure_version)
CMakeLists.txt:130 (find_package)

– Git revision found to be d70cc9d
– Found Git revision is: d70cc9d
– Building development version from Git clone.
– Searching for python dependencies…
– [1/5] Boost Python
– Boost Python found…
– [2/5] Python Libraries
– Found PythonLibs: -framework Python
– [3/5] Python Interpreter
– Found PythonInterp: /usr/bin/python2.5
– [4/5] Numpy Module
– Numpy headers found
– [5/5] SIP Module
– Found sip.h header…
– All python dependencies found - Python support enabled
– Threaded OpenGL rendering not enabled
– RPath support enabled for installed binaries and libraries
– Setting new boost python libraries
– Enabled python terminal
– Python site-packages directory: /Library/Python/2.5/site-packages
– docbook tools not found, doc targets disabled
– Configuring incomplete, errors occurred!

4

Dear all
I am trying to compile Avogadro on Mac OS X 10.5 with Python support
enabled (the release version compiles and runs). Could anyone confirm to
me that it is indeed possible to do so?
I ran into the following error at compile time. I cant tell for sure
where the reason for this error is, but there’s no sign of a “no such
file or directory” message, so I thought it might be something with the
code? I obtain the avogadro source with git, so it should be the latest
version of the code (notice the output when running Avogadro below).

mzh @ ~/build/avogadro $ bin/Avogadro.app/Contents/MacOS/Avogadro
“Avogadro version: 1.0.1 Git: d70cc9d
LibAvogadro version: 1.0.1 Git: d70cc9d”

I am issuing the following configure command:
cmake \

-DOPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0
-DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.3.dylib
-DOPENBABEL2_VERSION_MET=true
-DEIGEN_INCLUDE_DIR=~/src/eigen2
~/src/avogadro/

This is the last part of the make output before it crashes.

[ 59%] Built target propextension
[ 59%] Generating ui_pythonterminalwidget.h
[ 59%] Generating moc_pythonterminal.cxx
[ 59%] Generating moc_highlighter.cxx
Scanning dependencies of target pythonterminal
[ 59%] Building CXX object
libavogadro/src/extensions/CMakeFiles/pythonterminal.dir/pythonterminal.cpp.o
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:
In member function ‘virtual void
Avogadro::PythonTerminalEdit::keyPressEvent(QKeyEvent*)’:
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: ‘HEAD’ was not declared in this scope
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected ;' before ‘:’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘==’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘==’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘==’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘=’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:280: error: expected primary-expression before ‘}’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:280: error: expected ;’ before ‘}’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected `;’ before ‘:’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:283:
error: ‘text’ was not declared in this scope
make[2]: ***
[libavogadro/src/extensions/CMakeFiles/pythonterminal.dir/pythonterminal.cpp.o]
Error 1
make[1]: ***
[libavogadro/src/extensions/CMakeFiles/pythonterminal.dir/all] Error 2
make: *** [all] Error 2

5

One more thing: could you provide me with the exact kind of value for the -DOPENBABEL2_LIBRARIES option? Does it have to provide a library (i.e. .dylib, .3.dylib, .so file) or does it just have to provide the path to the library containing directory (i.e. /usr/local/lib/openbabel/2.2.3)?

If you have installed Open Babel, you do not need to supply the paths for INCLUDES or LIBRARIES. Cmake should find them automatically. I would omit these options.

Best regards,
-Geoff

6

Hi,

I just checked out the source and looked at pythonterminal.cpp. It appears
that there is a conflict in the code that was not resolved. Since I haven’t
setup my system yet, I’m gonna put the solution here and not in the git
repository (sorry for that). Around line 275 you’ll find

<<<<<<< HEAD:libavogadro/src/extensions/pythonterminal.cpp
}
else if(event->key() == Qt::Key_Return)
{

} else if(event->key() == Qt::Key_Return) {

1.0:libavogadro/src/extensions/pythonterminal.cpp

which is an unresolved issue that has not been taken care of by the
submitter. The <<<<<< lines and >>>>>> tells you where the issue and is not
part of c+++. Neither is =======.

It is an easy fix since you can comment out the stuff that you dont need so
//<<<<<<< HEAD:libavogadro/src/extensions/pythonterminal.cpp
// }
// else if(event->key() == Qt::Key_Return)
// {
//=======
} else if(event->key() == Qt::Key_Return) {
//>>>>>>> 1.0:libavogadro/src/extensions/pythonterminal.cpp

and you should be good to go again.

I hope that someone will put this fix into the repository soon though and I
am deeply sorry that I havent got the time to set up the repositories and
remotes with git - but I got my master thesis defence in less than a week
and therefore have other stuff to care about. :slight_smile:

best,
Casper

On Fri, Nov 27, 2009 at 3:54 PM, Martin Hediger ma.hed@bluewin.ch wrote:

Dear all
I am trying to compile Avogadro on Mac OS X 10.5 with Python support
enabled (the release version compiles and runs). Could anyone confirm to
me that it is indeed possible to do so?
I ran into the following error at compile time. I cant tell for sure
where the reason for this error is, but there’s no sign of a “no such
file or directory” message, so I thought it might be something with the
code? I obtain the avogadro source with git, so it should be the latest
version of the code (notice the output when running Avogadro below).

mzh @ ~/build/avogadro $ bin/Avogadro.app/Contents/MacOS/Avogadro
“Avogadro version: 1.0.1 Git: d70cc9d
LibAvogadro version: 1.0.1 Git: d70cc9d”

I am issuing the following configure command:
cmake \

-DOPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0
-DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.3.dylib
-DOPENBABEL2_VERSION_MET=true
-DEIGEN_INCLUDE_DIR=~/src/eigen2
~/src/avogadro/

This is the last part of the make output before it crashes.

[ 59%] Built target propextension
[ 59%] Generating ui_pythonterminalwidget.h
[ 59%] Generating moc_pythonterminal.cxx
[ 59%] Generating moc_highlighter.cxx
Scanning dependencies of target pythonterminal
[ 59%] Building CXX object

libavogadro/src/extensions/CMakeFiles/pythonterminal.dir/pythonterminal.cpp.o
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:
In member function ‘virtual void
Avogadro::PythonTerminalEdit::keyPressEvent(QKeyEvent*)’:
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected primary-expression before ‘<’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: ‘HEAD’ was not declared in this scope
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:275:
error: expected ;' before ‘:’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘==’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘==’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘==’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:279: error: expected primary-expression before ‘=’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:280: error: expected primary-expression before ‘}’ token /Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:280: error: expected ;’ before ‘}’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected primary-expression before ‘>’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:281:
error: expected `;’ before ‘:’ token
/Users/mzh/src/avogadro/libavogadro/src/extensions/pythonterminal.cpp:283:
error: ‘text’ was not declared in this scope
make[2]: ***

[libavogadro/src/extensions/CMakeFiles/pythonterminal.dir/pythonterminal.cpp.o]
Error 1
make[1]: ***
[libavogadro/src/extensions/CMakeFiles/pythonterminal.dir/all] Error 2
make: *** [all] Error 2

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