Re: building Slicer3 3.4

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Re: building Slicer3 3.4

Chris Gorman

On 2009-12-13, at 4:49 PM, Chris Gorman wrote:

Hello,

This didn't post properly.  Trying again.

On 2009-12-13, at 3:13 PM, Chris Gorman wrote:

Hello,

VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK option presented.  From VTK/CMakeLists.txt

SET(VTK_CAN_USE_TK)
IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
  IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
    SET(VTK_CAN_USE_TK 1)
  ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
                     "VTK_CAN_USE_TK" OFF)

The web page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build needs to be updated to inform users about this as it only mentions disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled by default now.  (At least it was on vtk 5.4.2.)

The next issue is building slicer3.  During configure I get 

CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
   Could not find tcl

I tried to hack in the value from my VTK configure, but this doesn't seem to be work, probably due to my lack of understanding of cmake grammar.  Setting it by 

SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")

in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set for vtk.  I also tried to set TCL_LIBRARY to point to the libtcl.dylib, but I think this causing problems too.  This allows the build to continue but not for long.  It fails.  

[  3%] Building CXX object Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx: In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*, const Nrrd*, double*)’:
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795: error: ‘BIFF_STRLEN’ was not declared in this scope
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802: error: ‘err’ was not declared in this scope
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806: error: ‘err’ was not declared in this scope
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810: error: ‘err’ was not declared in this scope
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815: error: ‘err’ was not declared in this scope
/Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824: error: ‘err’ was not declared in this scope
make[2]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
make: *** [all] Error 2

I did a quick google search to find where the declaration of BIFF_STRLEN, but wasn't able to find anything too useful.  My configuration is 

Darwin 10.2.0
cmake 2.8.0
tcl/tk 8.5 (from os x)
incrTcl 3.3 (from macports)
vtk 5.4.2 
itk 3.16.0
kwwidgets 1.0.0
teem 1.11.0
SlicerLibCurl 7.12.1
Slicer3 3.4

In summary.  I would like to find a solution to the cmake configure error, as I believe that is causing problems in addition to the build error.  If anyone has pointers, please let me know.  Thanks.

Chris Gorman



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Re: building Slicer3 3.4

pieper
Administrator
Hi Chris -

I added the note about VTK_USE_COCOA to the wiki page - thanks for the
feedback.  In general those pages about the manual configuration get out
of sync - if you run into problems you can compare your steps the ones
performed by the genlib script (it basically just automates the various
checkouts and cmake configures and builds).  If you want, feel free to
update the wiki with the latest info based on your experiences.

One thing I do know from recent experience is that you'll need to use
teem 1.10 with slicer 3.4 (in teem 1.11 the BIFF_STRLEN was removed).

-Steve

Chris Gorman wrote:

>
> On 2009-12-13, at 4:49 PM, Chris Gorman wrote:
>
>> Hello,
>>
>> This didn't post properly.  Trying again.
>>
>> On 2009-12-13, at 3:13 PM, Chris Gorman wrote:
>>
>>> Hello,
>>>
>>> VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK
>>> option presented.  From VTK/CMakeLists.txt
>>>
>>> SET(VTK_CAN_USE_TK)
>>> IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>   IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>     SET(VTK_CAN_USE_TK 1)
>>>   ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>> ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>> VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
>>>                      "VTK_CAN_USE_TK" OFF)
>>>
>>> The web
>>> page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build 
>>> needs to be updated to inform users about this as it only mentions
>>> disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled
>>> by default now.  (At least it was on vtk 5.4.2.)
>>>
>>> The next issue is building slicer3.  During configure I get
>>>
>>> CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
>>>    Could not find tcl
>>>
>>> I tried to hack in the value from my VTK configure, but this doesn't
>>> seem to be work, probably due to my lack of understanding of cmake
>>> grammar.  Setting it by
>>>
>>> SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")
>>>
>>> in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set
>>> for vtk.  I also tried to set TCL_LIBRARY to point to the
>>> libtcl.dylib, but I think this causing problems too.  This allows the
>>> build to continue but not for long.  It fails.  
>>>
>>> [  3%] Building CXX object
>>> Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:
>>> In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*,
>>> const Nrrd*, double*)’:
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795:
>>> error: ‘BIFF_STRLEN’ was not declared in this scope
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802:
>>> error: ‘err’ was not declared in this scope
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806:
>>> error: ‘err’ was not declared in this scope
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810:
>>> error: ‘err’ was not declared in this scope
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815:
>>> error: ‘err’ was not declared in this scope
>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824:
>>> error: ‘err’ was not declared in this scope
>>> make[2]: ***
>>> [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
>>> make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> I did a quick google search to find where the declaration of
>>> BIFF_STRLEN, but wasn't able to find anything too useful.  My
>>> configuration is
>>>
>>> Darwin 10.2.0
>>> cmake 2.8.0
>>> tcl/tk 8.5 (from os x)
>>> incrTcl 3.3 (from macports)
>>> vtk 5.4.2
>>> itk 3.16.0
>>> kwwidgets 1.0.0
>>> teem 1.11.0
>>> SlicerLibCurl 7.12.1
>>> Slicer3 3.4
>>>
>>> In summary.  I would like to find a solution to the cmake configure
>>> error, as I believe that is causing problems in addition to the build
>>> error.  If anyone has pointers, please let me know.  Thanks.
>>>
>>> Chris Gorman
>>
>
>
> ------------------------------------------------------------------------
>
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> slicer-devel mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
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Re: building Slicer3 3.4

Chris Gorman
Hello,

First off thank you for the pointer on teem 1.10 Steve.  It resolved the error that was occurring regarding BIFF_STRLEN.  My build went a bit further after that.  My next problem was the inability for the cmake command to find a TCL_LIBRARY.  Inspection of the build scripts indicated it was set as a tcl variable and passed to cmake.  I ran a grep through the source code and found a reference to it appeared to be used only in Applications/GUI/Slicer3.cxx amongst a few references in the .svn directories.  I then edited Applications/GUI/Slicer3.cxx and hard coded my tcl library in place of the build one.  Next I commented out the check for TCL_LIBRARY in Libs/SlicerIO/CMakeLists.txt and tried to build again.  I got a bit further but it still failed to build.

Linking C executable ../../bin/scat
cd /Users/chrisgorman/src/medical-imaging/slicer/bingcc/Libs/SlicerIO && /opt/local/bin/cmake -E cmake_link_script CMakeFiles/scat.dir/link.txt --verbose=1
/usr/bin/gcc   -mmacosx-version-min=10.6   -Wall -Wno-uninitialized -Wno-unused-parameter -no-cpp-precomp    -Wl,-search_paths_first -headerpad_max_install_names -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib     CMakeFiles/scat.dir/scat.c.o  -o ../../bin/scat  -L/usr/local/lib/InsightToolkit -L/usr/local/lib/KWWidgets -L/usr/local/lib/vtk-5.4 -L/usr/local/lib -L/Users/chrisgorman/src/medical-imaging/curl/bingcc/bin ../../lib/libslicerio.a
Undefined symbols:
  "_Tcl_DStringInit", referenced from:
      _slicerFgets in libslicerio.a(slicerio.c.o)
  "_Tcl_CreateInterp", referenced from:
      _slicerFopen in libslicerio.a(slicerio.c.o)
  "_Tcl_Gets", referenced from:
      _slicerFgets in libslicerio.a(slicerio.c.o)
  "_Tcl_Tell", referenced from:
      _slicerFtell in libslicerio.a(slicerio.c.o)
  "_Tcl_Flush", referenced from:
      _slicerFflush in libslicerio.a(slicerio.c.o)
  "_Tcl_ErrnoMsg", referenced from:
      _slicerFseek in libslicerio.a(slicerio.c.o)
      _slicerFtell in libslicerio.a(slicerio.c.o)
      _slicerUngetc in libslicerio.a(slicerio.c.o)
  "_Tcl_Seek", referenced from:
      _slicerFseek in libslicerio.a(slicerio.c.o)
  "_Tcl_Eof", referenced from:
      _slicerFeof in libslicerio.a(slicerio.c.o)
  "_Tcl_DStringFree", referenced from:
      _slicerFgets in libslicerio.a(slicerio.c.o)
  "_Tcl_OpenCommandChannel", referenced from:
      _slicerFopen in libslicerio.a(slicerio.c.o)
  "_Tcl_Read", referenced from:
      _slicerFread in libslicerio.a(slicerio.c.o)
      _slicerFgetc in libslicerio.a(slicerio.c.o)
  "_Tcl_Ungets", referenced from:
      _slicerUngetc in libslicerio.a(slicerio.c.o)
  "_Tcl_Free", referenced from:
      _slicerFopen in libslicerio.a(slicerio.c.o)
      _slicerFprintf in libslicerio.a(slicerio.c.o)
  "_Tcl_Write", referenced from:
      _slicerFwrite in libslicerio.a(slicerio.c.o)
      _slicerFputc in libslicerio.a(slicerio.c.o)
      _slicerFprintf in libslicerio.a(slicerio.c.o)
  "_Tcl_GetErrno", referenced from:
      _slicerFseek in libslicerio.a(slicerio.c.o)
      _slicerFtell in libslicerio.a(slicerio.c.o)
      _slicerUngetc in libslicerio.a(slicerio.c.o)
  "_Tcl_Close", referenced from:
      _slicerFclose in libslicerio.a(slicerio.c.o)
  "_Tcl_Alloc", referenced from:
      _slicerFprintf in libslicerio.a(slicerio.c.o)
  "_Tcl_GetStdChannel", referenced from:
      _slicerFwrite in libslicerio.a(slicerio.c.o)
  "_Tcl_SplitList", referenced from:
      _slicerFopen in libslicerio.a(slicerio.c.o)
  "_Tcl_DeleteInterp", referenced from:
      _slicerFclose in libslicerio.a(slicerio.c.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status

My original reason for doing the manual build was an error with one of the build steps trying to load a header from my system, tcl.h I think, and failing because it needed tcl.h from the build tree instead.  Unfortunately I didn't save any output.  So, I tried going around my system and hiding tcl/tk libraries and headers and tried the regular build process with getbuildtest.tcl and it worked.  I ended up with an alpha version, but otherwise what I wanted.  My next question is how do I install the build?  It seems that if I move anything around it can no longer find the libraries.  (This is not a big deal, I don't mind running it in place.)  It's too bad the manual build failed.  It would have been nice to be able to contribute the notes to the wiki.

