Release candidates available for testing

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Release candidates available for testing

Noel O'Boyle
Administrator
Hello all,

The release of Open Babel 2.3.0 is coming up soon. There have been
many changes so it would be great to get some feedback on whether the
current release candidates are working.

These are available at
http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
for Linux and http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
for Windows.

I'm responsible for the new compiling documentation, currently
available at http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
If there are any problems with these, please let us know also.

Regards,
   Noel

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Re: Release candidates available for testing

Igor Filippov
What is the equivalent of the option "--disable-dynamic-modules"  in
configure script for cmake?

Igor


On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:

> Hello all,
>
> The release of Open Babel 2.3.0 is coming up soon. There have been
> many changes so it would be great to get some feedback on whether the
> current release candidates are working.
>
> These are available at
> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
> for Linux and http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
> for Windows.
>
> I'm responsible for the new compiling documentation, currently
> available at http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
> If there are any problems with these, please let us know also.
>
> Regards,
>    Noel
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev 
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss



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Re: Release candidates available for testing

Geoffrey Hutchison
> What is the equivalent of the option "--disable-dynamic-modules"  in
> configure script for cmake?

cmake [...] -DBUILD_SHARED=OFF

Hope that helps,
-Geoff

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Re: Release candidates available for testing

Tim Vandermeersch
On Mon, Aug 23, 2010 at 6:06 PM, Geoffrey Hutchison
<[hidden email]> wrote:
>> What is the equivalent of the option "--disable-dynamic-modules"  in
>> configure script for cmake?
>
> cmake [...] -DBUILD_SHARED=OFF

This alone doesn't do very much.

I recently made some changes to the build system to get static
compiling to work in linux (gcc) and windows (MSVC). With these
changes it is possible to build distributable exe's for linux/windows
with no external dependencies. The changes are available on github but
I still have to port them to trunk.
(http://github.com/timvdm/openbabel-2.2.1-static) I used the
CMakeLists.txt files from trunk to build openbabel 2.2.1 but the
relevant changes should be easy to port.

I'll try to port them tonight.

Tim

> Hope that helps,
> -Geoff
>
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Re: Release candidates available for testing

Igor Filippov
In reply to this post by Geoffrey Hutchison
This created a static library libopenbabel.a but it looks like the
modules for different formats are still dynamic - i.e. smilesformat.so.

My use of "--disable-dynamic-modules" was to compile all the different
file formats into a single library. If it's a static library - all the
better, but I can live with a single shared library as well.

I will wait for Tim's port. Tim if there could be a single static
library it would be fantastic!

Igor

On Mon, 2010-08-23 at 12:06 -0400, Geoffrey Hutchison wrote:
> > What is the equivalent of the option "--disable-dynamic-modules"  in
> > configure script for cmake?
>
> cmake [...] -DBUILD_SHARED=OFF
>
> Hope that helps,
> -Geoff



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Re: Release candidates available for testing

Tim Vandermeersch
On Mon, Aug 23, 2010 at 6:37 PM, Igor Filippov
<[hidden email]> wrote:
> This created a static library libopenbabel.a but it looks like the
> modules for different formats are still dynamic - i.e. smilesformat.so.
>
> My use of "--disable-dynamic-modules" was to compile all the different
> file formats into a single library. If it's a static library - all the
> better, but I can live with a single shared library as well.
>
> I will wait for Tim's port. Tim if there could be a single static
> library it would be fantastic!

I didn't have time for this yesterday but I'll do it tonight.

