PYTHON_INCLUDE_DIR2 when building Slicer4

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PYTHON_INCLUDE_DIR2 when building Slicer4

Yi Gao-2
Dear all,

I just installed a fresh ubuntu (well it's actually lubuntu but I assume their only difference is the desktop environment) version 13.04.

Then of course the first thing is to build slicer. But I got some error in building the CTK.

The error message (using make without multithreads) is as follows:

[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[ 32%] No install step for 'ITKv4'
[ 32%] Completed 'ITKv4'
[ 34%] Built target ITKv4
[ 34%] Performing update step (git fetch) for 'SlicerExecutionModel'
-- SlicerExecutionModel update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-prefix/src/SlicerExecutionModel-stamp/SlicerExecutionModel-update-*.log

[ 34%] Performing configure step for 'SlicerExecutionModel'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-build
[ 35%] Performing build step for 'SlicerExecutionModel'
[  9%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameter.cxx.o
[ 18%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameterGroup.cxx.o
[ 27%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionUtilities.cxx.o
[ 36%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescription.cxx.o
[ 45%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
[ 54%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleProcessInformation.cxx.o
[ 63%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleLogo.cxx.o
[ 72%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleFactory.cxx.o
[ 81%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/BatchMakeUtilities.cxx.o
Linking CXX shared library bin/libModuleDescriptionParser.so
[ 81%] Built target ModuleDescriptionParser
[ 90%] Building CXX object GenerateCLP/CMakeFiles/GenerateCLP.dir/GenerateCLP.cxx.o
Linking CXX executable bin/GenerateCLP
[ 90%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 36%] No install step for 'SlicerExecutionModel'
[ 36%] Completed 'SlicerExecutionModel'
[ 38%] Built target SlicerExecutionModel
[ 38%] Performing update step (git fetch) for 'BRAINSTools'
-- BRAINSTools update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/BRAINSTools-prefix/src/BRAINSTools-stamp/BRAINSTools-update-*.log

[ 38%] No configure step for 'BRAINSTools'
[ 39%] No build step for 'BRAINSTools'
[ 40%] No install step for 'BRAINSTools'
[ 40%] Completed 'BRAINSTools'
[ 42%] Built target BRAINSTools
[ 42%] Performing update step (git fetch) for 'CTK'
-- CTK update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-prefix/src/CTK-stamp/CTK-update-*.log

[ 42%] Performing configure step for 'CTK'
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep.txt
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep-withext.txt
-- Could NOT find PythonLibs (missing:  PYTHON_INCLUDE_DIRS) (found version "2.7.3")
CMake Error at CMakeLists.txt:754 (message):
  PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
  CTK_LIB_Scripting/Python


-- Configuring incomplete, errors occurred!
make[2]: *** [CTK-prefix/src/CTK-stamp/CTK-configure] Error 1
make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
make: *** [all] Error 2
gaoyi@gaoyiXPS:~/usr/work/namic/S4/release20130430/Slicer-build$




I go to Slicer-build/CTK-build dir and did a "ccmake ." there, with advanced parameters.
The variable PYTHON_INCLUDE_DIR is pointing to
/home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7
which i assume is correct.

But after that, the is
PYTHON_INCLUDE_DIR2              PYTHON_INCLUDE_DIR2-NOTFOUND                                                                                                                                                                             


Then, in the CTK/CMakeLists.txt file, line 754 as suggested by the error message, I changed from
  if(NOT PYTHONLIBS_FOUND)
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

to

  if(NOT PYTHONLIBS_FOUND)
    message(${PYTHON_LIBRARIES})
    message(${PYTHON_INCLUDE_DIRS})
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

then in ccmake I hit "c" again and got:



 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/lib/libpython2.7.so

 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7PYTHON_INCLUDE_DIR2-NOTFOUND

 CMake Error at CMakeLists.txt:756 (message):
   PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
   CTK_LIB_Scripting/Python






Could I have some advice on how I should proceed next?

Thanks!

Best,
yi

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
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Re: PYTHON_INCLUDE_DIR2 when building Slicer4

Steve Pieper
Hi Yi - 

This PYTHON_INCLUDE_DIR2 variable looks like something unique to ubuntu's version of cmake[1]. Probably so they can find things in whatever the latest directory hierarchy is.

Did you try with a standard version of cmake?

