Avogadro-1.1.0 build error

General Discussion
1

Running Ubuntu 12.10 on an AMD64 machine, I have not been able to get
the “debichem” binary version (current 1.0.3) to work, and so thought I
would try a home-build of v.1.1.0. Cmake seems to find all the
requisite dependencies alright, but after a lot of “make -j2” work (most
not shown below), I get an opaque symbol lookup error (shown below),
which confounds building the binaries.

Can anyone point me to which lib/lib-version might satisfy the missing
symbol?

Thanks,

Bob W.

…
[ 11%] Generating moc_pythontool_p.cxx
[ 11%] Generating libavogadro_de.qm
/usr/bin/lconvert: symbol lookup error: /usr/bin/lconvert: undefined
symbol: _ZN16QCoreApplicationC1ERiPPci
make[2]: *** [libavogadro/src/libavogadro_de.qm] Error 127
make[1]: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs…
[ 11%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o
…

2

That’s rather interesting, I wish I could furnish some insight, but that’s not the case.

Let me suggest something, however, try compiling the subversion version of Pymol 1.6.0. I just compiled that yesterday evening straight ‘out of the box’, in Xubuntu 12.04, and it’s working!!!

Stephen P. Molnar, Ph.D. Life is a fuzzy set

Foundation for Chemistry Stochastic and multivariate

www.FoundationForChemistry.com

(614)312-7528 ©

Skype: smolnar1

From: Robert Wohlhueter [mailto:bobwohlhueter@earthlink.net]
Sent: Saturday, September 14, 2013 1:28 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] avogadro-1.1.0 build error

Running Ubuntu 12.10 on an AMD64 machine, I have not been able to get the “debichem” binary version (current 1.0.3) to work, and so thought I would try a home-build of v.1.1.0. Cmake seems to find all the requisite dependencies alright, but after a lot of “make -j2” work (most not shown below), I get an opaque symbol lookup error (shown below), which confounds building the binaries.

Can anyone point me to which lib/lib-version might satisfy the missing symbol?

Thanks,

Bob W.

…
[ 11%] Generating moc_pythontool_p.cxx
[ 11%] Generating libavogadro_de.qm
/usr/bin/lconvert: symbol lookup error: /usr/bin/lconvert: undefined symbol: _ZN16QCoreApplicationC1ERiPPci
make[2]: *** [libavogadro/src/libavogadro_de.qm] Error 127
make[1]: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs…
[ 11%] Building CXX object libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o
…

3

On Sat, Sep 14, 2013 at 1:28 PM, Robert Wohlhueter
bobwohlhueter@earthlink.net wrote:

Running Ubuntu 12.10 on an AMD64 machine, I have not been able to get the
“debichem” binary version (current 1.0.3) to work, and so thought I would
try a home-build of v.1.1.0. Cmake seems to find all the requisite
dependencies alright, but after a lot of “make -j2” work (most not shown
below), I get an opaque symbol lookup error (shown below), which confounds
building the binaries.

Can anyone point me to which lib/lib-version might satisfy the missing
symbol?

The /usr/bin/lconvert is a system tool, installed by Ubuntu. We use it
to build translations, I would imagine running it directly would cause
the same issue. You would need to fix that which is likely an Ubuntu
issue (the command works here). Did you try reinstalling whatever
package installs that file?

Marcus

4

Stephen,

Thanks for the observation – “interesting” is a tricky word.

Actually, I don’t use pymol (chimera – also Python-based – and VMD are
my stock molecular viewers.) Though I notice that pymol 1.6.0. is
available through synaptic: just installed it, and it doesn’t work!
Though the error is quite different (“freeglut (pymol): failed to open
display :0.0”. Interestingalso, since my DISPLAY variable is set to
“:0.0”, and no other applications seem to have trouble opening it.)
Lot’s of Python-based stuff does work on my machine.

So that’s another problem to divert me from real work (though not so
pressing). ldd avogadro shows all the library dependencies to be
satisfied, so at least I know what libs are needed, buta strategy for
finding some symbol that is supposed to be there but isn’t eludes me.

Bob W.

On 9/14/13 5:11 PM, Stephen P. Molnar wrote:

That’s rather interesting, I wish I could furnish some insight, but
that’s not the case.

Let me suggest something, however, try compiling the subversion
version of Pymol 1.6.0. I just compiled that yesterday evening
straight ‘out of the box’, in Xubuntu 12.04, and it’s working!!!

Stephen P. Molnar, Ph.D. Life is a
fuzzy set

Foundation for Chemistry Stochastic
and multivariate

www.FoundationForChemistry.com

(614)312-7528 (c)

Skype: smolnar1

*From:*Robert Wohlhueter [mailto:bobwohlhueter@earthlink.net]
Sent: Saturday, September 14, 2013 1:28 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] avogadro-1.1.0 build error

Running Ubuntu 12.10 on an AMD64 machine, I have not been able to get
the “debichem” binary version (current 1.0.3) to work, and so thought
I would try a home-build of v.1.1.0. Cmake seems to find all the
requisite dependencies alright, but after a lot of “make -j2” work
(most not shown below), I get an opaque symbol lookup error (shown
below), which confounds building the binaries.

Can anyone point me to which lib/lib-version might satisfy the missing
symbol?

Thanks,

Bob W.

…
[ 11%] Generating moc_pythontool_p.cxx
[ 11%] Generating libavogadro_de.qm
/usr/bin/lconvert: symbol lookup error: /usr/bin/lconvert: undefined
symbol: _ZN16QCoreApplicationC1ERiPPci
make[2]: *** [libavogadro/src/libavogadro_de.qm] Error 127
make[1]: *** [libavogadro/src/CMakeFiles/avogadro.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs…
[ 11%] Building CXX object
libavogadro/src/extensions/surfaces/openqube/CMakeFiles/OpenQube.dir/molecule.cpp.o
…

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