> Igor
>
> On Mon, 2010-08-23 at 12:06 -0400, Geoffrey Hutchison wrote:
>> > What is the equivalent of the option "--disable-dynamic-modules"  in
>> > configure script for cmake?
>>
>> cmake [...] -DBUILD_SHARED=OFF
>>
>> Hope that helps,
>> -Geoff
>
>
>
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>

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compiling release candidate

Eiso AB-2
In reply to this post by Igor Filippov
I'm trying to compile the release candidate and getting this:

[ 33%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.o
[ 34%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.o
/home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:28:23: error:
Eigen/Dense: No such file or directory
/home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp: In member function
'Eigen::Vector3d OpenBabel::OBAlign::MoveToOrigin(Eigen::MatrixXd&)':
/home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:74: error: invalid
use of undefined type 'const struct Eigen::PartialRedux<Eigen::Matrix<double,
10000, 10000, 2, 10000, 10000>, 1>'
/usr/local/include/eigen2/Eigen/src/Core/util/ForwardDeclarations.h:102: error:
declaration of 'const struct Eigen::PartialRedux<Eigen::Matrix<double, 10000,
10000, 2, 10000, 10000>, 1>'

[...] finally ends with:

/usr/local/include/eigen2/Eigen/src/Core/CwiseUnaryOp.h:75: error: using invalid
field 'Eigen::CwiseUnaryOp<UnaryOp, MatrixType>::m_functor'
make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
make: *** [all] Error 2


any idea what's wrong?

Eiso


Igor Filippov wrote:

> What is the equivalent of the option "--disable-dynamic-modules"  in
> configure script for cmake?
>
> Igor
>
>
> On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:
>> Hello all,
>>
>> The release of Open Babel 2.3.0 is coming up soon. There have been
>> many changes so it would be great to get some feedback on whether the
>> current release candidates are working.
>>
>> These are available at
>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
>> for Linux and http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
>> for Windows.
>>
>> I'm responsible for the new compiling documentation, currently
>> available at http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
>> If there are any problems with these, please let us know also.
>>
>> Regards,
>>     Noel
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
>
> ------------------------------------------------------------------------------
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>


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Re: compiling release candidate

Noel O'Boyle
Administrator
We just discussed this on openbabel-devel. It seems that it's a bug in
an older version of Eigen. You need to upgrade the version of Eigen
installed - meanwhile, we need to fix OpenBabel to workaround this
bug.

Just for the record, what version of Eigen exactly do you have
installed, and what OS is it?

- Noel

On 25 August 2010 11:16, Eiso AB <[hidden email]> wrote:

> I'm trying to compile the release candidate and getting this:
>
> [ 33%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.o
> [ 34%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.o
> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:28:23: error:
> Eigen/Dense: No such file or directory
> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp: In member function
> 'Eigen::Vector3d OpenBabel::OBAlign::MoveToOrigin(Eigen::MatrixXd&)':
> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:74: error: invalid
> use of undefined type 'const struct Eigen::PartialRedux<Eigen::Matrix<double,
> 10000, 10000, 2, 10000, 10000>, 1>'
> /usr/local/include/eigen2/Eigen/src/Core/util/ForwardDeclarations.h:102: error:
> declaration of 'const struct Eigen::PartialRedux<Eigen::Matrix<double, 10000,
> 10000, 2, 10000, 10000>, 1>'
>
> [...] finally ends with:
>
> /usr/local/include/eigen2/Eigen/src/Core/CwiseUnaryOp.h:75: error: using invalid
> field 'Eigen::CwiseUnaryOp<UnaryOp, MatrixType>::m_functor'
> make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
> make: *** [all] Error 2
>
>
> any idea what's wrong?
>
> Eiso
>
>
> Igor Filippov wrote:
>> What is the equivalent of the option "--disable-dynamic-modules"  in
>> configure script for cmake?
>>
>> Igor
>>
>>
>> On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:
>>> Hello all,
>>>
>>> The release of Open Babel 2.3.0 is coming up soon. There have been
>>> many changes so it would be great to get some feedback on whether the
>>> current release candidates are working.
>>>
>>> These are available at
>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
>>> for Linux and http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
>>> for Windows.
>>>
>>> I'm responsible for the new compiling documentation, currently
>>> available at http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
>>> If there are any problems with these, please let us know also.
>>>
>>> Regards,
>>>     Noel
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
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>>> OpenBabel-discuss mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
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Re: compiling release candidate

Eiso AB-2
hi Noel,

eigen2-2.0.5.tar.bz2

uname -a
Linux xxx.xxx.net 2.6.18-194.3.1.el5 #1 SMP Fri May 7 01:52:57 EDT 2010 i686
i686 i386 GNU/Linux

Eiso
ps. shouldn't the reply to field in this list be the list instead of the
sender?