-Steve



On Wed, May 1, 2013 at 7:01 AM, Gao, Yi <[hidden email]> wrote:
Dear all,

I just installed a fresh ubuntu (well it's actually lubuntu but I assume their only difference is the desktop environment) version 13.04.

Then of course the first thing is to build slicer. But I got some error in building the CTK.

The error message (using make without multithreads) is as follows:

[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[ 32%] No install step for 'ITKv4'
[ 32%] Completed 'ITKv4'
[ 34%] Built target ITKv4
[ 34%] Performing update step (git fetch) for 'SlicerExecutionModel'
-- SlicerExecutionModel update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-prefix/src/SlicerExecutionModel-stamp/SlicerExecutionModel-update-*.log

[ 34%] Performing configure step for 'SlicerExecutionModel'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-build
[ 35%] Performing build step for 'SlicerExecutionModel'
[  9%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameter.cxx.o
[ 18%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameterGroup.cxx.o
[ 27%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionUtilities.cxx.o
[ 36%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescription.cxx.o
[ 45%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
[ 54%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleProcessInformation.cxx.o
[ 63%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleLogo.cxx.o
[ 72%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleFactory.cxx.o
[ 81%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/BatchMakeUtilities.cxx.o
Linking CXX shared library bin/libModuleDescriptionParser.so
[ 81%] Built target ModuleDescriptionParser
[ 90%] Building CXX object GenerateCLP/CMakeFiles/GenerateCLP.dir/GenerateCLP.cxx.o
Linking CXX executable bin/GenerateCLP
[ 90%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 36%] No install step for 'SlicerExecutionModel'
[ 36%] Completed 'SlicerExecutionModel'
[ 38%] Built target SlicerExecutionModel
[ 38%] Performing update step (git fetch) for 'BRAINSTools'
-- BRAINSTools update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/BRAINSTools-prefix/src/BRAINSTools-stamp/BRAINSTools-update-*.log

[ 38%] No configure step for 'BRAINSTools'
[ 39%] No build step for 'BRAINSTools'
[ 40%] No install step for 'BRAINSTools'
[ 40%] Completed 'BRAINSTools'
[ 42%] Built target BRAINSTools
[ 42%] Performing update step (git fetch) for 'CTK'
-- CTK update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-prefix/src/CTK-stamp/CTK-update-*.log

[ 42%] Performing configure step for 'CTK'
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep.txt
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep-withext.txt
-- Could NOT find PythonLibs (missing:  PYTHON_INCLUDE_DIRS) (found version "2.7.3")
CMake Error at CMakeLists.txt:754 (message):
  PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
  CTK_LIB_Scripting/Python


-- Configuring incomplete, errors occurred!
make[2]: *** [CTK-prefix/src/CTK-stamp/CTK-configure] Error 1
make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
make: *** [all] Error 2
gaoyi@gaoyiXPS:~/usr/work/namic/S4/release20130430/Slicer-build$




I go to Slicer-build/CTK-build dir and did a "ccmake ." there, with advanced parameters.
The variable PYTHON_INCLUDE_DIR is pointing to
/home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7
which i assume is correct.

But after that, the is
PYTHON_INCLUDE_DIR2              PYTHON_INCLUDE_DIR2-NOTFOUND                                                                                                                                                                             


Then, in the CTK/CMakeLists.txt file, line 754 as suggested by the error message, I changed from
  if(NOT PYTHONLIBS_FOUND)
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

to

  if(NOT PYTHONLIBS_FOUND)
    message(${PYTHON_LIBRARIES})
    message(${PYTHON_INCLUDE_DIRS})
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

then in ccmake I hit "c" again and got:



 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/lib/libpython2.7.so

 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7PYTHON_INCLUDE_DIR2-NOTFOUND

 CMake Error at CMakeLists.txt:756 (message):
   PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
   CTK_LIB_Scripting/Python






Could I have some advice on how I should proceed next?

Thanks!

Best,
yi

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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|

Re: PYTHON_INCLUDE_DIR2 when building Slicer4

Yi Gao-2
Hi Steve,

I didn't... I just switched back to ubuntu 12.04 so that I can work on the real stuff quicker... Under 12.04 the version of the system's cmake does not meet Slicer's requirement so I used self-build cmake...