Chris Gorman

On 2009-12-13, at 9:06 PM, Steve Pieper wrote:

> Hi Chris -
>
> I added the note about VTK_USE_COCOA to the wiki page - thanks for the feedback.  In general those pages about the manual configuration get out of sync - if you run into problems you can compare your steps the ones performed by the genlib script (it basically just automates the various checkouts and cmake configures and builds).  If you want, feel free to update the wiki with the latest info based on your experiences.
>
> One thing I do know from recent experience is that you'll need to use teem 1.10 with slicer 3.4 (in teem 1.11 the BIFF_STRLEN was removed).
>
> -Steve
>
> Chris Gorman wrote:
>> On 2009-12-13, at 4:49 PM, Chris Gorman wrote:
>>> Hello,
>>>
>>> This didn't post properly.  Trying again.
>>>
>>> On 2009-12-13, at 3:13 PM, Chris Gorman wrote:
>>>
>>>> Hello,
>>>>
>>>> VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK option presented.  From VTK/CMakeLists.txt
>>>>
>>>> SET(VTK_CAN_USE_TK)
>>>> IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>  IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>    SET(VTK_CAN_USE_TK 1)
>>>>  ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>> ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>> VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
>>>>                     "VTK_CAN_USE_TK" OFF)
>>>>
>>>> The web page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build needs to be updated to inform users about this as it only mentions disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled by default now.  (At least it was on vtk 5.4.2.)
>>>>
>>>> The next issue is building slicer3.  During configure I get
>>>> CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
>>>>   Could not find tcl
>>>>
>>>> I tried to hack in the value from my VTK configure, but this doesn't seem to be work, probably due to my lack of understanding of cmake grammar.  Setting it by
>>>> SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")
>>>>
>>>> in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set for vtk.  I also tried to set TCL_LIBRARY to point to the libtcl.dylib, but I think this causing problems too.  This allows the build to continue but not for long.  It fails.  
>>>> [  3%] Building CXX object Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx: In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*, const Nrrd*, double*)’:
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795: error: ‘BIFF_STRLEN’ was not declared in this scope
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802: error: ‘err’ was not declared in this scope
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806: error: ‘err’ was not declared in this scope
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810: error: ‘err’ was not declared in this scope
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815: error: ‘err’ was not declared in this scope
>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824: error: ‘err’ was not declared in this scope
>>>> make[2]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
>>>> make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>>
>>>> I did a quick google search to find where the declaration of BIFF_STRLEN, but wasn't able to find anything too useful.  My configuration is
>>>> Darwin 10.2.0
>>>> cmake 2.8.0
>>>> tcl/tk 8.5 (from os x)
>>>> incrTcl 3.3 (from macports)
>>>> vtk 5.4.2 itk 3.16.0
>>>> kwwidgets 1.0.0
>>>> teem 1.11.0
>>>> SlicerLibCurl 7.12.1
>>>> Slicer3 3.4
>>>>
>>>> In summary.  I would like to find a solution to the cmake configure error, as I believe that is causing problems in addition to the build error.  If anyone has pointers, please let me know.  Thanks.
>>>>
>>>> Chris Gorman
>>>
>> ------------------------------------------------------------------------
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>> slicer-devel mailing list
>> [hidden email]
>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
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Re: building Slicer3 3.4

Chris Gorman
Hello again.

I have some updates on this.  First off I cannot reproduce the problems with errors caused by the tcl.h header, so you may want to disregard them.  I have disabled some macports ports which may have allowed me to bypass this problem.

The first problem I have building slicer3.4 with xcode 3.2.1 and darwin 10.2.0 is python2.5 it fails as gcc cannot find the switch -Wno-long-double.  Thanks to the macports folks (http://trac.macports.org/browser/trunk/dports/lang/python25/Portfile) I have some patches that get around this.  I applied ./patch-64bit.diff ./patch-configure-arch_only.diff ./patch-configure-badcflags.diff ./patch-Lib-cgi.py.diff ./patch-Lib-distutils-dist.py.diff ./patch-Makefile.pre.in.diff ./patch-setup.py.diff.  In my haste, I applied a few extra patches which I will try reverting to see if this gets the build to work they are ./not_used_in_macports/patch-FSIORefNum.diff ./not_used_in_macports/patch-Misc-setuid-prog.c.diff ./not_used_in_macports/patch-Modules-posixmodule.c.diff ./not_used_in_macports/patch-pyconfig.h.in.diff.

The build still fails although much further along.  There is no Slicer-real built, so it will not run.  Unfortunately I didn't do a build.log, but I can if anyone's interested.

running: sh /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Scripts/versioner.tcl
Slicer3_HOME is /Users/chrisgorman/src/medical-imaging/slicer/Slicer3

running: make Experimental
   Site: Macintosh.local
   Build name: Darwin-g++
Create new tag: 20091215-1938 - Experimental
Start processing tests
Configure project
   Each . represents 1024 bytes of output
    . Size of output: 0K
Build project
   Each symbol represents 1024 bytes of output.
   '!' represents an error and '*' a warning.
    ...! Size of output: 3K
Error(s) when building project
   3 Compiler errors
   1 Compiler warnings
Test project /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build
  1/ 95 Testing Parser1Test1                     Passed
  2/ 95 Testing Parser1Test2                     Passed
  3/ 95 Testing ModuleFactoryTest                Passed
  4/ 95 Testing Slicer3CLPExample1               Passed
  5/ 95 Testing Slicer3CLPExample2               Passed
  6/ 95 Testing Slicer3CLPExample3               Passed
  7/ 95 Testing LMParser1Test1                   Passed
  8/ 95 Testing LMParser1Test2                   Passed
  9/ 95 Testing VTKITKVectorReader               Passed
 10/ 95 Testing VTKITKBSplineTransform           Passed
 11/ 95 Testing Slicer3GUITest1               ***Failed
 12/ 95 Testing Slicer3GUITest2               ***Failed
 13/ 95 Testing Slicer3FiducialsTest1         ***Failed
 14/ 95 Testing Slicer3FiducialsTest2         ***Failed
 15/ 95 Testing QdecModuleLibs                ***Failed
 16/ 95 Testing TractographyTestGlyphs        ***Failed
 17/ 95 Testing ChangeTrackerCL_Help             Passed
 18/ 95 Testing ChangeTrackerCL_TestGlobalReg ***Failed
 19/ 95 Testing ChangeTrackerCL_TestFull_Inten***Failed
 20/ 95 Testing DiffusionEditorTest           ***Failed
 21/ 95 Testing DiffusionEditorGradients      ***Failed
 22/ 95 Testing DiffusionEditorGlyphsTracts   ***Failed
 23/ 95 Testing DiffusionEditorTensor         ***Failed
 24/ 95 Testing vtkEMSegmentMRMLManagerTest      Passed
 25/ 95 Testing vtkEMSegmentPreprocessingManag   Passed
 26/ 95 Testing vtkEMSegmentBlackBoxSegmentati   Passed
 27/ 95 Testing vtkEMSegmentBuildAndRunNewSegm   Passed
 28/ 95 Testing EMSegCL_Help                     Passed
 29/ 95 Testing EMSegCL_Version                  Passed
 30/ 95 Testing EMSegCL_RunDefaultNodes          Passed
 31/ 95 Testing EMSegCL_RunNormalize             Passed
 32/ 95 Testing EMSegCL_RunSetEverything         Passed
 33/ 95 Testing EMSegCL_DisableMultithreading    Passed
 34/ 95 Testing EMSegCL_EFBogusParameterNode     Passed
 35/ 95 Testing EMSegCL_EFBogusMRMLScene         Passed
 36/ 95 Testing EMSegCL_EFBogusTargetImages      Passed
 37/ 95 Testing EMSegCL_EFTooManyImages          Passed
 38/ 95 Testing EMSegCL_EFTooFewImages           Passed
 39/ 95 Testing EMSegCL_EFBogusResultStandardI   Passed
 40/ 95 Testing ModelIntoLabelVolumeTest      ***Failed
 41/ 95 Testing OrientImageTest1              ***Failed
 42/ 95 Testing OrientImageTest2              ***Failed
 43/ 95 Testing OrientImageTest3              ***Failed
 44/ 95 Testing AddTest                       ***Failed
 45/ 95 Testing ThresholdTest                 ***Failed
 46/ 95 Testing CheckerBoardTest              ***Failed
 47/ 95 Testing MedianImageFilterTest         ***Failed
 48/ 95 Testing GaussianBlurImageFilterTest   ***Failed
 49/ 95 Testing LinearRegistrationTest00      ***Failed
 50/ 95 Testing LinearRegistrationTest01      ***Failed
 51/ 95 Testing LinearRegistrationTest02      ***Failed
 52/ 95 Testing LinearRegistrationTest03      ***Failed
 53/ 95 Testing LinearRegistrationTest04      ***Failed
 54/ 95 Testing BSplineRegistrationTest00     ***Failed
 55/ 95 Testing TestGridTransformRegistrationT***Failed
 56/ 95 Testing AffineRegistrationTest        ***Failed
 57/ 95 Testing ConfidenceConnectedTest       ***Failed
 58/ 95 Testing CurvatureAnisotropicDiffusionT***Failed
 59/ 95 Testing DicomToNrrdConverterTest      ***Failed
 60/ 95 Testing DiffusionTensorEstimationTest ***Failed
 61/ 95 Testing DiffusionTensorMathematicsTest***Failed
 62/ 95 Testing DiffusionTensorTestTest       ***Failed
 63/ 95 Testing DiffusionWeightedTestTest     ***Failed
 64/ 95 Testing DWIDicomLoadTest              ***Failed
 65/ 95 Testing ExecutionModelTourTest        ***Failed
 66/ 95 Testing FreesurferSurfaceSectionExtrac***Failed
 67/ 95 Testing GradientAnisotropicDiffusionTe***Failed
 68/ 95 Testing GrayscaleFillHoleImageFilterTe***Failed
 69/ 95 Testing GrayscaleGrindPeakImageFilterT***Failed
 70/ 95 Testing GrayscaleModelMakerTest       ***Failed
 71/ 95 Testing HistogramMatchingTest         ***Failed
 72/ 95 Testing ImageLabelCombineTest         ***Failed
 73/ 95 Testing ImageReadDicomWriteTest       ***Failed
 74/ 95 Testing LabelMapSmoothingTest         ***Failed
 75/ 95 Testing ModelMakerTest                ***Failed
 76/ 95 Testing MultipleModelsExampleTest     ***Failed
 77/ 95 Testing OtsuThresholdImageFilterTest  ***Failed
 78/ 95 Testing OtsuThresholdSegmentationTest ***Failed
 79/ 95 Testing ResampleVolume2Test           ***Failed
 80/ 95 Testing ResampleVolumeTest            ***Failed
 81/ 95 Testing RigidRegistrationTest01       ***Failed
 82/ 95 Testing SubtractTest                  ***Failed
 83/ 95 Testing VotingBinaryHoleFillingImageFi***Failed
 84/ 95 Testing ZeroCrossingBasedEdgeDetection***Failed
 85/ 95 Testing Slicer3CLTest1                ***Failed
 86/ 95 Testing Slicer3CLTest2                ***Failed
 87/ 95 Testing Slicer3CLTest3                ***Failed
 88/ 95 Testing Slicer3CLTest4                ***Failed
 89/ 95 Testing Slicer3CLTest5                ***Failed
 90/ 95 Testing Slicer3CLTest6                ***Failed
 91/ 95 Testing Slicer3CLTest7                ***Failed
 92/ 95 Testing Slicer3ScrollTest             ***Failed
 93/ 95 Testing Slicer3MRMLUndo               ***Failed
 94/ 95 Testing Slicer3MRMLVolume             ***Failed
 95/ 95 Testing EventBrokerTest               ***Failed