Noel O'Boyle wrote:

> We just discussed this on openbabel-devel. It seems that it's a bug in
> an older version of Eigen. You need to upgrade the version of Eigen
> installed - meanwhile, we need to fix OpenBabel to workaround this
> bug.
>
> Just for the record, what version of Eigen exactly do you have
> installed, and what OS is it?
>
> - Noel
>
> On 25 August 2010 11:16, Eiso AB<[hidden email]>  wrote:
>> I'm trying to compile the release candidate and getting this:
>>
>> [ 33%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.o
>> [ 34%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.o
>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:28:23: error:
>> Eigen/Dense: No such file or directory
>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp: In member function
>> 'Eigen::Vector3d OpenBabel::OBAlign::MoveToOrigin(Eigen::MatrixXd&)':
>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:74: error: invalid
>> use of undefined type 'const struct Eigen::PartialRedux<Eigen::Matrix<double,
>> 10000, 10000, 2, 10000, 10000>, 1>'
>> /usr/local/include/eigen2/Eigen/src/Core/util/ForwardDeclarations.h:102: error:
>> declaration of 'const struct Eigen::PartialRedux<Eigen::Matrix<double, 10000,
>> 10000, 2, 10000, 10000>, 1>'
>>
>> [...] finally ends with:
>>
>> /usr/local/include/eigen2/Eigen/src/Core/CwiseUnaryOp.h:75: error: using invalid
>> field 'Eigen::CwiseUnaryOp<UnaryOp, MatrixType>::m_functor'
>> make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
>> make[2]: *** Waiting for unfinished jobs....
>> make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
>> make: *** [all] Error 2
>>
>>
>> any idea what's wrong?
>>
>> Eiso
>>
>>
>> Igor Filippov wrote:
>>> What is the equivalent of the option "--disable-dynamic-modules"  in
>>> configure script for cmake?
>>>
>>> Igor
>>>
>>>
>>> On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:
>>>> Hello all,
>>>>
>>>> The release of Open Babel 2.3.0 is coming up soon. There have been
>>>> many changes so it would be great to get some feedback on whether the
>>>> current release candidates are working.
>>>>
>>>> These are available at
>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
>>>> for Linux and http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
>>>> for Windows.
>>>>
>>>> I'm responsible for the new compiling documentation, currently
>>>> available at http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
>>>> If there are any problems with these, please let us know also.
>>>>
>>>> Regards,
>>>>      Noel
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by
>>>>
>>>> Make an app they can't live without
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>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>>>
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>>>
>>
>>
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>


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Re: compiling release candidate

Noel O'Boyle
Administrator
On 25 August 2010 12:18, Eiso AB <[hidden email]> wrote:
> hi Noel,
>
> eigen2-2.0.5.tar.bz2
>
> uname -a
> Linux xxx.xxx.net 2.6.18-194.3.1.el5 #1 SMP Fri May 7 01:52:57 EDT 2010 i686
> i686 i386 GNU/Linux

Thanks.

> Eiso
> ps. shouldn't the reply to field in this list be the list instead of the
> sender?

The field is set deliberately. Let's not start that discussion here :-)