Sorry that I didn't further dig into the problem but i'm happy that i have Slicer working now. :)

Best,
yi


On Wed, May 1, 2013 at 4:18 PM, Steve Pieper <[hidden email]> wrote:
Hi Yi - 

This PYTHON_INCLUDE_DIR2 variable looks like something unique to ubuntu's version of cmake[1]. Probably so they can find things in whatever the latest directory hierarchy is.

Did you try with a standard version of cmake?

-Steve



On Wed, May 1, 2013 at 7:01 AM, Gao, Yi <[hidden email]> wrote:
Dear all,

I just installed a fresh ubuntu (well it's actually lubuntu but I assume their only difference is the desktop environment) version 13.04.

Then of course the first thing is to build slicer. But I got some error in building the CTK.

The error message (using make without multithreads) is as follows:

[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[ 32%] No install step for 'ITKv4'
[ 32%] Completed 'ITKv4'
[ 34%] Built target ITKv4
[ 34%] Performing update step (git fetch) for 'SlicerExecutionModel'
-- SlicerExecutionModel update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-prefix/src/SlicerExecutionModel-stamp/SlicerExecutionModel-update-*.log

[ 34%] Performing configure step for 'SlicerExecutionModel'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-build
[ 35%] Performing build step for 'SlicerExecutionModel'
[  9%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameter.cxx.o
[ 18%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameterGroup.cxx.o
[ 27%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionUtilities.cxx.o
[ 36%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescription.cxx.o
[ 45%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
[ 54%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleProcessInformation.cxx.o
[ 63%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleLogo.cxx.o
[ 72%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleFactory.cxx.o
[ 81%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/BatchMakeUtilities.cxx.o
Linking CXX shared library bin/libModuleDescriptionParser.so
[ 81%] Built target ModuleDescriptionParser
[ 90%] Building CXX object GenerateCLP/CMakeFiles/GenerateCLP.dir/GenerateCLP.cxx.o
Linking CXX executable bin/GenerateCLP
[ 90%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 36%] No install step for 'SlicerExecutionModel'
[ 36%] Completed 'SlicerExecutionModel'
[ 38%] Built target SlicerExecutionModel
[ 38%] Performing update step (git fetch) for 'BRAINSTools'
-- BRAINSTools update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/BRAINSTools-prefix/src/BRAINSTools-stamp/BRAINSTools-update-*.log

[ 38%] No configure step for 'BRAINSTools'
[ 39%] No build step for 'BRAINSTools'
[ 40%] No install step for 'BRAINSTools'
[ 40%] Completed 'BRAINSTools'
[ 42%] Built target BRAINSTools
[ 42%] Performing update step (git fetch) for 'CTK'
-- CTK update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-prefix/src/CTK-stamp/CTK-update-*.log

[ 42%] Performing configure step for 'CTK'
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep.txt
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep-withext.txt
-- Could NOT find PythonLibs (missing:  PYTHON_INCLUDE_DIRS) (found version "2.7.3")
CMake Error at CMakeLists.txt:754 (message):
  PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
  CTK_LIB_Scripting/Python


-- Configuring incomplete, errors occurred!
make[2]: *** [CTK-prefix/src/CTK-stamp/CTK-configure] Error 1
make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
make: *** [all] Error 2
gaoyi@gaoyiXPS:~/usr/work/namic/S4/release20130430/Slicer-build$




I go to Slicer-build/CTK-build dir and did a "ccmake ." there, with advanced parameters.
The variable PYTHON_INCLUDE_DIR is pointing to
/home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7
which i assume is correct.

But after that, the is
PYTHON_INCLUDE_DIR2              PYTHON_INCLUDE_DIR2-NOTFOUND                                                                                                                                                                             


Then, in the CTK/CMakeLists.txt file, line 754 as suggested by the error message, I changed from
  if(NOT PYTHONLIBS_FOUND)
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

to

  if(NOT PYTHONLIBS_FOUND)
    message(${PYTHON_LIBRARIES})
    message(${PYTHON_INCLUDE_DIRS})
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

then in ccmake I hit "c" again and got:



 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/lib/libpython2.7.so

 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7PYTHON_INCLUDE_DIR2-NOTFOUND

 CMake Error at CMakeLists.txt:756 (message):
   PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
   CTK_LIB_Scripting/Python






Could I have some advice on how I should proceed next?

Thanks!