28% tests passed, 68 tests failed out of 95

The following tests FAILED:
         11 - Slicer3GUITest1 (Failed)
         12 - Slicer3GUITest2 (Failed)
         13 - Slicer3FiducialsTest1 (Failed)
         14 - Slicer3FiducialsTest2 (Failed)
         15 - QdecModuleLibs (Failed)
         16 - TractographyTestGlyphs (Failed)
         18 - ChangeTrackerCL_TestGlobalReg (Failed)
         19 - ChangeTrackerCL_TestFull_Intensity (Failed)
         20 - DiffusionEditorTest (Failed)
         21 - DiffusionEditorGradients (Failed)
         22 - DiffusionEditorGlyphsTracts (Failed)
         23 - DiffusionEditorTensor (Failed)
         40 - ModelIntoLabelVolumeTest (Failed)
         41 - OrientImageTest1 (Failed)
         42 - OrientImageTest2 (Failed)
         43 - OrientImageTest3 (Failed)
         44 - AddTest (Failed)
         45 - ThresholdTest (Failed)
         46 - CheckerBoardTest (Failed)
         47 - MedianImageFilterTest (Failed)
         48 - GaussianBlurImageFilterTest (Failed)
         49 - LinearRegistrationTest00 (Failed)
         50 - LinearRegistrationTest01 (Failed)
         51 - LinearRegistrationTest02 (Failed)
         52 - LinearRegistrationTest03 (Failed)
         53 - LinearRegistrationTest04 (Failed)
         54 - BSplineRegistrationTest00 (Failed)
         55 - TestGridTransformRegistrationTest00 (Failed)
         56 - AffineRegistrationTest (Failed)
         57 - ConfidenceConnectedTest (Failed)
         58 - CurvatureAnisotropicDiffusionTest (Failed)
         59 - DicomToNrrdConverterTest (Failed)
         60 - DiffusionTensorEstimationTest (Failed)
         61 - DiffusionTensorMathematicsTest (Failed)
         62 - DiffusionTensorTestTest (Failed)
         63 - DiffusionWeightedTestTest (Failed)
         64 - DWIDicomLoadTest (Failed)
         65 - ExecutionModelTourTest (Failed)
         66 - FreesurferSurfaceSectionExtractionTest (Failed)
         67 - GradientAnisotropicDiffusionTest (Failed)
         68 - GrayscaleFillHoleImageFilterTest (Failed)
         69 - GrayscaleGrindPeakImageFilterTest (Failed)
         70 - GrayscaleModelMakerTest (Failed)
         71 - HistogramMatchingTest (Failed)
         72 - ImageLabelCombineTest (Failed)
         73 - ImageReadDicomWriteTest (Failed)
         74 - LabelMapSmoothingTest (Failed)
         75 - ModelMakerTest (Failed)
         76 - MultipleModelsExampleTest (Failed)
         77 - OtsuThresholdImageFilterTest (Failed)
         78 - OtsuThresholdSegmentationTest (Failed)
         79 - ResampleVolume2Test (Failed)
         80 - ResampleVolumeTest (Failed)
         81 - RigidRegistrationTest01 (Failed)
         82 - SubtractTest (Failed)
         83 - VotingBinaryHoleFillingImageFilterTest (Failed)
         84 - ZeroCrossingBasedEdgeDetectionImageFilterTest (Failed)
         85 - Slicer3CLTest1 (Failed)
         86 - Slicer3CLTest2 (Failed)
         87 - Slicer3CLTest3 (Failed)
         88 - Slicer3CLTest4 (Failed)
         89 - Slicer3CLTest5 (Failed)
         90 - Slicer3CLTest6 (Failed)
         91 - Slicer3CLTest7 (Failed)
         92 - Slicer3ScrollTest (Failed)
         93 - Slicer3MRMLUndo (Failed)
         94 - Slicer3MRMLVolume (Failed)
         95 - EventBrokerTest (Failed)
Performing coverage
 Cannot find any coverage files. Ignoring Coverage request.
Submit files (using http)
   Using HTTP submit method
   Drop site: http://www.cdash.org/CDash/submit.php?project=Slicer3
   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Build.xml
   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Configure.xml
   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Test.xml
   Submission successful
Errors while running CTest
make[3]: *** [CMakeFiles/Experimental] Error 8
make[2]: *** [CMakeFiles/Experimental.dir/all] Error 2
make[1]: *** [CMakeFiles/Experimental.dir/rule] Error 2
make: *** [Experimental] Error 2

child process exited abnormally

Results:
build of "Experimental" failed  

As to the Slicer3.5 alpha build, it will build and run on my system, but some problems occur.  Trying out the Slicer3Minute tutorial, the display shows no change on the once the dataset is loaded.  The Slicer3Visualization tutorial the volume loads and is displayed, but some of the other effects don't work, for example loading the label map (tutorial page 38 part 2) shows no change on the images.  I haven't tried anything else yet.  

Chris Gorman

Macports patches.



In my patches directory and applied in haste, no longer part of the macports python 2.5 build.





On 2009-12-15, at 9:07 AM, Chris Gorman wrote:

