Build slicer from source - missing library

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Build slicer from source - missing library

Richter, Daniel Dr.
Hi,

I am stuck with building slicer from source on linux 64bit, Debian 5. The super build process stops when configuring for NUMPY:

-- NUMPY_DIR: /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY
-- NUMPY_SETUP_CMD: setup.py;config
NUMPY Errors detected:

/u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython)

CMake Error at /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_environment.cmake:63 (message):
  Error in configure step of NUMPY.  See
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_output.txt
  and
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_error.txt
Call Stack (most recent call first):
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step.cmake:13 (numpy_setup_command)

I had a look at the cmake file which calls the customPython executable and tried to reproduce the problem running just this command with the same arguments as in the cmake file on the terminal but I do not get the same error, in fact the program does not seem to do anything then. Anyways, I understand that it is some kind of wrapper program for python. The lib it complains about was in fact missing because the Debian I use did not provide it. I installed it in some directory and added that one to the LD_LIBRARY_PATH, but no success, same error when rerunning make. Does anyone have an idea how to solve this? This is about to drive me crazy...:-D

Is there an efficient way of just rerunning the configure process and clean up the mess for NUMPY to start over? I would like to avoid to rebuild everything from scratch every time...


Thank you so much,

best,
Daniel



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Re: Build slicer from source - missing library

Sharp, Gregory C.
Hi Daniel,
 
I don't know about your shared library mismatch.  Do you have
multiple gcc versions installed?
 
Anyway, regarding the partial re-build.  What I usually do is delete the relevant
directories, then re-run cmake.  For example:
 
rm -rf python* && cmake . && make
 
Greg
 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Richter, Daniel Dr.
Sent: Wednesday, September 11, 2013 9:43 AM
To: [hidden email]
Subject: [slicer-users] Build slicer from source - missing library

Hi,

I am stuck with building slicer from source on linux 64bit, Debian 5. The super build process stops when configuring for NUMPY:

-- NUMPY_DIR: /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY
-- NUMPY_SETUP_CMD: setup.py;config
NUMPY Errors detected:

/u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython)

CMake Error at /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_environment.cmake:63 (message):
  Error in configure step of NUMPY.  See
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_output.txt
  and
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_error.txt
Call Stack (most recent call first):
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step.cmake:13 (numpy_setup_command)

I had a look at the cmake file which calls the customPython executable and tried to reproduce the problem running just this command with the same arguments as in the cmake file on the terminal but I do not get the same error, in fact the program does not seem to do anything then. Anyways, I understand that it is some kind of wrapper program for python. The lib it complains about was in fact missing because the Debian I use did not provide it. I installed it in some directory and added that one to the LD_LIBRARY_PATH, but no success, same error when rerunning make. Does anyone have an idea how to solve this? This is about to drive me crazy...:-D

Is there an efficient way of just rerunning the configure process and clean up the mess for NUMPY to start over? I would like to avoid to rebuild everything from scratch every time...


Thank you so much,

best,
Daniel



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Re: Build slicer from source - missing library

Jean-Christophe Fillion-Robin
Hi Richter, 


Let us know what are you findings.

Hth
Jc


On Wed, Sep 11, 2013 at 10:05 AM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Daniel,
 
I don't know about your shared library mismatch.  Do you have
multiple gcc versions installed?
 
Anyway, regarding the partial re-build.  What I usually do is delete the relevant
directories, then re-run cmake.  For example:
 
rm -rf python* && cmake . && make
 
Greg
 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Richter, Daniel Dr.
Sent: Wednesday, September 11, 2013 9:43 AM
To: [hidden email]
Subject: [slicer-users] Build slicer from source - missing library

Hi,

I am stuck with building slicer from source on linux 64bit, Debian 5. The super build process stops when configuring for NUMPY:

-- NUMPY_DIR: /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY
-- NUMPY_SETUP_CMD: setup.py;config
NUMPY Errors detected:

/u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython)

CMake Error at /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_environment.cmake:63 (message):
  Error in configure step of NUMPY.  See
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_output.txt
  and
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_error.txt
Call Stack (most recent call first):
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step.cmake:13 (numpy_setup_command)

I had a look at the cmake file which calls the customPython executable and tried to reproduce the problem running just this command with the same arguments as in the cmake file on the terminal but I do not get the same error, in fact the program does not seem to do anything then. Anyways, I understand that it is some kind of wrapper program for python. The lib it complains about was in fact missing because the Debian I use did not provide it. I installed it in some directory and added that one to the LD_LIBRARY_PATH, but no success, same error when rerunning make. Does anyone have an idea how to solve this? This is about to drive me crazy...:-D

Is there an efficient way of just rerunning the configure process and clean up the mess for NUMPY to start over? I would like to avoid to rebuild everything from scratch every time...


Thank you so much,

best,
Daniel



_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/FAQ



--
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Re: Build slicer from source - missing library

Richter, Daniel Dr.
Thank you both,

I tried the things you added to the wiki and my standard libraries do not have the GLIBCXX version required. However, I thought by installing a more recent version of the library I could fix the problem which I somehow can not. I installed everything locally as I do not have ROOT rights but changed the ld library path accordingly. During the build process the newer library is still not found. I am probably missing some important step.

Well, I'll try on a newer system now first, to see if I get Slicer to build there.

best,
Daniel

--
Dr. Daniel Richter
Biophysics Department

Room SB3.3.195

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From: Jean-Christophe Fillion-Robin [[hidden email]]
Sent: 11 September 2013 17:19
To: Sharp, Gregory C.
Cc: Richter, Daniel Dr.; [hidden email]
Subject: Re: [slicer-users] Build slicer from source - missing library

Hi Richter, 


Let us know what are you findings.

Hth
Jc


On Wed, Sep 11, 2013 at 10:05 AM, Sharp, Gregory C. <[hidden email]> wrote:
Hi Daniel,
 
I don't know about your shared library mismatch.  Do you have
multiple gcc versions installed?
 
Anyway, regarding the partial re-build.  What I usually do is delete the relevant
directories, then re-run cmake.  For example:
 
rm -rf python* && cmake . && make
 
Greg
 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Richter, Daniel Dr.
Sent: Wednesday, September 11, 2013 9:43 AM
To: [hidden email]
Subject: [slicer-users] Build slicer from source - missing library

Hi,

I am stuck with building slicer from source on linux 64bit, Debian 5. The super build process stops when configuring for NUMPY:

-- NUMPY_DIR: /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY
-- NUMPY_SETUP_CMD: setup.py;config
NUMPY Errors detected:

/u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/python-install/bin/customPython)

CMake Error at /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_environment.cmake:63 (message):
  Error in configure step of NUMPY.  See
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_output.txt
  and
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step_error.txt
Call Stack (most recent call first):
  /u/drichter/AIXd/user/drichter/share/Slicer-Superbuild-Debug/NUMPY_configure_step.cmake:13 (numpy_setup_command)

I had a look at the cmake file which calls the customPython executable and tried to reproduce the problem running just this command with the same arguments as in the cmake file on the terminal but I do not get the same error, in fact the program does not seem to do anything then. Anyways, I understand that it is some kind of wrapper program for python. The lib it complains about was in fact missing because the Debian I use did not provide it. I installed it in some directory and added that one to the LD_LIBRARY_PATH, but no success, same error when rerunning make. Does anyone have an idea how to solve this? This is about to drive me crazy...:-D

Is there an efficient way of just rerunning the configure process and clean up the mess for NUMPY to start over? I would like to avoid to rebuild everything from scratch every time...


Thank you so much,

best,
Daniel



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/FAQ



--
+1 919 869 8849

_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/FAQ