Best,
yi

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: PYTHON_INCLUDE_DIR2 when building Slicer4

Ranveer Joyseeree-2
Hi Slicer Developers,

I have the exact same problem. In summary, pythonLibs is not found during the build process, thereby producing an error. The problem appeared when I upgraded to ubuntu v13.04 and tried to install slicer4 from scratch. I am using the standard version of cmake-2.8.10.1. Going back to ubuntu v12.04 is not an option for me so I would like to request that we find a proper solution to the issue. Many thanks!

Best regards,
Randy



On 02.05.2013 21:48, Gao, Yi wrote:
Hi Steve,

I didn't... I just switched back to ubuntu 12.04 so that I can work on the real stuff quicker... Under 12.04 the version of the system's cmake does not meet Slicer's requirement so I used self-build cmake...

Sorry that I didn't further dig into the problem but i'm happy that i have Slicer working now. :)

Best,
yi


On Wed, May 1, 2013 at 4:18 PM, Steve Pieper <[hidden email]> wrote:
Hi Yi - 

This PYTHON_INCLUDE_DIR2 variable looks like something unique to ubuntu's version of cmake[1]. Probably so they can find things in whatever the latest directory hierarchy is.

Did you try with a standard version of cmake?

-Steve



On Wed, May 1, 2013 at 7:01 AM, Gao, Yi <[hidden email]> wrote:
Dear all,

I just installed a fresh ubuntu (well it's actually lubuntu but I assume their only difference is the desktop environment) version 13.04.

Then of course the first thing is to build slicer. But I got some error in building the CTK.

The error message (using make without multithreads) is as follows:

[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[ 32%] No install step for 'ITKv4'
[ 32%] Completed 'ITKv4'
[ 34%] Built target ITKv4
[ 34%] Performing update step (git fetch) for 'SlicerExecutionModel'
-- SlicerExecutionModel update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-prefix/src/SlicerExecutionModel-stamp/SlicerExecutionModel-update-*.log

[ 34%] Performing configure step for 'SlicerExecutionModel'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-build
[ 35%] Performing build step for 'SlicerExecutionModel'
[  9%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameter.cxx.o
[ 18%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameterGroup.cxx.o
[ 27%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionUtilities.cxx.o
[ 36%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescription.cxx.o
[ 45%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
[ 54%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleProcessInformation.cxx.o
[ 63%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleLogo.cxx.o
[ 72%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleFactory.cxx.o
[ 81%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/BatchMakeUtilities.cxx.o
Linking CXX shared library bin/libModuleDescriptionParser.so
[ 81%] Built target ModuleDescriptionParser
[ 90%] Building CXX object GenerateCLP/CMakeFiles/GenerateCLP.dir/GenerateCLP.cxx.o
Linking CXX executable bin/GenerateCLP
[ 90%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 36%] No install step for 'SlicerExecutionModel'
[ 36%] Completed 'SlicerExecutionModel'
[ 38%] Built target SlicerExecutionModel
[ 38%] Performing update step (git fetch) for 'BRAINSTools'
-- BRAINSTools update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/BRAINSTools-prefix/src/BRAINSTools-stamp/BRAINSTools-update-*.log

[ 38%] No configure step for 'BRAINSTools'
[ 39%] No build step for 'BRAINSTools'
[ 40%] No install step for 'BRAINSTools'
[ 40%] Completed 'BRAINSTools'
[ 42%] Built target BRAINSTools
[ 42%] Performing update step (git fetch) for 'CTK'
-- CTK update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-prefix/src/CTK-stamp/CTK-update-*.log

[ 42%] Performing configure step for 'CTK'
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep.txt
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep-withext.txt
-- Could NOT find PythonLibs (missing:  PYTHON_INCLUDE_DIRS) (found version "2.7.3")
CMake Error at CMakeLists.txt:754 (message):
  PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
  CTK_LIB_Scripting/Python


-- Configuring incomplete, errors occurred!
make[2]: *** [CTK-prefix/src/CTK-stamp/CTK-configure] Error 1
make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
make: *** [all] Error 2
gaoyi@gaoyiXPS:~/usr/work/namic/S4/release20130430/Slicer-build$




I go to Slicer-build/CTK-build dir and did a "ccmake ." there, with advanced parameters.
The variable PYTHON_INCLUDE_DIR is pointing to
/home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7
which i assume is correct.