> Hello,
>
> First off thank you for the pointer on teem 1.10 Steve.  It resolved the error that was occurring regarding BIFF_STRLEN.  My build went a bit further after that.  My next problem was the inability for the cmake command to find a TCL_LIBRARY.  Inspection of the build scripts indicated it was set as a tcl variable and passed to cmake.  I ran a grep through the source code and found a reference to it appeared to be used only in Applications/GUI/Slicer3.cxx amongst a few references in the .svn directories.  I then edited Applications/GUI/Slicer3.cxx and hard coded my tcl library in place of the build one.  Next I commented out the check for TCL_LIBRARY in Libs/SlicerIO/CMakeLists.txt and tried to build again.  I got a bit further but it still failed to build.
>
> Linking C executable ../../bin/scat
> cd /Users/chrisgorman/src/medical-imaging/slicer/bingcc/Libs/SlicerIO && /opt/local/bin/cmake -E cmake_link_script CMakeFiles/scat.dir/link.txt --verbose=1
> /usr/bin/gcc   -mmacosx-version-min=10.6   -Wall -Wno-uninitialized -Wno-unused-parameter -no-cpp-precomp    -Wl,-search_paths_first -headerpad_max_install_names -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib     CMakeFiles/scat.dir/scat.c.o  -o ../../bin/scat  -L/usr/local/lib/InsightToolkit -L/usr/local/lib/KWWidgets -L/usr/local/lib/vtk-5.4 -L/usr/local/lib -L/Users/chrisgorman/src/medical-imaging/curl/bingcc/bin ../../lib/libslicerio.a
> Undefined symbols:
>  "_Tcl_DStringInit", referenced from:
>      _slicerFgets in libslicerio.a(slicerio.c.o)
>  "_Tcl_CreateInterp", referenced from:
>      _slicerFopen in libslicerio.a(slicerio.c.o)
>  "_Tcl_Gets", referenced from:
>      _slicerFgets in libslicerio.a(slicerio.c.o)
>  "_Tcl_Tell", referenced from:
>      _slicerFtell in libslicerio.a(slicerio.c.o)
>  "_Tcl_Flush", referenced from:
>      _slicerFflush in libslicerio.a(slicerio.c.o)
>  "_Tcl_ErrnoMsg", referenced from:
>      _slicerFseek in libslicerio.a(slicerio.c.o)
>      _slicerFtell in libslicerio.a(slicerio.c.o)
>      _slicerUngetc in libslicerio.a(slicerio.c.o)
>  "_Tcl_Seek", referenced from:
>      _slicerFseek in libslicerio.a(slicerio.c.o)
>  "_Tcl_Eof", referenced from:
>      _slicerFeof in libslicerio.a(slicerio.c.o)
>  "_Tcl_DStringFree", referenced from:
>      _slicerFgets in libslicerio.a(slicerio.c.o)
>  "_Tcl_OpenCommandChannel", referenced from:
>      _slicerFopen in libslicerio.a(slicerio.c.o)
>  "_Tcl_Read", referenced from:
>      _slicerFread in libslicerio.a(slicerio.c.o)
>      _slicerFgetc in libslicerio.a(slicerio.c.o)
>  "_Tcl_Ungets", referenced from:
>      _slicerUngetc in libslicerio.a(slicerio.c.o)
>  "_Tcl_Free", referenced from:
>      _slicerFopen in libslicerio.a(slicerio.c.o)
>      _slicerFprintf in libslicerio.a(slicerio.c.o)
>  "_Tcl_Write", referenced from:
>      _slicerFwrite in libslicerio.a(slicerio.c.o)
>      _slicerFputc in libslicerio.a(slicerio.c.o)
>      _slicerFprintf in libslicerio.a(slicerio.c.o)
>  "_Tcl_GetErrno", referenced from:
>      _slicerFseek in libslicerio.a(slicerio.c.o)
>      _slicerFtell in libslicerio.a(slicerio.c.o)
>      _slicerUngetc in libslicerio.a(slicerio.c.o)
>  "_Tcl_Close", referenced from:
>      _slicerFclose in libslicerio.a(slicerio.c.o)
>  "_Tcl_Alloc", referenced from:
>      _slicerFprintf in libslicerio.a(slicerio.c.o)
>  "_Tcl_GetStdChannel", referenced from:
>      _slicerFwrite in libslicerio.a(slicerio.c.o)
>  "_Tcl_SplitList", referenced from:
>      _slicerFopen in libslicerio.a(slicerio.c.o)
>  "_Tcl_DeleteInterp", referenced from:
>      _slicerFclose in libslicerio.a(slicerio.c.o)
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
>
> My original reason for doing the manual build was an error with one of the build steps trying to load a header from my system, tcl.h I think, and failing because it needed tcl.h from the build tree instead.  Unfortunately I didn't save any output.  So, I tried going around my system and hiding tcl/tk libraries and headers and tried the regular build process with getbuildtest.tcl and it worked.  I ended up with an alpha version, but otherwise what I wanted.  My next question is how do I install the build?  It seems that if I move anything around it can no longer find the libraries.  (This is not a big deal, I don't mind running it in place.)  It's too bad the manual build failed.  It would have been nice to be able to contribute the notes to the wiki.
>
> Chris Gorman
>
> On 2009-12-13, at 9:06 PM, Steve Pieper wrote:
>
>> Hi Chris -
>>
>> I added the note about VTK_USE_COCOA to the wiki page - thanks for the feedback.  In general those pages about the manual configuration get out of sync - if you run into problems you can compare your steps the ones performed by the genlib script (it basically just automates the various checkouts and cmake configures and builds).  If you want, feel free to update the wiki with the latest info based on your experiences.
>>
>> One thing I do know from recent experience is that you'll need to use teem 1.10 with slicer 3.4 (in teem 1.11 the BIFF_STRLEN was removed).
>>
>> -Steve
>>
>> Chris Gorman wrote:
>>> On 2009-12-13, at 4:49 PM, Chris Gorman wrote:
>>>> Hello,
>>>>
>>>> This didn't post properly.  Trying again.
>>>>
>>>> On 2009-12-13, at 3:13 PM, Chris Gorman wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK option presented.  From VTK/CMakeLists.txt
>>>>>
>>>>> SET(VTK_CAN_USE_TK)
>>>>> IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>> IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>   SET(VTK_CAN_USE_TK 1)
>>>>> ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>> ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>> VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
>>>>>                    "VTK_CAN_USE_TK" OFF)
>>>>>
>>>>> The web page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build needs to be updated to inform users about this as it only mentions disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled by default now.  (At least it was on vtk 5.4.2.)
>>>>>
>>>>> The next issue is building slicer3.  During configure I get
>>>>> CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
>>>>>  Could not find tcl
>>>>>
>>>>> I tried to hack in the value from my VTK configure, but this doesn't seem to be work, probably due to my lack of understanding of cmake grammar.  Setting it by
>>>>> SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")
>>>>>
>>>>> in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set for vtk.  I also tried to set TCL_LIBRARY to point to the libtcl.dylib, but I think this causing problems too.  This allows the build to continue but not for long.  It fails.  
>>>>> [  3%] Building CXX object Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx: In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*, const Nrrd*, double*)’:
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795: error: ‘BIFF_STRLEN’ was not declared in this scope
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802: error: ‘err’ was not declared in this scope
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806: error: ‘err’ was not declared in this scope
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810: error: ‘err’ was not declared in this scope
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815: error: ‘err’ was not declared in this scope
>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824: error: ‘err’ was not declared in this scope
>>>>> make[2]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
>>>>> make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
>>>>> make: *** [all] Error 2
>>>>>
>>>>> I did a quick google search to find where the declaration of BIFF_STRLEN, but wasn't able to find anything too useful.  My configuration is
>>>>> Darwin 10.2.0
>>>>> cmake 2.8.0
>>>>> tcl/tk 8.5 (from os x)
>>>>> incrTcl 3.3 (from macports)
>>>>> vtk 5.4.2 itk 3.16.0
>>>>> kwwidgets 1.0.0
>>>>> teem 1.11.0
>>>>> SlicerLibCurl 7.12.1
>>>>> Slicer3 3.4
>>>>>
>>>>> In summary.  I would like to find a solution to the cmake configure error, as I believe that is causing problems in addition to the build error.  If anyone has pointers, please let me know.  Thanks.
>>>>>
>>>>> Chris Gorman
>>>>
>>> ------------------------------------------------------------------------
>>> _______________________________________________
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>

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Re: building Slicer3 3.4

Chris Gorman
Hello,

Just a quick note python needs all the patches included with the previous email to build.

Chris Gorman

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Re: building Slicer3 3.4

pieper
Administrator
In reply to this post by Chris Gorman
Hi Chris -

Yes, sometimes it is threading the needle to get all the right versions
of the OS, python, tcl, etc building with the right flags.  I believe
the --Wno-long-double was introduced for compatibility with OSX 10.6 so
I'm not sure about 10.2.  Also we typically build our own tcl/tk 8.4 so
I don't know if it's possible to build with the OS's 10.5 (I'm guissing
not).  If you could generate a build log for your system that might help
track down the remaining issues.

Regarding your earlier question, you can run 'make package' in the
Slicer3-build directory to get a tar.gz of an installable slicer (or
specify --pack argument to getbuildtest).  Essentially you will get a
directory tree that you can copy to wherever you want it.  As long as
the contents are in the same relative locations everything should work.

Best,
Steve

Chris Gorman wrote:

