Build Problem

Leandro_Boscariol · January 22, 2009, 11:57pm

Hi guys!

Today was the first time I’ve tried to build since it has moved to github.

When building, I’ve got the following:

/home/alfeto/workspace/svn/avogadro/libavogadro/src/camera.cpp:35: error:
expected class-name before ‘{’ token
make[2]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/camera.cpp.o]
Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

So, any ideas about it?

Cheers!

–
Leandro A. Boscariol

Tim_Vandermeersch · January 23, 2009, 12:39am

Hi,

What Eigen version are you using? Eigen::WithAlignedOperatorNew has
been removed from Eigen2-rc1. The git repo currently (or avogadro
version 0.9.0) requires beta6.

However, the WithAlignedOperatorNew needs to be replaced with the
equivalent macro. I’ll look at this now.

Cheers,
Tim

On Fri, Jan 23, 2009 at 12:57 AM, Leandro Boscariol
leandroboscariol@gmail.com wrote:

Hi guys!

Today was the first time I’ve tried to build since it has moved to github.

When building, I’ve got the following:

/home/alfeto/workspace/svn/avogadro/libavogadro/src/camera.cpp:35: error:
expected class-name before ‘{’ token
make[2]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/camera.cpp.o]
Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

So, any ideas about it?

Cheers!

–
Leandro A. Boscariol

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Leandro_Boscariol · January 23, 2009, 9:49pm

Hi Tim,
Actually, I´m using the latest eigen2 from the svn.

Sure that’s Eigen related stuff?

Cheers!

On Thu, Jan 22, 2009 at 22:39, Tim Vandermeersch <
tim.vandermeersch@gmail.com> wrote:

Hi,

What Eigen version are you using? Eigen::WithAlignedOperatorNew has
been removed from Eigen2-rc1. The git repo currently (or avogadro
version 0.9.0) requires beta6.

However, the WithAlignedOperatorNew needs to be replaced with the
equivalent macro. I’ll look at this now.

Cheers,
Tim

On Fri, Jan 23, 2009 at 12:57 AM, Leandro Boscariol
leandroboscariol@gmail.com wrote:

Hi guys!

Today was the first time I’ve tried to build since it has moved to
github.

When building, I’ve got the following:

/home/alfeto/workspace/svn/avogadro/libavogadro/src/camera.cpp:35: error:
expected class-name before ‘{’ token
make[2]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/camera.cpp.o]
Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

So, any ideas about it?

Cheers!

–
Leandro A. Boscariol

This SF.net email is sponsored by:
SourcForge Community
SourceForge wants to tell your story.
http://p.sf.net/sfu/sf-spreadtheword

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

–
Leandro A. Boscariol

Tim_Vandermeersch · January 23, 2009, 9:59pm

Hi,

On Fri, Jan 23, 2009 at 10:49 PM, Leandro Boscariol
leandroboscariol@gmail.com wrote:

Hi Tim,
Actually, I´m using the latest eigen2 from the svn.

I know it is not optimal but now having the latest eigen2 actually
breaks avogadro 0.9.0.

Sure that’s Eigen related stuff?

Yes, I updated Eigen2 to svn yesterday and got the same problem.
However, I did commit the fix to my repo which will be taken up by
cryos’ main branch. (see
replace WithAlignedOperatorNew with EIGEN_MAKE_ALIGNED_OPERATOR_NEW. · timvdm/avogadro@fd8f075 · GitHub)

Cheers,
Tim

Cheers!

On Thu, Jan 22, 2009 at 22:39, Tim Vandermeersch
tim.vandermeersch@gmail.com wrote:

Hi,

What Eigen version are you using? Eigen::WithAlignedOperatorNew has
been removed from Eigen2-rc1. The git repo currently (or avogadro
version 0.9.0) requires beta6.

However, the WithAlignedOperatorNew needs to be replaced with the
equivalent macro. I’ll look at this now.

Cheers,
Tim

On Fri, Jan 23, 2009 at 12:57 AM, Leandro Boscariol
leandroboscariol@gmail.com wrote:

Hi guys!

Today was the first time I’ve tried to build since it has moved to
github.

When building, I’ve got the following:

/home/alfeto/workspace/svn/avogadro/libavogadro/src/camera.cpp:35:
error:
expected class-name before ‘{’ token
make[2]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/camera.cpp.o]
Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

So, any ideas about it?

Cheers!

