Environment variables definition and compile error

Development
1

Hey guys,
I tried to download and install avogadro from svn today. I have two probelms
with that:

  1. (a person named bjacob on the irc channel told me to adress this
    to “geoff”)
    Could you please leave some information about the openbabel folders (esp.
    environment variable BABEL_LIBDIR and cmake flag DOPENBABEL2_INCLUDE_DIR) on
    the compile-page of the wiki? Because people that have e. g. openbabel
    already locally installed like me have to guess now which folders that might
    be for them. Maybe put sth like “thats the folder where your files x and y
    are” there…

  2. Could you help me solve this compile error (I don’t know much about coding,
    sorry)
    xaver@xav-desktop:~/Programme/avogadro/build$ cmake
    … -DOPENBABEL2_INCLUDE_DIR=/usr/include/openbabel-2.0/ -DOPENBABEL2_LIBRARIES=/usr/lib/libopenbabel.so -DOPENBABEL2_VERSION_MET=true
    – Found Qt-Version 4.3.2
    – Found lupdate: /usr/bin/lupdate-qt4
    – Found lrelease: /usr/bin/lrelease-qt4
    – Configuring done
    – Generating done
    – Build files have been written to: /home/xaver/Programme/avogadro/build
    xaver@xav-desktop:~/Programme/avogadro/build$ make
    Scanning dependencies of target avogadro-lib
    [ 0%] Building CXX object libavogadro/src/CMakeFiles/avogadro-lib.dir/color.o
    [ 1%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/periodictableview.o
    [ 1%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/glpainter.o
    [ 2%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/cylinder.o
    [ 2%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/painter.o
    [ 3%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/primitiveitemmodel.o
    /home/xaver/Programme/avogadro/libavogadro/src/primitiveitemmodel.cpp: In
    member function »virtual QVariant Avogadro::PrimitiveItemModel::data(const
    QModelIndex&, int) const«:
    /home/xaver/Programme/avogadro/libavogadro/src/primitiveitemmodel.cpp:254:
    Fehler: »class Avogadro::Residue« hat kein Element namens »GetNumString«
    make[2]: ***
    [libavogadro/src/CMakeFiles/avogadro-lib.dir/primitiveitemmodel.o] Fehler 1
    make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Fehler 2
    make: *** [all] Fehler 2

Other information, if needed: Ubuntu 7.10, cmake version 2.4-patch 7,
Openbabel 2.1.1-0ubuntu2, same version for libopenbabel2 and
libopenbabel-dev, libqt4-dev 4.3.2-0ubuntu3.1, libeigen-dev 1.0.5-0ubuntu2

Thanks!
Xaver W.

2

Could you please leave some information about the openbabel folders
(esp.
environment variable BABEL_LIBDIR and cmake flag
DOPENBABEL2_INCLUDE_DIR) on
the compile-page of the wiki?

Well, it’s actually Donald that put those flags into Cmake. If you’ve
installed the SVN version of Open Babel (which is my recommendation),
you don’t need to worry about any of that.

Other information, if needed: Ubuntu 7.10, cmake version 2.4-patch 7,
Openbabel 2.1.1-0ubuntu2, same version for libopenbabel2 and
libopenbabel-dev, libqt4-dev 4.3.2-0ubuntu3.1, libeigen-dev
1.0.5-0ubuntu2

That’s the problem. At the moment, Avogadro is tightly tied to the
Open Babel 2.2.0 development (SVN) code. I thought that was pretty
clear on the wiki, but I’d be happy to make that clearer if needed.

There are a lot of bugs, feature enhancements, etc. in OB-2.2 that are
worthwhile for Avogadro – and many of the Avogadro developers are
also OB developers.

One reason that I haven’t pushed hard for an Avogadro 0.3 release is
that there isn’t an appropriate Open Babel release ready yet.
Hopefully in the near future, there will be new releases for both.

Hope that helps,
-Geoff

3

Xaver,

Those flags were added so if you were doing openbabel development along with avogadro, it made your life easier. If you have installed openbabel then there should be no problem.

Your compile error looks as if you’re using an older version of openbabel. Hope I didn’t repeat too much of what geoff said.