> Hello again.
>
> I have some updates on this.  First off I cannot reproduce the problems with errors caused by the tcl.h header, so you may want to disregard them.  I have disabled some macports ports which may have allowed me to bypass this problem.
>
> The first problem I have building slicer3.4 with xcode 3.2.1 and darwin 10.2.0 is python2.5 it fails as gcc cannot find the switch -Wno-long-double.  Thanks to the macports folks (http://trac.macports.org/browser/trunk/dports/lang/python25/Portfile) I have some patches that get around this.  I applied ./patch-64bit.diff ./patch-configure-arch_only.diff ./patch-configure-badcflags.diff ./patch-Lib-cgi.py.diff ./patch-Lib-distutils-dist.py.diff ./patch-Makefile.pre.in.diff ./patch-setup.py.diff.  In my haste, I applied a few extra patches which I will try reverting to see if this gets the build to work they are ./not_used_in_macports/patch-FSIORefNum.diff ./not_used_in_macports/patch-Misc-setuid-prog.c.diff ./not_used_in_macports/patch-Modules-posixmodule.c.diff ./not_used_in_macports/patch-pyconfig.h.in.diff.
>
> The build still fails although much further along.  There is no Slicer-real built, so it will not run.  Unfortunately I didn't do a build.log, but I can if anyone's interested.
>
> running: sh /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Scripts/versioner.tcl
> Slicer3_HOME is /Users/chrisgorman/src/medical-imaging/slicer/Slicer3
>
> running: make Experimental
>    Site: Macintosh.local
>    Build name: Darwin-g++
> Create new tag: 20091215-1938 - Experimental
> Start processing tests
> Configure project
>    Each . represents 1024 bytes of output
>     . Size of output: 0K
> Build project
>    Each symbol represents 1024 bytes of output.
>    '!' represents an error and '*' a warning.
>     ...! Size of output: 3K
> Error(s) when building project
>    3 Compiler errors
>    1 Compiler warnings
> Test project /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build
>   1/ 95 Testing Parser1Test1                     Passed
>   2/ 95 Testing Parser1Test2                     Passed
>   3/ 95 Testing ModuleFactoryTest                Passed
>   4/ 95 Testing Slicer3CLPExample1               Passed
>   5/ 95 Testing Slicer3CLPExample2               Passed
>   6/ 95 Testing Slicer3CLPExample3               Passed
>   7/ 95 Testing LMParser1Test1                   Passed
>   8/ 95 Testing LMParser1Test2                   Passed
>   9/ 95 Testing VTKITKVectorReader               Passed
>  10/ 95 Testing VTKITKBSplineTransform           Passed
>  11/ 95 Testing Slicer3GUITest1               ***Failed
>  12/ 95 Testing Slicer3GUITest2               ***Failed
>  13/ 95 Testing Slicer3FiducialsTest1         ***Failed
>  14/ 95 Testing Slicer3FiducialsTest2         ***Failed
>  15/ 95 Testing QdecModuleLibs                ***Failed
>  16/ 95 Testing TractographyTestGlyphs        ***Failed
>  17/ 95 Testing ChangeTrackerCL_Help             Passed
>  18/ 95 Testing ChangeTrackerCL_TestGlobalReg ***Failed
>  19/ 95 Testing ChangeTrackerCL_TestFull_Inten***Failed
>  20/ 95 Testing DiffusionEditorTest           ***Failed
>  21/ 95 Testing DiffusionEditorGradients      ***Failed
>  22/ 95 Testing DiffusionEditorGlyphsTracts   ***Failed
>  23/ 95 Testing DiffusionEditorTensor         ***Failed
>  24/ 95 Testing vtkEMSegmentMRMLManagerTest      Passed
>  25/ 95 Testing vtkEMSegmentPreprocessingManag   Passed
>  26/ 95 Testing vtkEMSegmentBlackBoxSegmentati   Passed
>  27/ 95 Testing vtkEMSegmentBuildAndRunNewSegm   Passed
>  28/ 95 Testing EMSegCL_Help                     Passed
>  29/ 95 Testing EMSegCL_Version                  Passed
>  30/ 95 Testing EMSegCL_RunDefaultNodes          Passed
>  31/ 95 Testing EMSegCL_RunNormalize             Passed
>  32/ 95 Testing EMSegCL_RunSetEverything         Passed
>  33/ 95 Testing EMSegCL_DisableMultithreading    Passed
>  34/ 95 Testing EMSegCL_EFBogusParameterNode     Passed
>  35/ 95 Testing EMSegCL_EFBogusMRMLScene         Passed
>  36/ 95 Testing EMSegCL_EFBogusTargetImages      Passed
>  37/ 95 Testing EMSegCL_EFTooManyImages          Passed
>  38/ 95 Testing EMSegCL_EFTooFewImages           Passed
>  39/ 95 Testing EMSegCL_EFBogusResultStandardI   Passed
>  40/ 95 Testing ModelIntoLabelVolumeTest      ***Failed
>  41/ 95 Testing OrientImageTest1              ***Failed
>  42/ 95 Testing OrientImageTest2              ***Failed
>  43/ 95 Testing OrientImageTest3              ***Failed
>  44/ 95 Testing AddTest                       ***Failed
>  45/ 95 Testing ThresholdTest                 ***Failed
>  46/ 95 Testing CheckerBoardTest              ***Failed
>  47/ 95 Testing MedianImageFilterTest         ***Failed
>  48/ 95 Testing GaussianBlurImageFilterTest   ***Failed
>  49/ 95 Testing LinearRegistrationTest00      ***Failed
>  50/ 95 Testing LinearRegistrationTest01      ***Failed
>  51/ 95 Testing LinearRegistrationTest02      ***Failed
>  52/ 95 Testing LinearRegistrationTest03      ***Failed
>  53/ 95 Testing LinearRegistrationTest04      ***Failed
>  54/ 95 Testing BSplineRegistrationTest00     ***Failed
>  55/ 95 Testing TestGridTransformRegistrationT***Failed
>  56/ 95 Testing AffineRegistrationTest        ***Failed
>  57/ 95 Testing ConfidenceConnectedTest       ***Failed
>  58/ 95 Testing CurvatureAnisotropicDiffusionT***Failed
>  59/ 95 Testing DicomToNrrdConverterTest      ***Failed
>  60/ 95 Testing DiffusionTensorEstimationTest ***Failed
>  61/ 95 Testing DiffusionTensorMathematicsTest***Failed
>  62/ 95 Testing DiffusionTensorTestTest       ***Failed
>  63/ 95 Testing DiffusionWeightedTestTest     ***Failed
>  64/ 95 Testing DWIDicomLoadTest              ***Failed
>  65/ 95 Testing ExecutionModelTourTest        ***Failed
>  66/ 95 Testing FreesurferSurfaceSectionExtrac***Failed
>  67/ 95 Testing GradientAnisotropicDiffusionTe***Failed
>  68/ 95 Testing GrayscaleFillHoleImageFilterTe***Failed
>  69/ 95 Testing GrayscaleGrindPeakImageFilterT***Failed
>  70/ 95 Testing GrayscaleModelMakerTest       ***Failed
>  71/ 95 Testing HistogramMatchingTest         ***Failed
>  72/ 95 Testing ImageLabelCombineTest         ***Failed
>  73/ 95 Testing ImageReadDicomWriteTest       ***Failed
>  74/ 95 Testing LabelMapSmoothingTest         ***Failed
>  75/ 95 Testing ModelMakerTest                ***Failed
>  76/ 95 Testing MultipleModelsExampleTest     ***Failed
>  77/ 95 Testing OtsuThresholdImageFilterTest  ***Failed
>  78/ 95 Testing OtsuThresholdSegmentationTest ***Failed
>  79/ 95 Testing ResampleVolume2Test           ***Failed
>  80/ 95 Testing ResampleVolumeTest            ***Failed
>  81/ 95 Testing RigidRegistrationTest01       ***Failed
>  82/ 95 Testing SubtractTest                  ***Failed
>  83/ 95 Testing VotingBinaryHoleFillingImageFi***Failed
>  84/ 95 Testing ZeroCrossingBasedEdgeDetection***Failed
>  85/ 95 Testing Slicer3CLTest1                ***Failed
>  86/ 95 Testing Slicer3CLTest2                ***Failed
>  87/ 95 Testing Slicer3CLTest3                ***Failed
>  88/ 95 Testing Slicer3CLTest4                ***Failed
>  89/ 95 Testing Slicer3CLTest5                ***Failed
>  90/ 95 Testing Slicer3CLTest6                ***Failed
>  91/ 95 Testing Slicer3CLTest7                ***Failed
>  92/ 95 Testing Slicer3ScrollTest             ***Failed
>  93/ 95 Testing Slicer3MRMLUndo               ***Failed
>  94/ 95 Testing Slicer3MRMLVolume             ***Failed
>  95/ 95 Testing EventBrokerTest               ***Failed
>
> 28% tests passed, 68 tests failed out of 95
>
> The following tests FAILED:
> 11 - Slicer3GUITest1 (Failed)
> 12 - Slicer3GUITest2 (Failed)
> 13 - Slicer3FiducialsTest1 (Failed)
> 14 - Slicer3FiducialsTest2 (Failed)
> 15 - QdecModuleLibs (Failed)
> 16 - TractographyTestGlyphs (Failed)
> 18 - ChangeTrackerCL_TestGlobalReg (Failed)
> 19 - ChangeTrackerCL_TestFull_Intensity (Failed)
> 20 - DiffusionEditorTest (Failed)
> 21 - DiffusionEditorGradients (Failed)
> 22 - DiffusionEditorGlyphsTracts (Failed)
> 23 - DiffusionEditorTensor (Failed)
> 40 - ModelIntoLabelVolumeTest (Failed)
> 41 - OrientImageTest1 (Failed)
> 42 - OrientImageTest2 (Failed)
> 43 - OrientImageTest3 (Failed)
> 44 - AddTest (Failed)
> 45 - ThresholdTest (Failed)
> 46 - CheckerBoardTest (Failed)
> 47 - MedianImageFilterTest (Failed)
> 48 - GaussianBlurImageFilterTest (Failed)
> 49 - LinearRegistrationTest00 (Failed)
> 50 - LinearRegistrationTest01 (Failed)
> 51 - LinearRegistrationTest02 (Failed)
> 52 - LinearRegistrationTest03 (Failed)
> 53 - LinearRegistrationTest04 (Failed)
> 54 - BSplineRegistrationTest00 (Failed)
> 55 - TestGridTransformRegistrationTest00 (Failed)
> 56 - AffineRegistrationTest (Failed)
> 57 - ConfidenceConnectedTest (Failed)
> 58 - CurvatureAnisotropicDiffusionTest (Failed)
> 59 - DicomToNrrdConverterTest (Failed)
> 60 - DiffusionTensorEstimationTest (Failed)
> 61 - DiffusionTensorMathematicsTest (Failed)
> 62 - DiffusionTensorTestTest (Failed)
> 63 - DiffusionWeightedTestTest (Failed)
> 64 - DWIDicomLoadTest (Failed)
> 65 - ExecutionModelTourTest (Failed)
> 66 - FreesurferSurfaceSectionExtractionTest (Failed)
> 67 - GradientAnisotropicDiffusionTest (Failed)
> 68 - GrayscaleFillHoleImageFilterTest (Failed)
> 69 - GrayscaleGrindPeakImageFilterTest (Failed)
> 70 - GrayscaleModelMakerTest (Failed)
> 71 - HistogramMatchingTest (Failed)
> 72 - ImageLabelCombineTest (Failed)
> 73 - ImageReadDicomWriteTest (Failed)
> 74 - LabelMapSmoothingTest (Failed)
> 75 - ModelMakerTest (Failed)
> 76 - MultipleModelsExampleTest (Failed)
> 77 - OtsuThresholdImageFilterTest (Failed)
> 78 - OtsuThresholdSegmentationTest (Failed)
> 79 - ResampleVolume2Test (Failed)
> 80 - ResampleVolumeTest (Failed)
> 81 - RigidRegistrationTest01 (Failed)
> 82 - SubtractTest (Failed)
> 83 - VotingBinaryHoleFillingImageFilterTest (Failed)
> 84 - ZeroCrossingBasedEdgeDetectionImageFilterTest (Failed)
> 85 - Slicer3CLTest1 (Failed)
> 86 - Slicer3CLTest2 (Failed)
> 87 - Slicer3CLTest3 (Failed)
> 88 - Slicer3CLTest4 (Failed)
> 89 - Slicer3CLTest5 (Failed)
> 90 - Slicer3CLTest6 (Failed)
> 91 - Slicer3CLTest7 (Failed)
> 92 - Slicer3ScrollTest (Failed)
> 93 - Slicer3MRMLUndo (Failed)
> 94 - Slicer3MRMLVolume (Failed)
> 95 - EventBrokerTest (Failed)
> Performing coverage