> Noel O'Boyle wrote:
>>
>> We just discussed this on openbabel-devel. It seems that it's a bug in
>> an older version of Eigen. You need to upgrade the version of Eigen
>> installed - meanwhile, we need to fix OpenBabel to workaround this
>> bug.
>>
>> Just for the record, what version of Eigen exactly do you have
>> installed, and what OS is it?
>>
>> - Noel
>>
>> On 25 August 2010 11:16, Eiso AB<[hidden email]>  wrote:
>>>
>>> I'm trying to compile the release candidate and getting this:
>>>
>>> [ 33%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.o
>>> [ 34%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.o
>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:28:23:
>>> error:
>>> Eigen/Dense: No such file or directory
>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp: In member
>>> function
>>> 'Eigen::Vector3d OpenBabel::OBAlign::MoveToOrigin(Eigen::MatrixXd&)':
>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:74: error:
>>> invalid
>>> use of undefined type 'const struct
>>> Eigen::PartialRedux<Eigen::Matrix<double,
>>> 10000, 10000, 2, 10000, 10000>, 1>'
>>> /usr/local/include/eigen2/Eigen/src/Core/util/ForwardDeclarations.h:102:
>>> error:
>>> declaration of 'const struct Eigen::PartialRedux<Eigen::Matrix<double,
>>> 10000,
>>> 10000, 2, 10000, 10000>, 1>'
>>>
>>> [...] finally ends with:
>>>
>>> /usr/local/include/eigen2/Eigen/src/Core/CwiseUnaryOp.h:75: error: using
>>> invalid
>>> field 'Eigen::CwiseUnaryOp<UnaryOp, MatrixType>::m_functor'
>>> make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
>>> make[2]: *** Waiting for unfinished jobs....
>>> make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>>
>>> any idea what's wrong?
>>>
>>> Eiso
>>>
>>>
>>> Igor Filippov wrote:
>>>>
>>>> What is the equivalent of the option "--disable-dynamic-modules"  in
>>>> configure script for cmake?
>>>>
>>>> Igor
>>>>
>>>>
>>>> On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:
>>>>>
>>>>> Hello all,
>>>>>
>>>>> The release of Open Babel 2.3.0 is coming up soon. There have been
>>>>> many changes so it would be great to get some feedback on whether the
>>>>> current release candidates are working.
>>>>>
>>>>> These are available at
>>>>>
>>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
>>>>> for Linux and
>>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
>>>>> for Windows.
>>>>>
>>>>> I'm responsible for the new compiling documentation, currently
>>>>> available at
>>>>> http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
>>>>> If there are any problems with these, please let us know also.
>>>>>
>>>>> Regards,
>>>>>     Noel
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by
>>>>>
>>>>> Make an app they can't live without
>>>>> Enter the BlackBerry Developer Challenge
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Re: compiling release candidate

Eiso AB-2
Noel O'Boyle wrote:
> On 25 August 2010 12:18, Eiso AB<[hidden email]>  wrote:
>> hi Noel,
>>
>> eigen2-2.0.5.tar.bz2

eigen-2.0.15 looks ok.

it's confusing that eigen has no installation instructions.
mkdir build ; cd build ; cmake ../ ; make ; make install
seems to do the trick.

