Make -j2 Error

General Discussion
1

Dear All,

I am a newbie to Ubuntu and my first course of action was to install
Avogadro. I followed the instructions from the install file and when
I type make -j2 command after some time I get the following lines…

[95%] Building CXX object avogadro/src/CMakeFiles/avogadro-app.dir/qrc
avogadro.cxx.o
Linking CXX executable …/…/bin/avogadro
[95%] Built target avogadro-app
make: ***[all] Error 2

Can you help me out with this? What am I doing wrong? Thanks in advance.

BM

2

I think you can get avogadro on ubuntu the easy way…
Look in the system area for ubuntu software center; you can install avogadro from there: get software; science & engineering;
chemistry. (On lucid lynx netbook remix, this is where you’ll find it, but there is something similar for previous version of ubuntu as
well.)
Steve Williams

----- Original Message -----
From: Benjamin Moritz benjaminmoritz2013@u.northwestern.edu
Date: Sunday, June 6, 2010 4:25 pm
Subject: [Avogadro-Discuss] Make -j2 Error
To: avogadro-discuss@lists.sourceforge.net

Dear All,

I am a newbie to Ubuntu and my first course of action was to install
Avogadro. I followed the instructions from the install file and when
I type make -j2 command after some time I get the following lines…

[95%] Building CXX object avogadro/src/CMakeFiles/avogadro-app.dir/qrc
avogadro.cxx.o
Linking CXX executable …/…/bin/avogadro
[95%] Built target avogadro-app
make: ***[all] Error 2

Can you help me out with this? What am I doing wrong? Thanks in
advance.
BM

ThinkGeek and WIRED’s GeekDad team up for the Ultimate
GeekDad Father’s Day Giveaway. ONE MASSIVE PRIZE to the
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3

On Jun 6, 2010, at 2:11 PM, Benjamin Moritz wrote:

[95%] Building CXX object avogadro/src/CMakeFiles/avogadro-app.dir/qrc
avogadro.cxx.o
Linking CXX executable …/…/bin/avogadro
[95%] Built target avogadro-app
make: ***[all] Error 2

As Steve mentioned, there are packages available for Ubuntu. But if you want to compile yourself, you’ll need to give us a few more lines. Try running “make” (i.e., not -j2) and give us the last 5-10 lines.

Thanks,
-Geoff

4

Steve, Geoff,

Thanks for the quick replies. My first attempt with Avogadro was
through the software center download. Once Avogadro was installed
every time I clicked on it, it would never launch. All I would get is
the “mouse pointer waiting” circle and the program would never launch.

I then decided that if I wanted to learn the UNIX environment then I
should do it the hard way and try to compile myself. So far I have
successfully installed Openbabel, Eigen and Qt4 with little problems.
But Avogadro isn’t as easy. I ran the “make” command and here are the
following lines…

[ 78%] Building CXX object
libavogadro/src/python/CMakeFiles/python-module.dir/sip.cpp.o
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:
In static member function ‘static PyObject*
QClass_converters::QClass_to_PyQt::convert(const T&)’:
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:143:
error: ‘const struct sipAPIDef’ has no member named
‘api_convert_from_instance’
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:
In static member function ‘static PyObject*
QClass_converters::QClass_to_PyQt::convert(T*)’:
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:167:
error: ‘const struct sipAPIDef’ has no member named
‘api_convert_from_instance’
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:
In static member function ‘static void*
QClass_converters::QClass_from_PyQt(PyObject*)’:
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:187:
error: ‘const struct sipAPIDef’ has no member named
‘api_wrapper_check’
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:195:
error: ‘const struct sipAPIDef’ has no member named ‘api_transfer’
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:205:
error: ‘struct sipWrapper’ has no member named ‘u’
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:
In static member function ‘static PyObject*
QList_QAction_to_python_list_PyQt::convert(const QList<QAction*>&)’:
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:245:
error: ‘const struct _sipAPIDef’ has no member named
‘api_convert_from_instance’
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:
In function ‘PyObject* toPyQt(T*)’:
/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:383:
error: ‘const struct sipAPIDef’ has no member named
‘api_convert_from_instance’
make[2]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/sip.cpp.o]
Error 1
make[1]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/all] Error 2
make: *** [all] Error 2

Thanks for your help.