>  Cannot find any coverage files. Ignoring Coverage request.
> Submit files (using http)
>    Using HTTP submit method
>    Drop site: http://www.cdash.org/CDash/submit.php?project=Slicer3
>    Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Build.xml
>    Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Configure.xml
>    Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Test.xml
>    Submission successful
> Errors while running CTest
> make[3]: *** [CMakeFiles/Experimental] Error 8
> make[2]: *** [CMakeFiles/Experimental.dir/all] Error 2
> make[1]: *** [CMakeFiles/Experimental.dir/rule] Error 2
> make: *** [Experimental] Error 2
>
> child process exited abnormally
>
> Results:
> build of "Experimental" failed  
>
> As to the Slicer3.5 alpha build, it will build and run on my system, but some problems occur.  Trying out the Slicer3Minute tutorial, the display shows no change on the once the dataset is loaded.  The Slicer3Visualization tutorial the volume loads and is displayed, but some of the other effects don't work, for example loading the label map (tutorial page 38 part 2) shows no change on the images.  I haven't tried anything else yet.  
>
> Chris Gorman
>
> Macports patches.
>
>
> ------------------------------------------------------------------------
>
>
>
> In my patches directory and applied in haste, no longer part of the macports python 2.5 build.
>
>
> ------------------------------------------------------------------------
>
>
>
>
> On 2009-12-15, at 9:07 AM, Chris Gorman wrote:
>
>> Hello,
>>
>> First off thank you for the pointer on teem 1.10 Steve.  It resolved the error that was occurring regarding BIFF_STRLEN.  My build went a bit further after that.  My next problem was the inability for the cmake command to find a TCL_LIBRARY.  Inspection of the build scripts indicated it was set as a tcl variable and passed to cmake.  I ran a grep through the source code and found a reference to it appeared to be used only in Applications/GUI/Slicer3.cxx amongst a few references in the .svn directories.  I then edited Applications/GUI/Slicer3.cxx and hard coded my tcl library in place of the build one.  Next I commented out the check for TCL_LIBRARY in Libs/SlicerIO/CMakeLists.txt and tried to build again.  I got a bit further but it still failed to build.
>>
>> Linking C executable ../../bin/scat
>> cd /Users/chrisgorman/src/medical-imaging/slicer/bingcc/Libs/SlicerIO && /opt/local/bin/cmake -E cmake_link_script CMakeFiles/scat.dir/link.txt --verbose=1
>> /usr/bin/gcc   -mmacosx-version-min=10.6   -Wall -Wno-uninitialized -Wno-unused-parameter -no-cpp-precomp    -Wl,-search_paths_first -headerpad_max_install_names -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib     CMakeFiles/scat.dir/scat.c.o  -o ../../bin/scat  -L/usr/local/lib/InsightToolkit -L/usr/local/lib/KWWidgets -L/usr/local/lib/vtk-5.4 -L/usr/local/lib -L/Users/chrisgorman/src/medical-imaging/curl/bingcc/bin ../../lib/libslicerio.a
>> Undefined symbols:
>>  "_Tcl_DStringInit", referenced from:
>>      _slicerFgets in libslicerio.a(slicerio.c.o)
>>  "_Tcl_CreateInterp", referenced from:
>>      _slicerFopen in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Gets", referenced from:
>>      _slicerFgets in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Tell", referenced from:
>>      _slicerFtell in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Flush", referenced from:
>>      _slicerFflush in libslicerio.a(slicerio.c.o)
>>  "_Tcl_ErrnoMsg", referenced from:
>>      _slicerFseek in libslicerio.a(slicerio.c.o)
>>      _slicerFtell in libslicerio.a(slicerio.c.o)
>>      _slicerUngetc in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Seek", referenced from:
>>      _slicerFseek in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Eof", referenced from:
>>      _slicerFeof in libslicerio.a(slicerio.c.o)
>>  "_Tcl_DStringFree", referenced from:
>>      _slicerFgets in libslicerio.a(slicerio.c.o)
>>  "_Tcl_OpenCommandChannel", referenced from:
>>      _slicerFopen in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Read", referenced from:
>>      _slicerFread in libslicerio.a(slicerio.c.o)
>>      _slicerFgetc in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Ungets", referenced from:
>>      _slicerUngetc in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Free", referenced from:
>>      _slicerFopen in libslicerio.a(slicerio.c.o)
>>      _slicerFprintf in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Write", referenced from:
>>      _slicerFwrite in libslicerio.a(slicerio.c.o)
>>      _slicerFputc in libslicerio.a(slicerio.c.o)
>>      _slicerFprintf in libslicerio.a(slicerio.c.o)
>>  "_Tcl_GetErrno", referenced from:
>>      _slicerFseek in libslicerio.a(slicerio.c.o)
>>      _slicerFtell in libslicerio.a(slicerio.c.o)
>>      _slicerUngetc in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Close", referenced from:
>>      _slicerFclose in libslicerio.a(slicerio.c.o)
>>  "_Tcl_Alloc", referenced from:
>>      _slicerFprintf in libslicerio.a(slicerio.c.o)
>>  "_Tcl_GetStdChannel", referenced from:
>>      _slicerFwrite in libslicerio.a(slicerio.c.o)
>>  "_Tcl_SplitList", referenced from:
>>      _slicerFopen in libslicerio.a(slicerio.c.o)
>>  "_Tcl_DeleteInterp", referenced from:
>>      _slicerFclose in libslicerio.a(slicerio.c.o)
>> ld: symbol(s) not found
>> collect2: ld returned 1 exit status
>>
>> My original reason for doing the manual build was an error with one of the build steps trying to load a header from my system, tcl.h I think, and failing because it needed tcl.h from the build tree instead.  Unfortunately I didn't save any output.  So, I tried going around my system and hiding tcl/tk libraries and headers and tried the regular build process with getbuildtest.tcl and it worked.  I ended up with an alpha version, but otherwise what I wanted.  My next question is how do I install the build?  It seems that if I move anything around it can no longer find the libraries.  (This is not a big deal, I don't mind running it in place.)  It's too bad the manual build failed.  It would have been nice to be able to contribute the notes to the wiki.
>>
>> Chris Gorman
>>
>> On 2009-12-13, at 9:06 PM, Steve Pieper wrote:
>>
>>> Hi Chris -
>>>
>>> I added the note about VTK_USE_COCOA to the wiki page - thanks for the feedback.  In general those pages about the manual configuration get out of sync - if you run into problems you can compare your steps the ones performed by the genlib script (it basically just automates the various checkouts and cmake configures and builds).  If you want, feel free to update the wiki with the latest info based on your experiences.
>>>
>>> One thing I do know from recent experience is that you'll need to use teem 1.10 with slicer 3.4 (in teem 1.11 the BIFF_STRLEN was removed).
>>>
>>> -Steve
>>>
>>> Chris Gorman wrote:
>>>> On 2009-12-13, at 4:49 PM, Chris Gorman wrote:
>>>>> Hello,
>>>>>
>>>>> This didn't post properly.  Trying again.
>>>>>
>>>>> On 2009-12-13, at 3:13 PM, Chris Gorman wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK option presented.  From VTK/CMakeLists.txt
>>>>>>
>>>>>> SET(VTK_CAN_USE_TK)
>>>>>> IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>>> IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>>   SET(VTK_CAN_USE_TK 1)
>>>>>> ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>> ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>>> VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
>>>>>>                    "VTK_CAN_USE_TK" OFF)
>>>>>>
>>>>>> The web page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build needs to be updated to inform users about this as it only mentions disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled by default now.  (At least it was on vtk 5.4.2.)
>>>>>>
>>>>>> The next issue is building slicer3.  During configure I get
>>>>>> CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
>>>>>>  Could not find tcl
>>>>>>
>>>>>> I tried to hack in the value from my VTK configure, but this doesn't seem to be work, probably due to my lack of understanding of cmake grammar.  Setting it by
>>>>>> SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")
>>>>>>
>>>>>> in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set for vtk.  I also tried to set TCL_LIBRARY to point to the libtcl.dylib, but I think this causing problems too.  This allows the build to continue but not for long.  It fails.  
>>>>>> [  3%] Building CXX object Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx: In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*, const Nrrd*, double*)’:
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795: error: ‘BIFF_STRLEN’ was not declared in this scope
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802: error: ‘err’ was not declared in this scope
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806: error: ‘err’ was not declared in this scope
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810: error: ‘err’ was not declared in this scope
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815: error: ‘err’ was not declared in this scope
>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824: error: ‘err’ was not declared in this scope
>>>>>> make[2]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
>>>>>> make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
>>>>>> make: *** [all] Error 2
>>>>>>
>>>>>> I did a quick google search to find where the declaration of BIFF_STRLEN, but wasn't able to find anything too useful.  My configuration is
>>>>>> Darwin 10.2.0
>>>>>> cmake 2.8.0
>>>>>> tcl/tk 8.5 (from os x)
>>>>>> incrTcl 3.3 (from macports)
>>>>>> vtk 5.4.2 itk 3.16.0
>>>>>> kwwidgets 1.0.0
>>>>>> teem 1.11.0
>>>>>> SlicerLibCurl 7.12.1
>>>>>> Slicer3 3.4
>>>>>>
>>>>>> In summary.  I would like to find a solution to the cmake configure error, as I believe that is causing problems in addition to the build error.  If anyone has pointers, please let me know.  Thanks.
>>>>>>
>>>>>> Chris Gorman
>>>> ------------------------------------------------------------------------
>>>> _______________________________________________
>>>> 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: building Slicer3 3.4