Eiso




>>
>> uname -a
>> Linux xxx.xxx.net 2.6.18-194.3.1.el5 #1 SMP Fri May 7 01:52:57 EDT 2010 i686
>> i686 i386 GNU/Linux
>
> Thanks.
>
>> Eiso
>> ps. shouldn't the reply to field in this list be the list instead of the
>> sender?
>
> The field is set deliberately. Let's not start that discussion here :-)
>
>> Noel O'Boyle wrote:
>>>
>>> We just discussed this on openbabel-devel. It seems that it's a bug in
>>> an older version of Eigen. You need to upgrade the version of Eigen
>>> installed - meanwhile, we need to fix OpenBabel to workaround this
>>> bug.
>>>
>>> Just for the record, what version of Eigen exactly do you have
>>> installed, and what OS is it?
>>>
>>> - Noel
>>>
>>> On 25 August 2010 11:16, Eiso AB<[hidden email]>    wrote:
>>>>
>>>> I'm trying to compile the release candidate and getting this:
>>>>
>>>> [ 33%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.o
>>>> [ 34%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.o
>>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:28:23:
>>>> error:
>>>> Eigen/Dense: No such file or directory
>>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp: In member
>>>> function
>>>> 'Eigen::Vector3d OpenBabel::OBAlign::MoveToOrigin(Eigen::MatrixXd&)':
>>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:74: error:
>>>> invalid
>>>> use of undefined type 'const struct
>>>> Eigen::PartialRedux<Eigen::Matrix<double,
>>>> 10000, 10000, 2, 10000, 10000>, 1>'
>>>> /usr/local/include/eigen2/Eigen/src/Core/util/ForwardDeclarations.h:102:
>>>> error:
>>>> declaration of 'const struct Eigen::PartialRedux<Eigen::Matrix<double,
>>>> 10000,
>>>> 10000, 2, 10000, 10000>, 1>'
>>>>
>>>> [...] finally ends with:
>>>>
>>>> /usr/local/include/eigen2/Eigen/src/Core/CwiseUnaryOp.h:75: error: using
>>>> invalid
>>>> field 'Eigen::CwiseUnaryOp<UnaryOp, MatrixType>::m_functor'
>>>> make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
>>>> make[2]: *** Waiting for unfinished jobs....
>>>> make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>>
>>>>
>>>> any idea what's wrong?
>>>>
>>>> Eiso
>>>>
>>>>
>>>> Igor Filippov wrote:
>>>>>
>>>>> What is the equivalent of the option "--disable-dynamic-modules"  in
>>>>> configure script for cmake?
>>>>>
>>>>> Igor
>>>>>
>>>>>
>>>>> On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:
>>>>>>
>>>>>> Hello all,
>>>>>>
>>>>>> The release of Open Babel 2.3.0 is coming up soon. There have been
>>>>>> many changes so it would be great to get some feedback on whether the
>>>>>> current release candidates are working.
>>>>>>
>>>>>> These are available at
>>>>>>
>>>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
>>>>>> for Linux and
>>>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
>>>>>> for Windows.
>>>>>>
>>>>>> I'm responsible for the new compiling documentation, currently
>>>>>> available at
>>>>>> http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
>>>>>> If there are any problems with these, please let us know also.
>>>>>>
>>>>>> Regards,
>>>>>>      Noel
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by
>>>>>>
>>>>>> Make an app they can't live without
>>>>>> Enter the BlackBerry Developer Challenge
>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>> _______________________________________________
>>>>>> OpenBabel-discuss mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by
>>>>>
>>>>> Make an app they can't live without
>>>>> Enter the BlackBerry Developer Challenge
>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>> _______________________________________________
>>>>> OpenBabel-discuss mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
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>>>> worldwide. Take advantage of special opportunities to increase revenue
>>>> and
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>>>>
>>>
>>
>>
>


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Re: compiling release candidate

Noel O'Boyle
Administrator
On 25 August 2010 13:55, Eiso AB <[hidden email]> wrote:

> Noel O'Boyle wrote:
>>
>> On 25 August 2010 12:18, Eiso AB<[hidden email]>  wrote:
>>>
>>> hi Noel,
>>>
>>> eigen2-2.0.5.tar.bz2
>
> eigen-2.0.15 looks ok.
>
> it's confusing that eigen has no installation instructions.
> mkdir build ; cd build ; cmake ../ ; make ; make install
> seems to do the trick.

You're right - it might be good to pass this on to the Eigen
developers. When I used it, I just used it directly from the zip
(-DEIGEN2_INCLUDE_DIR=wherever).