Donald

-----Original Message-----
From: Xaver Wurzenberger xaver.xn@web.de

Date: Sat, 12 Jan 2008 17:25:56
To:avogadro-devel@lists.sourceforge.net
Subject: [Avogadro-devel] Environment variables definition and compile error

Hey guys,
I tried to download and install avogadro from svn today. I have two probelms
with that:

  1. (a person named bjacob on the irc channel told me to adress this
    to “geoff”)
    Could you please leave some information about the openbabel folders (esp.
    environment variable BABEL_LIBDIR and cmake flag DOPENBABEL2_INCLUDE_DIR) on
    the compile-page of the wiki? Because people that have e. g. openbabel
    already locally installed like me have to guess now which folders that might
    be for them. Maybe put sth like “thats the folder where your files x and y
    are” there…

  2. Could you help me solve this compile error (I don’t know much about coding,
    sorry)
    xaver@xav-desktop:~/Programme/avogadro/build$ cmake
    … -DOPENBABEL2_INCLUDE_DIR=/usr/include/openbabel-2.0/ -DOPENBABEL2_LIBRARIES=/usr/lib/libopenbabel.so -DOPENBABEL2_VERSION_MET=true
    – Found Qt-Version 4.3.2
    – Found lupdate: /usr/bin/lupdate-qt4
    – Found lrelease: /usr/bin/lrelease-qt4
    – Configuring done
    – Generating done
    – Build files have been written to: /home/xaver/Programme/avogadro/build
    xaver@xav-desktop:~/Programme/avogadro/build$ make
    Scanning dependencies of target avogadro-lib
    [ 0%] Building CXX object libavogadro/src/CMakeFiles/avogadro-lib.dir/color.o
    [ 1%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/periodictableview.o
    [ 1%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/glpainter.o
    [ 2%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/cylinder.o
    [ 2%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/painter.o
    [ 3%] Building CXX object
    libavogadro/src/CMakeFiles/avogadro-lib.dir/primitiveitemmodel.o
    /home/xaver/Programme/avogadro/libavogadro/src/primitiveitemmodel.cpp: In
    member function »virtual QVariant Avogadro::PrimitiveItemModel::data(const
    QModelIndex&, int) const«:
    /home/xaver/Programme/avogadro/libavogadro/src/primitiveitemmodel.cpp:254:
    Fehler: »class Avogadro::Residue« hat kein Element namens »GetNumString«
    make[2]: ***
    [libavogadro/src/CMakeFiles/avogadro-lib.dir/primitiveitemmodel.o] Fehler 1
    make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Fehler 2
    make: *** [all] Fehler 2

Other information, if needed: Ubuntu 7.10, cmake version 2.4-patch 7,
Openbabel 2.1.1-0ubuntu2, same version for libopenbabel2 and
libopenbabel-dev, libqt4-dev 4.3.2-0ubuntu3.1, libeigen-dev 1.0.5-0ubuntu2

Thanks!
Xaver W.

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4

Hey guys,
thanks for the quick answer.
I understand now that only the combination svn-openbabel and svn-avogardo
makes sense atm.

Geoff: Yes, please but that in big fat red letters on the wiki - I rather
doubt that anyone with a local, stable openbabel install can figure it out
that it’s too old atm.

Donald: OK, you’re right I shouldn’t have to worry about the folders with the
svn version. But eventually the stable openbabel version will be recent
enough - and then more people will need the same information I asked for now.

Benoit: Thanks, but I already figured it out. My idea was to put the folder
information on the wiki - and if it’s not too much trouble, a bit more than
what you wrote (BABEL_LIBDIR -> libs and OPENBABEL2_INCLUDE_DIR -> headers),
because you really have to have some knowledge about coding to know what
lib and header files might look like.

Anyway, i don’t wanna bug you guys, thats just what I think might help people
get to know Avogadro - and I think interest will grow since it’s kinda the
proposed application on the official GAMESS (US) site now.

Also, I’d generally like to help you guys with development, but I don’t know
how as I’m not a coder. Maybe if I could supply you with some kind of
chemistry information. And maybe not too much before april, because that’s
when my ‘master of chemistry’ exams will be… :wink:

Regards, Xaver

5

Anyway, i don’t wanna bug you guys, thats just what I think might
help people
get to know Avogadro - and I think interest will grow since it’s
kinda the
proposed application on the official GAMESS (US) site now.

Ooh, I didn’t see that before. It’d be nice if there were some help
with surfaces/orbitals from GAMESS, then. :slight_smile:

Also, I’d generally like to help you guys with development, but I
don’t know
how as I’m not a coder.

There’s plenty of ways to help. One way is to help with chemistry
information in the translations. For example, I’m not sure if the
GAMESS input has been translated into German.

Of course bug testing, feature suggestions are also always welcome.

Cheers,
-Geoff

6

Perhaps it is best to remove things like the docking extension from
the build file. The corresponding openbabel OBDock class is still
under active development. This way developers can add it to the build
files if they want it, end-users don’t have to update openbabel for
each change in these files.

Tim