Chris Gorman
Hello again.

Per Steve's suggestion I've attached a two build.logs.  I need to include 2 because the build fails half way through with the python issue and I needed to apply some patches.  As to the gcc error, apparently it is a gcc 3 switch that has been deprecated.  At least it is as of gcc 4.2 which is the default compiler from XCode 3.2.1.  As to the os versions I believe I unintentionally misled Steve.  Darwin is the kernel and is not the same version as the operating system.  Darwin 10.2.0 is actually OS X 10.6.2.  Who knows why versioning was done this way but it is.    So it appears that building on 10.6.2 won't work for 3.4 but it does mostly for 3.5 alpha.  It is likely that your builds  are built on 10.5 with XCode 3.1.3 or something like that.  I made the jump to 10.6, but am actually regretting it.  Hopefully in a few months more things will build properly on 10.6.  I would consider that it may not be a good use of time to debug why the build for Slicer 3.4 doesn't work, since an Intel binary is available if needed, and instead to target efforts to why the 3.5 alpha build doesn't display some of the loaded data.  Thanks for all the help.

Chris Gorman



On 2009-12-15, at 8:03 PM, Steve Pieper wrote:

> Hi Chris -
>
> Yes, sometimes it is threading the needle to get all the right versions of the OS, python, tcl, etc building with the right flags.  I believe the --Wno-long-double was introduced for compatibility with OSX 10.6 so I'm not sure about 10.2.  Also we typically build our own tcl/tk 8.4 so I don't know if it's possible to build with the OS's 10.5 (I'm guissing not).  If you could generate a build log for your system that might help track down the remaining issues.
>
> Regarding your earlier question, you can run 'make package' in the Slicer3-build directory to get a tar.gz of an installable slicer (or specify --pack argument to getbuildtest).  Essentially you will get a directory tree that you can copy to wherever you want it.  As long as the contents are in the same relative locations everything should work.
>
> Best,
> Steve
>
> Chris Gorman wrote:
>> Hello again.
>> I have some updates on this.  First off I cannot reproduce the problems with errors caused by the tcl.h header, so you may want to disregard them.  I have disabled some macports ports which may have allowed me to bypass this problem.
>> The first problem I have building slicer3.4 with xcode 3.2.1 and darwin 10.2.0 is python2.5 it fails as gcc cannot find the switch -Wno-long-double.  Thanks to the macports folks (http://trac.macports.org/browser/trunk/dports/lang/python25/Portfile) I have some patches that get around this.  I applied ./patch-64bit.diff ./patch-configure-arch_only.diff ./patch-configure-badcflags.diff ./patch-Lib-cgi.py.diff ./patch-Lib-distutils-dist.py.diff ./patch-Makefile.pre.in.diff ./patch-setup.py.diff.  In my haste, I applied a few extra patches which I will try reverting to see if this gets the build to work they are ./not_used_in_macports/patch-FSIORefNum.diff ./not_used_in_macports/patch-Misc-setuid-prog.c.diff ./not_used_in_macports/patch-Modules-posixmodule.c.diff ./not_used_in_macports/patch-pyconfig.h.in.diff.
>> The build still fails although much further along.  There is no Slicer-real built, so it will not run.  Unfortunately I didn't do a build.log, but I can if anyone's interested. running: sh /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Scripts/versioner.tcl
>> Slicer3_HOME is /Users/chrisgorman/src/medical-imaging/slicer/Slicer3
>> running: make Experimental
>>   Site: Macintosh.local
>>   Build name: Darwin-g++
>> Create new tag: 20091215-1938 - Experimental
>> Start processing tests
>> Configure project
>>   Each . represents 1024 bytes of output
>>    . Size of output: 0K
>> Build project
>>   Each symbol represents 1024 bytes of output.
>>   '!' represents an error and '*' a warning.
>>    ...! Size of output: 3K
>> Error(s) when building project
>>   3 Compiler errors
>>   1 Compiler warnings
>> Test project /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build
>>  1/ 95 Testing Parser1Test1                     Passed
>>  2/ 95 Testing Parser1Test2                     Passed
>>  3/ 95 Testing ModuleFactoryTest                Passed
>>  4/ 95 Testing Slicer3CLPExample1               Passed
>>  5/ 95 Testing Slicer3CLPExample2               Passed
>>  6/ 95 Testing Slicer3CLPExample3               Passed
>>  7/ 95 Testing LMParser1Test1                   Passed
>>  8/ 95 Testing LMParser1Test2                   Passed
>>  9/ 95 Testing VTKITKVectorReader               Passed
>> 10/ 95 Testing VTKITKBSplineTransform           Passed
>> 11/ 95 Testing Slicer3GUITest1               ***Failed  12/ 95 Testing Slicer3GUITest2               ***Failed  13/ 95 Testing Slicer3FiducialsTest1         ***Failed  14/ 95 Testing Slicer3FiducialsTest2         ***Failed  15/ 95 Testing QdecModuleLibs                ***Failed  16/ 95 Testing TractographyTestGlyphs        ***Failed  17/ 95 Testing ChangeTrackerCL_Help             Passed
>> 18/ 95 Testing ChangeTrackerCL_TestGlobalReg ***Failed  19/ 95 Testing ChangeTrackerCL_TestFull_Inten***Failed  20/ 95 Testing DiffusionEditorTest           ***Failed  21/ 95 Testing DiffusionEditorGradients      ***Failed  22/ 95 Testing DiffusionEditorGlyphsTracts   ***Failed  23/ 95 Testing DiffusionEditorTensor         ***Failed  24/ 95 Testing vtkEMSegmentMRMLManagerTest      Passed
>> 25/ 95 Testing vtkEMSegmentPreprocessingManag   Passed
>> 26/ 95 Testing vtkEMSegmentBlackBoxSegmentati   Passed
>> 27/ 95 Testing vtkEMSegmentBuildAndRunNewSegm   Passed
>> 28/ 95 Testing EMSegCL_Help                     Passed
>> 29/ 95 Testing EMSegCL_Version                  Passed
>> 30/ 95 Testing EMSegCL_RunDefaultNodes          Passed
>> 31/ 95 Testing EMSegCL_RunNormalize             Passed
>> 32/ 95 Testing EMSegCL_RunSetEverything         Passed
>> 33/ 95 Testing EMSegCL_DisableMultithreading    Passed
>> 34/ 95 Testing EMSegCL_EFBogusParameterNode     Passed
>> 35/ 95 Testing EMSegCL_EFBogusMRMLScene         Passed
>> 36/ 95 Testing EMSegCL_EFBogusTargetImages      Passed
>> 37/ 95 Testing EMSegCL_EFTooManyImages          Passed
>> 38/ 95 Testing EMSegCL_EFTooFewImages           Passed
>> 39/ 95 Testing EMSegCL_EFBogusResultStandardI   Passed
>> 40/ 95 Testing ModelIntoLabelVolumeTest      ***Failed  41/ 95 Testing OrientImageTest1              ***Failed  42/ 95 Testing OrientImageTest2              ***Failed  43/ 95 Testing OrientImageTest3              ***Failed  44/ 95 Testing AddTest                       ***Failed  45/ 95 Testing ThresholdTest                 ***Failed  46/ 95 Testing CheckerBoardTest              ***Failed  47/ 95 Testing MedianImageFilterTest         ***Failed  48/ 95 Testing GaussianBlurImageFilterTest   ***Failed  49/ 95 Testing LinearRegistrationTest00      ***Failed  50/ 95 Testing LinearRegistrationTest01      ***Failed  51/ 95 Testing LinearRegistrationTest02      ***Failed  52/ 95 Testing LinearRegistrationTest03      ***Failed  53/ 95 Testing LinearRegistrationTest04      ***Failed  54/ 95 Testing BSplineRegistrationTest00     ***Failed  55/ 95 Testing TestGridTransformRegistrationT***Failed  56/ 95 Testing AffineRegistrationTest        ***Failed  57/ 95 Testing ConfidenceConnectedTest       ***Failed  58/ 95 Testing CurvatureAnisotropicDiffusionT***Failed  59/ 95 Testing DicomToNrrdConverterTest      ***Failed  60/ 95 Testing DiffusionTensorEstimationTest ***Failed  61/ 95 Testing DiffusionTensorMathematicsTest***Failed  62/ 95 Testing DiffusionTensorTestTest       ***Failed  63/ 95 Testing DiffusionWeightedTestTest     ***Failed  64/ 95 Testing DWIDicomLoadTest              ***Failed  65/ 95 Testing ExecutionModelTourTest        ***Failed  66/ 95 Testing FreesurferSurfaceSectionExtrac***Failed  67/ 95 Testing GradientAnisotropicDiffusionTe***Failed  68/ 95 Testing GrayscaleFillHoleImageFilterTe***Failed  69/ 95 Testing GrayscaleGrindPeakImageFilterT***Failed  70/ 95 Testing GrayscaleModelMakerTest       ***Failed  71/ 95 Testing HistogramMatchingTest         ***Failed  72/ 95 Testing ImageLabelCombineTest         ***Failed  73/ 95 Testing ImageReadDicomWriteTest       ***Failed  74/ 95 Testing LabelMapSmoothingTest         ***Failed  75/ 95 Testing ModelMakerTest                ***Failed  76/ 95 Testing MultipleModelsExampleTest     ***Failed  77/ 95 Testing OtsuThresholdImageFilterTest  ***Failed  78/ 95 Testing OtsuThresholdSegmentationTest ***Failed  79/ 95 Testing ResampleVolume2Test           ***Failed  80/ 95 Testing ResampleVolumeTest            ***Failed  81/ 95 Testing RigidRegistrationTest01       ***Failed  82/ 95 Testing SubtractTest                  ***Failed  83/ 95 Testing VotingBinaryHoleFillingImageFi***Failed  84/ 95 Testing ZeroCrossingBasedEdgeDetection***Failed  85/ 95 Testing Slicer3CLTest1                ***Failed  86/ 95 Testing Slicer3CLTest2                ***Failed  87/ 95 Testing Slicer3CLTest3                ***Failed  88/ 95 Testing Slicer3CLTest4                ***Failed  89/ 95 Testing Slicer3CLTest5                ***Failed  90/ 95 Testing Slicer3CLTest6                ***Failed  91/ 95 Testing Slicer3CLTest7                ***Failed  92/ 95 Testing Slicer3ScrollTest             ***Failed  93/ 95 Testing Slicer3MRMLUndo               ***Failed  94/ 95 Testing Slicer3MRMLVolume             ***Failed  95/ 95 Testing EventBrokerTest               ***Failed 28% tests passed, 68 tests failed out of 95
>> The following tests FAILED:
>> 11 - Slicer3GUITest1 (Failed)
>> 12 - Slicer3GUITest2 (Failed)
>> 13 - Slicer3FiducialsTest1 (Failed)
>> 14 - Slicer3FiducialsTest2 (Failed)
>> 15 - QdecModuleLibs (Failed)
>> 16 - TractographyTestGlyphs (Failed)
>> 18 - ChangeTrackerCL_TestGlobalReg (Failed)
>> 19 - ChangeTrackerCL_TestFull_Intensity (Failed)
>> 20 - DiffusionEditorTest (Failed)
>> 21 - DiffusionEditorGradients (Failed)
>> 22 - DiffusionEditorGlyphsTracts (Failed)
>> 23 - DiffusionEditorTensor (Failed)
>> 40 - ModelIntoLabelVolumeTest (Failed)
>> 41 - OrientImageTest1 (Failed)
>> 42 - OrientImageTest2 (Failed)
>> 43 - OrientImageTest3 (Failed)
>> 44 - AddTest (Failed)
>> 45 - ThresholdTest (Failed)
>> 46 - CheckerBoardTest (Failed)
>> 47 - MedianImageFilterTest (Failed)
