It looks like 'slicer' is not captitalized in SuperBuild/External_CTK.cmake - can you try fixing that an trying the build again?

if(Slicer_USE_PYTHONQT)
list(APPEND optional_ep_args
-DPYTHON_LIBRARY:FILEPATH=${slicer_PYTHON_LIBRARY}
-DPYTHON_INCLUDE_DIR:PATH=${slicer_PYTHON_INCLUDE}
-DPYTHON_EXECUTABLE:FILEPATH=${slicer_PYTHON_EXECUTABLE}
-DCTK_LIB_Scripting/Python/Core:BOOL=${Slicer_USE_PYTHONQT}

It now says

46%] Performing configure step for 'CTK'
-- Generated: /software/Slicer4/superbuild/CTK-build/DGraphInput-alldep.txt
-- Generated: /software/Slicer4/superbuild/CTK-build/DGraphInput-alldep-withext.txt

-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE)
CMake Error at CMakeLists.txt:750 (message):
PYTHON_EXECUTABLE variable 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

and from what I can see Python compiled fine

Did you fix the capitalization of all three variables?

  -DPYTHON_EXECUTABLE:FILEPATH=${slicer_PYTHON_EXECUTABLE}

Yes , here is their current definition

-DPYTHON_LIBRARY:FILEPATH=${Slicer_PYTHON_LIBRARY}
-DPYTHON_INCLUDE_DIR:PATH=${Slicer_PYTHON_INCLUDE}
-DPYTHON_EXECUTABLE:FILEPATH=${Slicer_PYTHON_EXECUTABLE}

Actually it looks like that one (slicer_PYTHON_EXECUTABLE) is meant to be lower case, but the others should be upper case. Can you try that combination?

-Steve

Then I get

-- Found PythonInterp: /software/Slicer4/superbuild/python-install/bin/customPython (found version "2.7.3")
-- Could NOT find PythonLibs (missing: PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS)
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

We should probably give up this remote debugging, but I will try one more time:

Can you PLEASE be explicit about that you changed and what that resulted in?

I assume by the recent sequence of comments that you now have this:

-DPYTHON_LIBRARY:FILEPATH=${Slicer_PYTHON_LIBRARY}
-DPYTHON_INCLUDE_DIR:PATH=${Slicer_PYTHON_INCLUDE}
-DPYTHON_EXECUTABLE:FILEPATH=${slicer_PYTHON_EXECUTABLE}

but that leads to the same error message as you got when you used:

-DPYTHON_LIBRARY:FILEPATH=${slicer_PYTHON_LIBRARY}
-DPYTHON_INCLUDE_DIR:PATH=${slicer_PYTHON_INCLUDE}
-DPYTHON_EXECUTABLE:FILEPATH=${slicer_PYTHON_EXECUTABLE}

This does not make sense to me.

What I suggest is that you make a github fork of slicer and that you create a branch with the specific changes and then then provide the link to those changes along with the compile output you get. That way there will be no ambiguity about which changes lead to which error messages.

yes, what you say is exactly correct lower and upper letter do not matter. However if I set
-DPYTHON_LIBRARY:FILEPATH=${Slicer_PYTHON_LIBRARY}
-DPYTHON_INCLUDE_DIR:PATH=${Slicer_PYTHON_INCLUDE}
-DPYTHON_EXECUTABLE:FILEPATH=${slicer_PYTHON_EXECUTABLE}

on a machine where Slicer compiles the change breaks the compilation. If I do a grep on trunk/Superbuild then

-DPYTHON_LIBRARY:FILEPATH=${slicer_PYTHON_LIBRARY}
-DPYTHON_INCLUDE_DIR:PATH=${slicer_PYTHON_INCLUDE}
-DPYTHON_EXECUTABLE:FILEPATH=${slicer_PYTHON_EXECUTABLE}

is the correct definition . Sorry for any confusion I have caused

also when I set before those lines

message( "=====> ${slicer_PYTHON_LIBRARY} ${slicer_PYTHON_INCLUDE} ${slicer_PYTHON_EXECUTABLE}" )

then I get

=====> /software/Slicer4/superbuild/python-install/lib/libpython2.7.so /software/Slicer4/superbuild/python-install/include/python2.7 /software/Slicer4/superbuild/python-install/bin/customPython

which seems correct - so lower case is the way to go . In addition the three directories / files exist on my drive

I was able to replicate this by launching an amazon ec2 instance running ubuntu 13.04 (ami-1e831d77) .

The issue seems to be with the version of cmake that is shipped with ubuntu (apparently it is a custom version).

When I rebuilt using my own build of the standard cmake from git I was able to build and run slicer with no problem.

ubuntu@ip-10-149-6-112:~/xvdf/cmake$ /usr/local/bin/cmake --version
cmake version 2.8.10.20130509-gae431

I suggest building (or downloading) your own cmake as a workaround.

yes it now works for me too

Wiki prerequisites have been updated to point out the issue.

http://www.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/Developers/Build_Instructions/Prerequisites&curid=7132&diff=31601&oldid=31188

http://www.slicer.org/slicerWiki/index.php?title=Documentation/4.2/Developers/Build_Instructions/Prerequisites&curid=7486&diff=31599&oldid=30279

Thanks to Steve. Wiki has been updated to explain the developer he should install a different version of cmake.

Ideally, the system should detect that an incorrect version of FindPythonLibs.cmake is used. See 0003116

Hi,

I got the same issue and fixed it by updating CMake version.
However, I'm still interested in knowing why previous cmake version is not working.
What is the difference ?

Thank you.

@Laurent: The need for "clean" version of CMake is explained here: 0003116