> Eiso
>
>
>
>
>>>
>>> uname -a
>>> Linux xxx.xxx.net 2.6.18-194.3.1.el5 #1 SMP Fri May 7 01:52:57 EDT 2010
>>> i686
>>> i686 i386 GNU/Linux
>>
>> Thanks.
>>
>>> Eiso
>>> ps. shouldn't the reply to field in this list be the list instead of the
>>> sender?
>>
>> The field is set deliberately. Let's not start that discussion here :-)
>>
>>> Noel O'Boyle wrote:
>>>>
>>>> We just discussed this on openbabel-devel. It seems that it's a bug in
>>>> an older version of Eigen. You need to upgrade the version of Eigen
>>>> installed - meanwhile, we need to fix OpenBabel to workaround this
>>>> bug.
>>>>
>>>> Just for the record, what version of Eigen exactly do you have
>>>> installed, and what OS is it?
>>>>
>>>> - Noel
>>>>
>>>> On 25 August 2010 11:16, Eiso AB<[hidden email]>    wrote:
>>>>>
>>>>> I'm trying to compile the release candidate and getting this:
>>>>>
>>>>> [ 33%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.o
>>>>> [ 34%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.o
>>>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:28:23:
>>>>> error:
>>>>> Eigen/Dense: No such file or directory
>>>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp: In member
>>>>> function
>>>>> 'Eigen::Vector3d OpenBabel::OBAlign::MoveToOrigin(Eigen::MatrixXd&)':
>>>>> /home/e.ab/software/src/openbabel-2.3.0b2/src/math/align.cpp:74: error:
>>>>> invalid
>>>>> use of undefined type 'const struct
>>>>> Eigen::PartialRedux<Eigen::Matrix<double,
>>>>> 10000, 10000, 2, 10000, 10000>, 1>'
>>>>>
>>>>> /usr/local/include/eigen2/Eigen/src/Core/util/ForwardDeclarations.h:102:
>>>>> error:
>>>>> declaration of 'const struct Eigen::PartialRedux<Eigen::Matrix<double,
>>>>> 10000,
>>>>> 10000, 2, 10000, 10000>, 1>'
>>>>>
>>>>> [...] finally ends with:
>>>>>
>>>>> /usr/local/include/eigen2/Eigen/src/Core/CwiseUnaryOp.h:75: error:
>>>>> using
>>>>> invalid
>>>>> field 'Eigen::CwiseUnaryOp<UnaryOp, MatrixType>::m_functor'
>>>>> make[2]: *** [src/CMakeFiles/openbabel.dir/math/align.o] Error 1
>>>>> make[2]: *** Waiting for unfinished jobs....
>>>>> make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
>>>>> make: *** [all] Error 2
>>>>>
>>>>>
>>>>> any idea what's wrong?
>>>>>
>>>>> Eiso
>>>>>
>>>>>
>>>>> Igor Filippov wrote:
>>>>>>
>>>>>> What is the equivalent of the option "--disable-dynamic-modules"  in
>>>>>> configure script for cmake?
>>>>>>
>>>>>> Igor
>>>>>>
>>>>>>
>>>>>> On Sat, 2010-08-21 at 15:03 -0400, Noel O'Boyle wrote:
>>>>>>>
>>>>>>> Hello all,
>>>>>>>
>>>>>>> The release of Open Babel 2.3.0 is coming up soon. There have been
>>>>>>> many changes so it would be great to get some feedback on whether the
>>>>>>> current release candidates are working.
>>>>>>>
>>>>>>> These are available at
>>>>>>>
>>>>>>>
>>>>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download
>>>>>>> for Linux and
>>>>>>>
>>>>>>> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-18/OpenBabel2.3.0rc2_Windows_Installer.exe/download
>>>>>>> for Windows.
>>>>>>>
>>>>>>> I'm responsible for the new compiling documentation, currently
>>>>>>> available at
>>>>>>>
>>>>>>> http://baoilleach.webfactional.com/site_media/ob-docs/Installation/install.html#compiling-open-babel.
>>>>>>> If there are any problems with these, please let us know also.
>>>>>>>
>>>>>>> Regards,
>>>>>>>     Noel
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> This SF.net email is sponsored by
>>>>>>>
>>>>>>> Make an app they can't live without
>>>>>>> Enter the BlackBerry Developer Challenge
>>>>>>> http://p.sf.net/sfu/RIM-dev2dev
>>>>>>> _______________________________________________
>>>>>>> OpenBabel-discuss mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by
>>>>>>
>>>>>> Make an app they can't live without
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>>>>>> _______________________________________________
>>>>>> OpenBabel-discuss mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>> users
>>>>> worldwide. Take advantage of special opportunities to increase revenue
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>>>>> [hidden email]
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>>>>>
>>>>
>>>
>>>
>>
>
>

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