But after that, the is
PYTHON_INCLUDE_DIR2              PYTHON_INCLUDE_DIR2-NOTFOUND                                                                                                                                                           &nbs p; & nbsp;               


Then, in the CTK/CMakeLists.txt file, line 754 as suggested by the error message, I changed from
  if(NOT PYTHONLIBS_FOUND)
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

to

  if(NOT PYTHONLIBS_FOUND)
    message(${PYTHON_LIBRARIES})
    message(${PYTHON_INCLUDE_DIRS})
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

then in ccmake I hit "c" again and got:



 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/lib/libpython2.7.so

 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7PYTHON_INCLUDE_DIR2-NOTFOUND

 CMake Error at CMakeLists.txt:756 (message):
   PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
   CTK_LIB_Scripting/Python






Could I have some advice on how I should proceed next?

Thanks!

Best,
yi

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Re: PYTHON_INCLUDE_DIR2 when building Slicer4

Kilian Pohl-2
Please see

http://na-mic.org/Mantis/view.php?id=3103

K


On 5/7/2013 12:30 PM, Ranveer Joyseeree wrote:
Hi Slicer Developers,

I have the exact same problem. In summary, pythonLibs is not found during the build process, thereby producing an error. The problem appeared when I upgraded to ubuntu v13.04 and tried to install slicer4 from scratch. I am using the standard version of cmake-2.8.10.1. Going back to ubuntu v12.04 is not an option for me so I would like to request that we find a proper solution to the issue. Many thanks!

Best regards,
Randy



On 02.05.2013 21:48, Gao, Yi wrote:
Hi Steve,

I didn't... I just switched back to ubuntu 12.04 so that I can work on the real stuff quicker... Under 12.04 the version of the system's cmake does not meet Slicer's requirement so I used self-build cmake...

Sorry that I didn't further dig into the problem but i'm happy that i have Slicer working now. :)

Best,
yi


On Wed, May 1, 2013 at 4:18 PM, Steve Pieper <[hidden email]> wrote:
Hi Yi - 

This PYTHON_INCLUDE_DIR2 variable looks like something unique to ubuntu's version of cmake[1]. Probably so they can find things in whatever the latest directory hierarchy is.

Did you try with a standard version of cmake?

-Steve



On Wed, May 1, 2013 at 7:01 AM, Gao, Yi <[hidden email]> wrote:
Dear all,

I just installed a fresh ubuntu (well it's actually lubuntu but I assume their only difference is the desktop environment) version 13.04.

Then of course the first thing is to build slicer. But I got some error in building the CTK.

The error message (using make without multithreads) is as follows:

[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[ 32%] No install step for 'ITKv4'
[ 32%] Completed 'ITKv4'
[ 34%] Built target ITKv4
[ 34%] Performing update step (git fetch) for 'SlicerExecutionModel'
-- SlicerExecutionModel update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-prefix/src/SlicerExecutionModel-stamp/SlicerExecutionModel-update-*.log

[ 34%] Performing configure step for 'SlicerExecutionModel'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-build
[ 35%] Performing build step for 'SlicerExecutionModel'
[  9%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameter.cxx.o
[ 18%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameterGroup.cxx.o
[ 27%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionUtilities.cxx.o
[ 36%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescription.cxx.o
[ 45%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
[ 54%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleProcessInformation.cxx.o
[ 63%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleLogo.cxx.o
[ 72%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleFactory.cxx.o
[ 81%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/BatchMakeUtilities.cxx.o
Linking CXX shared library bin/libModuleDescriptionParser.so
[ 81%] Built target ModuleDescriptionParser
[ 90%] Building CXX object GenerateCLP/CMakeFiles/GenerateCLP.dir/GenerateCLP.cxx.o
Linking CXX executable bin/GenerateCLP
[ 90%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 36%] No install step for 'SlicerExecutionModel'
[ 36%] Completed 'SlicerExecutionModel'
[ 38%] Built target SlicerExecutionModel
[ 38%] Performing update step (git fetch) for 'BRAINSTools'
-- BRAINSTools update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/BRAINSTools-prefix/src/BRAINSTools-stamp/BRAINSTools-update-*.log