–
Leandro A. Boscariol

This SF.net email is sponsored by:
SourcForge Community
SourceForge wants to tell your story.
http://p.sf.net/sfu/sf-spreadtheword

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

–
Leandro A. Boscariol

mhanwell · January 24, 2009, 12:02am

Tim Vandermeersch wrote:

Yes, I updated Eigen2 to svn yesterday and got the same problem.
However, I did commit the fix to my repo which will be taken up by
cryos’ main branch. (see
replace WithAlignedOperatorNew with EIGEN_MAKE_ALIGNED_OPERATOR_NEW. · timvdm/avogadro@fd8f075 · GitHub)

Tim, you are marked as a collaborator and as such can push changes to
the cryos/avogadro master yourself. With limited connectivity until I
get back please feel free to do this, especially for fixes like this
where master doesn’t currently compile against Eigen trunk. I wouldn’t
have tagged had I known Eigen would break API…

I am back on Sunday evening, but certainly feel free to merge in your
changes. I think this is less confusing to users wanting these fixes
when using Avogadro trunk too.

Thanks,

Marcus

Leandro_Boscariol · January 24, 2009, 12:12pm

Hi Tim.

Well, looks like u did as Marcus said, and updated the master branch on
github, and I have not that issue anymore!

But, now I’ve got this:

/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference to forkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference to openpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.9.0] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

And, I guess that’s something related to my installation. What should I have
to avoid it? Should I update python or something?

Cheers!

On Fri, Jan 23, 2009 at 19:59, Tim Vandermeersch <
tim.vandermeersch@gmail.com> wrote:

Hi,

On Fri, Jan 23, 2009 at 10:49 PM, Leandro Boscariol
leandroboscariol@gmail.com wrote:

Hi Tim,
Actually, I´m using the latest eigen2 from the svn.

I know it is not optimal but now having the latest eigen2 actually
breaks avogadro 0.9.0.

Sure that’s Eigen related stuff?

Yes, I updated Eigen2 to svn yesterday and got the same problem.
However, I did commit the fix to my repo which will be taken up by
cryos’ main branch. (see

replace WithAlignedOperatorNew with EIGEN_MAKE_ALIGNED_OPERATOR_NEW. · timvdm/avogadro@fd8f075 · GitHub
)

Cheers,
Tim

Cheers!

On Thu, Jan 22, 2009 at 22:39, Tim Vandermeersch
tim.vandermeersch@gmail.com wrote:

Hi,

What Eigen version are you using? Eigen::WithAlignedOperatorNew has
been removed from Eigen2-rc1. The git repo currently (or avogadro
version 0.9.0) requires beta6.

However, the WithAlignedOperatorNew needs to be replaced with the
equivalent macro. I’ll look at this now.

Cheers,
Tim

On Fri, Jan 23, 2009 at 12:57 AM, Leandro Boscariol
leandroboscariol@gmail.com wrote:

Hi guys!

Today was the first time I’ve tried to build since it has moved to
github.

When building, I’ve got the following:

/home/alfeto/workspace/svn/avogadro/libavogadro/src/camera.cpp:35:
error:
expected class-name before ‘{’ token
make[2]: ***
[libavogadro/src/CMakeFiles/avogadro-lib.dir/camera.cpp.o]
Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

So, any ideas about it?

Cheers!

–
Leandro A. Boscariol

This SF.net email is sponsored by:
SourcForge Community
SourceForge wants to tell your story.
http://p.sf.net/sfu/sf-spreadtheword

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

–
Leandro A. Boscariol

–
Leandro A. Boscariol

mhanwell · January 24, 2009, 1:59pm

Leandro Boscariol wrote:

Hi Tim.

Well, looks like u did as Marcus said, and updated the master branch
on github, and I have not that issue anymore!

But, now I’ve got this:

/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference to forkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference to openpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.9.0] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2
I am afraid that this is a known issue with CMake’s module that finds
Python. It is hardwired to expect the non-standard layout used by
Debian, most other distros use (what I believe) is the standard layout
Python upstream uses. Your distro could patch their CMake, I am going to
see what I can do to get this fixed upstream once I get back home too.

For now you could disable Python support to check everything else out.

Thanks,

Marcus

Leandro_Boscariol · January 24, 2009, 2:12pm

Hi Marcus.

On Sat, Jan 24, 2009 at 11:59, Marcus D. Hanwell marcus@cryos.org wrote:

Leandro Boscariol wrote:

Hi Tim.