BM

On 6/6/10, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

On Jun 6, 2010, at 2:11 PM, Benjamin Moritz wrote:

[95%] Building CXX object avogadro/src/CMakeFiles/avogadro-app.dir/qrc
avogadro.cxx.o
Linking CXX executable …/…/bin/avogadro
[95%] Built target avogadro-app
make: ***[all] Error 2

As Steve mentioned, there are packages available for Ubuntu. But if you want
to compile yourself, you’ll need to give us a few more lines. Try running
“make” (i.e., not -j2) and give us the last 5-10 lines.

Thanks,
-Geoff

ThinkGeek and WIRED’s GeekDad team up for the Ultimate
GeekDad Father’s Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo

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Avogadro-Discuss@lists.sourceforge.net
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5

Looking at your errors, I suspect you have an old version of SIP or PyQt installed. I’d be curious to know what version of those packages you’re using.

In the meantime, you can get rid of those errors by re-running “cmake” and adding -DENABLE_PYTHON=false to the command-line when calling cmake. This will turn off the Python features.

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:383:
error: ‘const struct sipAPIDef’ has no member named
‘api_convert_from_instance’
make[2]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/sip.cpp.o]
Error 1
make[1]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/all] Error 2
make: *** [all] Error 2

6

Geoff,

That worked, but I get the following error after I try and launch Avogadro…

QStackedLayout::setCurrentWidget: Widget 0x8499838 not contained in stack
QGLTempContext: No GL capable X visuals available.
Segmentation fault

Any ideas?

BM

On 6/7/10, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

Looking at your errors, I suspect you have an old version of SIP or PyQt
installed. I’d be curious to know what version of those packages you’re
using.

In the meantime, you can get rid of those errors by re-running “cmake” and
adding -DENABLE_PYTHON=false to the command-line when calling cmake. This
will turn off the Python features.

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/sip.cpp:383:
error: ‘const struct sipAPIDef’ has no member named
‘api_convert_from_instance’
make[2]: ***
[libavogadro/src/python/CMakeFiles/python-module.dir/sip.cpp.o]
Error 1
make[1]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/all]
Error 2
make: *** [all] Error 2

ThinkGeek and WIRED’s GeekDad team up for the Ultimate
GeekDad Father’s Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo

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7

It looks like your OpenGL drivers are not set up correctly. Does glxgears
work? Can you paste the output frem glxinfo, and let us know what graphics
card/driver you are trying to use?

Marcus

On Monday 07 June 2010 11:55:44 Benjamin Moritz wrote:

Geoff,

That worked, but I get the following error after I try and launch
Avogadro…

QStackedLayout::setCurrentWidget: Widget 0x8499838 not contained in stack
QGLTempContext: No GL capable X visuals available.
Segmentation fault

Any ideas?

BM

On 6/7/10, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

Looking at your errors, I suspect you have an old version of SIP or PyQt
installed. I’d be curious to know what version of those packages you’re
using.

In the meantime, you can get rid of those errors by re-running “cmake”
and adding -DENABLE_PYTHON=false to the command-line when calling cmake.
This will turn off the Python features.

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

/home/bmoritz/Programs/Avogadro/avogadro-1.0.0/libavogadro/src/python/si
p.cpp:383: error: ‘const struct sipAPIDef’ has no member named
‘api_convert_from_instance’
make[2]: ***
[libavogadro/src/python/CMakeFiles/python-module.dir/sip.cpp.o]
Error 1
make[1]: *** [libavogadro/src/python/CMakeFiles/python-module.dir/all]
Error 2
make: *** [all] Error 2

----- ThinkGeek and WIRED’s GeekDad team up for the Ultimate
GeekDad Father’s Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo

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Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

— ThinkGeek and WIRED’s GeekDad team up for the Ultimate
GeekDad Father’s Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options