[ 38%] No configure step for 'BRAINSTools'
[ 39%] No build step for 'BRAINSTools'
[ 40%] No install step for 'BRAINSTools'
[ 40%] Completed 'BRAINSTools'
[ 42%] Built target BRAINSTools
[ 42%] Performing update step (git fetch) for 'CTK'
-- CTK update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-prefix/src/CTK-stamp/CTK-update-*.log

[ 42%] Performing configure step for 'CTK'
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep.txt
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep-withext.txt
-- Could NOT find PythonLibs (missing:  PYTHON_INCLUDE_DIRS) (found version "2.7.3")
CMake Error at CMakeLists.txt:754 (message):
  PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
  CTK_LIB_Scripting/Python


-- Configuring incomplete, errors occurred!
make[2]: *** [CTK-prefix/src/CTK-stamp/CTK-configure] Error 1
make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
make: *** [all] Error 2
gaoyi@gaoyiXPS:~/usr/work/namic/S4/release20130430/Slicer-build$




I go to Slicer-build/CTK-build dir and did a "ccmake ." there, with advanced parameters.
The variable PYTHON_INCLUDE_DIR is pointing to
/home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7
which i assume is correct.

But after that, the is
PYTHON_INCLUDE_DIR2              PYTHON_INCLUDE_DIR2-NOTFOUND                                                                                                                                                           &a mp;nbs p; & nbsp;               


Then, in the CTK/CMakeLists.txt file, line 754 as suggested by the error message, I changed from
  if(NOT PYTHONLIBS_FOUND)
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

to

  if(NOT PYTHONLIBS_FOUND)
    message(${PYTHON_LIBRARIES})
    message(${PYTHON_INCLUDE_DIRS})
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

then in ccmake I hit "c" again and got:



 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/lib/libpython2.7.so

 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7PYTHON_INCLUDE_DIR2-NOTFOUND

 CMake Error at CMakeLists.txt:756 (message):
   PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
   CTK_LIB_Scripting/Python






Could I have some advice on how I should proceed next?

Thanks!

Best,
yi

_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject




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Re: PYTHON_INCLUDE_DIR2 when building Slicer4

Jean-Christophe Fillion-Robin
For reference: 

  Issue #3101 has been closed and, thanks to Steve, the wiki has been updated to mention that official CMake version should be used.

  A separate issue (3116) has been created to track the fact either Slicer build system could be improved or FindPythonLibs.cmake provided by Ubuntu could be improved as explained here [1]. More specifically, "PYTHON_INCLUDE_DIR" could be added to the list of path search while trying to set PYTHON_INCLUDE_DIR2.


Would be great if somebody could help testing the suggested solution and then proposing a patch to ubuntu/debian maintainer.



Thanks
Jc




On Tue, May 7, 2013 at 12:37 PM, Kilian Pohl <[hidden email]> wrote:
Please see

http://na-mic.org/Mantis/view.php?id=3103

K



On 5/7/2013 12:30 PM, Ranveer Joyseeree wrote:
Hi Slicer Developers,

I have the exact same problem. In summary, pythonLibs is not found during the build process, thereby producing an error. The problem appeared when I upgraded to ubuntu v13.04 and tried to install slicer4 from scratch. I am using the standard version of cmake-2.8.10.1. Going back to ubuntu v12.04 is not an option for me so I would like to request that we find a proper solution to the issue. Many thanks!

Best regards,
Randy



On 02.05.2013 21:48, Gao, Yi wrote:
Hi Steve,

I didn't... I just switched back to ubuntu 12.04 so that I can work on the real stuff quicker... Under 12.04 the version of the system's cmake does not meet Slicer's requirement so I used self-build cmake...

Sorry that I didn't further dig into the problem but i'm happy that i have Slicer working now. :)

Best,
yi


On Wed, May 1, 2013 at 4:18 PM, Steve Pieper <[hidden email]> wrote:
Hi Yi - 

This PYTHON_INCLUDE_DIR2 variable looks like something unique to ubuntu's version of cmake[1]. Probably so they can find things in whatever the latest directory hierarchy is.

Did you try with a standard version of cmake?

-Steve



On Wed, May 1, 2013 at 7:01 AM, Gao, Yi <[hidden email]> wrote:
Dear all,

I just installed a fresh ubuntu (well it's actually lubuntu but I assume their only difference is the desktop environment) version 13.04.

Then of course the first thing is to build slicer. But I got some error in building the CTK.