Well, looks like u did as Marcus said, and updated the master branch
on github, and I have not that issue anymore!

But, now I’ve got this:

/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference to forkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference to openpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.9.0] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2
I am afraid that this is a known issue with CMake’s module that finds
Python. It is hardwired to expect the non-standard layout used by
Debian, most other distros use (what I believe) is the standard layout
Python upstream uses. Your distro could patch their CMake, I am going to
see what I can do to get this fixed upstream once I get back home too.

I think that you told me that before. Maybe its the same issue. I will look
through the older emails and see if I can fix it.

Thanks for all

Cheers!

–
Leandro A. Boscariol

Leandro_Boscariol · January 29, 2009, 1:51am

Hi!

On Sat, Jan 24, 2009 at 12:12, Leandro Boscariol <leandroboscariol@gmail.com

wrote:

Hi Marcus.

On Sat, Jan 24, 2009 at 11:59, Marcus D. Hanwell marcus@cryos.org wrote:

Leandro Boscariol wrote:

Hi Tim.

Well, looks like u did as Marcus said, and updated the master branch
on github, and I have not that issue anymore!

But, now I’ve got this:

/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_forkpty': posixmodule.c:(.text+0x3a49): undefined reference to forkpty’
/usr/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function
posix_openpty': posixmodule.c:(.text+0x3ad8): undefined reference to openpty’
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.9.0] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2
I am afraid that this is a known issue with CMake’s module that finds
Python. It is hardwired to expect the non-standard layout used by
Debian, most other distros use (what I believe) is the standard layout
Python upstream uses. Your distro could patch their CMake, I am going to
see what I can do to get this fixed upstream once I get back home too.

I think that you told me that before. Maybe its the same issue. I will look
through the older emails and see if I can fix it.

I found it:

You could add a -DPYTHON_LIBRARIES=/usr/lib/python2.5/libpythson2.5.so or

something to that effect. It is trying to using the static lib in the
config
directory that virtually no distro uses and is not the way the default
Python
build system installs it

So, I’ve changed this

/usr/lib/python2.5/config/libpython2.5.a

for this

/usr/lib/libpython2.5.so

Now, I guess there another issue related to eigen:

Linking CXX shared library
libavogadro.so

alfeto@amebamovel:~/workspace/svn/avogadro/build$

alfeto@amebamovel:~/workspace/svn/avogadro/build$ vim
CMakeCache.txt~

alfeto@amebamovel:~/workspace/svn/avogadro/build$ vim
CMakeCache.txt

alfeto@amebamovel:~/workspace/svn/avogadro/build$ cat
errors

CMakeFiles/avogadro-lib.dir/cylinder.cpp.o: In function
`Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/cylinder.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/pluginmanager.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/pluginmanager.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/textrenderer.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/textrenderer.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/glwidget.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/glwidget.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/glgraphicsview.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/glgraphicsview.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/molecule.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/molecule.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/extension.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/extension.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/meshgenerator.cpp.o: In function Eigen::Scaling(float)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/meshgenerator.cpp.o: In function Eigen::Scaling(double)':

/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/camera.cpp.o: In function Eigen::Scaling(float)‘:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/camera.cpp.o: In function Eigen::Scaling(double)’:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/boxcontrol.cpp.o: In function Eigen::Scaling(float)‘:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/boxcontrol.cpp.o: In function Eigen::Scaling(double)’:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/glpainter.cpp.o: In function Eigen::Scaling(float)‘:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/glpainter.cpp.o: In function Eigen::Scaling(double)’:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
Eigen::Scaling(double)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: first defined here CMakeFiles/avogadro-lib.dir/engines/bsdyengine.cpp.o: In function Eigen::Scaling(float)‘:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: multiple definition of
Eigen::Scaling(float)' CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:123: first defined here CMakeFiles/avogadro-lib.dir/engines/bsdyengine.cpp.o: In function Eigen::Scaling(double)’:
/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125: multiple definition of
`Eigen::Scaling(double)’
CMakeFiles/avogadro-lib.dir/navigate.cpp.o:/usr/include/eigen2/Eigen/src/Geometry/Scaling.h:125:
first defined here
collect2: ld returned 1 exit status
make[2]: *** [libavogadro/src/libavogadro.so.0.9.0] Error 1
make[1]: *** [libavogadro/src/CMakeFiles/avogadro-lib.dir/all] Error 2
make: *** [all] Error 2

Oh, again, is the latest from svn.

Cheers!

Leandro A. Boscariol