The error message (using make without multithreads) is as follows:

[100%] Built target ITKVideoIO
[100%] Built target ITKVideoIO-all
[ 32%] No install step for 'ITKv4'
[ 32%] Completed 'ITKv4'
[ 34%] Built target ITKv4
[ 34%] Performing update step (git fetch) for 'SlicerExecutionModel'
-- SlicerExecutionModel update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-prefix/src/SlicerExecutionModel-stamp/SlicerExecutionModel-update-*.log

[ 34%] Performing configure step for 'SlicerExecutionModel'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/SlicerExecutionModel-build
[ 35%] Performing build step for 'SlicerExecutionModel'
[  9%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameter.cxx.o
[ 18%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleParameterGroup.cxx.o
[ 27%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionUtilities.cxx.o
[ 36%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescription.cxx.o
[ 45%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
[ 54%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleProcessInformation.cxx.o
[ 63%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleLogo.cxx.o
[ 72%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleFactory.cxx.o
[ 81%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/BatchMakeUtilities.cxx.o
Linking CXX shared library bin/libModuleDescriptionParser.so
[ 81%] Built target ModuleDescriptionParser
[ 90%] Building CXX object GenerateCLP/CMakeFiles/GenerateCLP.dir/GenerateCLP.cxx.o
Linking CXX executable bin/GenerateCLP
[ 90%] Built target GenerateCLP
[100%] Built target GenerateCLPLauncher
[ 36%] No install step for 'SlicerExecutionModel'
[ 36%] Completed 'SlicerExecutionModel'
[ 38%] Built target SlicerExecutionModel
[ 38%] Performing update step (git fetch) for 'BRAINSTools'
-- BRAINSTools update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/BRAINSTools-prefix/src/BRAINSTools-stamp/BRAINSTools-update-*.log

[ 38%] No configure step for 'BRAINSTools'
[ 39%] No build step for 'BRAINSTools'
[ 40%] No install step for 'BRAINSTools'
[ 40%] Completed 'BRAINSTools'
[ 42%] Built target BRAINSTools
[ 42%] Performing update step (git fetch) for 'CTK'
-- CTK update command succeeded.  See also /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-prefix/src/CTK-stamp/CTK-update-*.log

[ 42%] Performing configure step for 'CTK'
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep.txt
-- Generated: /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/CTK-build/DGraphInput-alldep-withext.txt
-- Could NOT find PythonLibs (missing:  PYTHON_INCLUDE_DIRS) (found version "2.7.3")
CMake Error at CMakeLists.txt:754 (message):
  PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
  CTK_LIB_Scripting/Python


-- Configuring incomplete, errors occurred!
make[2]: *** [CTK-prefix/src/CTK-stamp/CTK-configure] Error 1
make[1]: *** [CMakeFiles/CTK.dir/all] Error 2
make: *** [all] Error 2
gaoyi@gaoyiXPS:~/usr/work/namic/S4/release20130430/Slicer-build$




I go to Slicer-build/CTK-build dir and did a "ccmake ." there, with advanced parameters.
The variable PYTHON_INCLUDE_DIR is pointing to
/home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7
which i assume is correct.

But after that, the is
PYTHON_INCLUDE_DIR2              PYTHON_INCLUDE_DIR2-NOTFOUND                                                                                                                                                           &a mp;nbs p; & nbsp;               


Then, in the CTK/CMakeLists.txt file, line 754 as suggested by the error message, I changed from
  if(NOT PYTHONLIBS_FOUND)
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

to

  if(NOT PYTHONLIBS_FOUND)
    message(${PYTHON_LIBRARIES})
    message(${PYTHON_INCLUDE_DIRS})
    message(FATAL_ERROR "PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build CTK_LIB_Scripting/Python")
  endif()
endif()

then in ccmake I hit "c" again and got:



 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/lib/libpython2.7.so

 /home/gaoyi/usr/work/namic/S4/release20130430/Slicer-build/python-install/include/python2.7PYTHON_INCLUDE_DIR2-NOTFOUND

 CMake Error at CMakeLists.txt:756 (message):
   PYTHON_LIBRARIES and PYTHON_INCLUDE_DIRS should be set to build
   CTK_LIB_Scripting/Python






Could I have some advice on how I should proceed next?

Thanks!

Best,
yi

_______________________________________________
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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject




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