>> 48 - GaussianBlurImageFilterTest (Failed)
>> 49 - LinearRegistrationTest00 (Failed)
>> 50 - LinearRegistrationTest01 (Failed)
>> 51 - LinearRegistrationTest02 (Failed)
>> 52 - LinearRegistrationTest03 (Failed)
>> 53 - LinearRegistrationTest04 (Failed)
>> 54 - BSplineRegistrationTest00 (Failed)
>> 55 - TestGridTransformRegistrationTest00 (Failed)
>> 56 - AffineRegistrationTest (Failed)
>> 57 - ConfidenceConnectedTest (Failed)
>> 58 - CurvatureAnisotropicDiffusionTest (Failed)
>> 59 - DicomToNrrdConverterTest (Failed)
>> 60 - DiffusionTensorEstimationTest (Failed)
>> 61 - DiffusionTensorMathematicsTest (Failed)
>> 62 - DiffusionTensorTestTest (Failed)
>> 63 - DiffusionWeightedTestTest (Failed)
>> 64 - DWIDicomLoadTest (Failed)
>> 65 - ExecutionModelTourTest (Failed)
>> 66 - FreesurferSurfaceSectionExtractionTest (Failed)
>> 67 - GradientAnisotropicDiffusionTest (Failed)
>> 68 - GrayscaleFillHoleImageFilterTest (Failed)
>> 69 - GrayscaleGrindPeakImageFilterTest (Failed)
>> 70 - GrayscaleModelMakerTest (Failed)
>> 71 - HistogramMatchingTest (Failed)
>> 72 - ImageLabelCombineTest (Failed)
>> 73 - ImageReadDicomWriteTest (Failed)
>> 74 - LabelMapSmoothingTest (Failed)
>> 75 - ModelMakerTest (Failed)
>> 76 - MultipleModelsExampleTest (Failed)
>> 77 - OtsuThresholdImageFilterTest (Failed)
>> 78 - OtsuThresholdSegmentationTest (Failed)
>> 79 - ResampleVolume2Test (Failed)
>> 80 - ResampleVolumeTest (Failed)
>> 81 - RigidRegistrationTest01 (Failed)
>> 82 - SubtractTest (Failed)
>> 83 - VotingBinaryHoleFillingImageFilterTest (Failed)
>> 84 - ZeroCrossingBasedEdgeDetectionImageFilterTest (Failed)
>> 85 - Slicer3CLTest1 (Failed)
>> 86 - Slicer3CLTest2 (Failed)
>> 87 - Slicer3CLTest3 (Failed)
>> 88 - Slicer3CLTest4 (Failed)
>> 89 - Slicer3CLTest5 (Failed)
>> 90 - Slicer3CLTest6 (Failed)
>> 91 - Slicer3CLTest7 (Failed)
>> 92 - Slicer3ScrollTest (Failed)
>> 93 - Slicer3MRMLUndo (Failed)
>> 94 - Slicer3MRMLVolume (Failed)
>> 95 - EventBrokerTest (Failed)
>> Performing coverage
>> Cannot find any coverage files. Ignoring Coverage request.
>> Submit files (using http)
>>   Using HTTP submit method
>>   Drop site: http://www.cdash.org/CDash/submit.php?project=Slicer3
>>   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Build.xml
>>   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Configure.xml
>>   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Test.xml
>>   Submission successful
>> Errors while running CTest
>> make[3]: *** [CMakeFiles/Experimental] Error 8
>> make[2]: *** [CMakeFiles/Experimental.dir/all] Error 2
>> make[1]: *** [CMakeFiles/Experimental.dir/rule] Error 2
>> make: *** [Experimental] Error 2
>> child process exited abnormally
>> Results: build of "Experimental" failed  As to the Slicer3.5 alpha build, it will build and run on my system, but some problems occur.  Trying out the Slicer3Minute tutorial, the display shows no change on the once the dataset is loaded.  The Slicer3Visualization tutorial the volume loads and is displayed, but some of the other effects don't work, for example loading the label map (tutorial page 38 part 2) shows no change on the images.  I haven't tried anything else yet.  Chris Gorman
>> Macports patches.
>> ------------------------------------------------------------------------
>> In my patches directory and applied in haste, no longer part of the macports python 2.5 build.
>> ------------------------------------------------------------------------
>> On 2009-12-15, at 9:07 AM, Chris Gorman wrote:
>>> Hello,
>>>
>>> First off thank you for the pointer on teem 1.10 Steve.  It resolved the error that was occurring regarding BIFF_STRLEN.  My build went a bit further after that.  My next problem was the inability for the cmake command to find a TCL_LIBRARY.  Inspection of the build scripts indicated it was set as a tcl variable and passed to cmake.  I ran a grep through the source code and found a reference to it appeared to be used only in Applications/GUI/Slicer3.cxx amongst a few references in the .svn directories.  I then edited Applications/GUI/Slicer3.cxx and hard coded my tcl library in place of the build one.  Next I commented out the check for TCL_LIBRARY in Libs/SlicerIO/CMakeLists.txt and tried to build again.  I got a bit further but it still failed to build.
>>>
>>> Linking C executable ../../bin/scat
>>> cd /Users/chrisgorman/src/medical-imaging/slicer/bingcc/Libs/SlicerIO && /opt/local/bin/cmake -E cmake_link_script CMakeFiles/scat.dir/link.txt --verbose=1
>>> /usr/bin/gcc   -mmacosx-version-min=10.6   -Wall -Wno-uninitialized -Wno-unused-parameter -no-cpp-precomp    -Wl,-search_paths_first -headerpad_max_install_names -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib     CMakeFiles/scat.dir/scat.c.o  -o ../../bin/scat  -L/usr/local/lib/InsightToolkit -L/usr/local/lib/KWWidgets -L/usr/local/lib/vtk-5.4 -L/usr/local/lib -L/Users/chrisgorman/src/medical-imaging/curl/bingcc/bin ../../lib/libslicerio.a Undefined symbols:
>>> "_Tcl_DStringInit", referenced from:
>>>     _slicerFgets in libslicerio.a(slicerio.c.o)
>>> "_Tcl_CreateInterp", referenced from:
>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Gets", referenced from:
>>>     _slicerFgets in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Tell", referenced from:
>>>     _slicerFtell in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Flush", referenced from:
>>>     _slicerFflush in libslicerio.a(slicerio.c.o)
>>> "_Tcl_ErrnoMsg", referenced from:
>>>     _slicerFseek in libslicerio.a(slicerio.c.o)
>>>     _slicerFtell in libslicerio.a(slicerio.c.o)
>>>     _slicerUngetc in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Seek", referenced from:
>>>     _slicerFseek in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Eof", referenced from:
>>>     _slicerFeof in libslicerio.a(slicerio.c.o)
>>> "_Tcl_DStringFree", referenced from:
>>>     _slicerFgets in libslicerio.a(slicerio.c.o)
>>> "_Tcl_OpenCommandChannel", referenced from:
>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Read", referenced from:
>>>     _slicerFread in libslicerio.a(slicerio.c.o)
>>>     _slicerFgetc in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Ungets", referenced from:
>>>     _slicerUngetc in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Free", referenced from:
>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>>     _slicerFprintf in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Write", referenced from:
>>>     _slicerFwrite in libslicerio.a(slicerio.c.o)
>>>     _slicerFputc in libslicerio.a(slicerio.c.o)
>>>     _slicerFprintf in libslicerio.a(slicerio.c.o)
>>> "_Tcl_GetErrno", referenced from:
>>>     _slicerFseek in libslicerio.a(slicerio.c.o)
>>>     _slicerFtell in libslicerio.a(slicerio.c.o)
>>>     _slicerUngetc in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Close", referenced from:
>>>     _slicerFclose in libslicerio.a(slicerio.c.o)
>>> "_Tcl_Alloc", referenced from:
>>>     _slicerFprintf in libslicerio.a(slicerio.c.o)
>>> "_Tcl_GetStdChannel", referenced from:
>>>     _slicerFwrite in libslicerio.a(slicerio.c.o)
>>> "_Tcl_SplitList", referenced from:
>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>> "_Tcl_DeleteInterp", referenced from:
>>>     _slicerFclose in libslicerio.a(slicerio.c.o)
>>> ld: symbol(s) not found
>>> collect2: ld returned 1 exit status
>>>
>>> My original reason for doing the manual build was an error with one of the build steps trying to load a header from my system, tcl.h I think, and failing because it needed tcl.h from the build tree instead.  Unfortunately I didn't save any output.  So, I tried going around my system and hiding tcl/tk libraries and headers and tried the regular build process with getbuildtest.tcl and it worked.  I ended up with an alpha version, but otherwise what I wanted.  My next question is how do I install the build?  It seems that if I move anything around it can no longer find the libraries.  (This is not a big deal, I don't mind running it in place.)  It's too bad the manual build failed.  It would have been nice to be able to contribute the notes to the wiki.
>>>
>>> Chris Gorman
>>>
>>> On 2009-12-13, at 9:06 PM, Steve Pieper wrote:
>>>
>>>> Hi Chris -
>>>>
>>>> I added the note about VTK_USE_COCOA to the wiki page - thanks for the feedback.  In general those pages about the manual configuration get out of sync - if you run into problems you can compare your steps the ones performed by the genlib script (it basically just automates the various checkouts and cmake configures and builds).  If you want, feel free to update the wiki with the latest info based on your experiences.
>>>>
>>>> One thing I do know from recent experience is that you'll need to use teem 1.10 with slicer 3.4 (in teem 1.11 the BIFF_STRLEN was removed).
>>>>
>>>> -Steve
>>>>
>>>> Chris Gorman wrote:
>>>>> On 2009-12-13, at 4:49 PM, Chris Gorman wrote:
>>>>>> Hello,
>>>>>>
>>>>>> This didn't post properly.  Trying again.
>>>>>>
>>>>>> On 2009-12-13, at 3:13 PM, Chris Gorman wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK option presented.  From VTK/CMakeLists.txt
>>>>>>>
>>>>>>> SET(VTK_CAN_USE_TK)
>>>>>>> IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>>>> IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>>>  SET(VTK_CAN_USE_TK 1)
>>>>>>> ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>>> ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>>>> VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
>>>>>>>                   "VTK_CAN_USE_TK" OFF)
>>>>>>>
>>>>>>> The web page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build needs to be updated to inform users about this as it only mentions disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled by default now.  (At least it was on vtk 5.4.2.)
>>>>>>>
>>>>>>> The next issue is building slicer3.  During configure I get CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
>>>>>>> Could not find tcl
>>>>>>>
>>>>>>> I tried to hack in the value from my VTK configure, but this doesn't seem to be work, probably due to my lack of understanding of cmake grammar.  Setting it by SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")
>>>>>>>
>>>>>>> in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set for vtk.  I also tried to set TCL_LIBRARY to point to the libtcl.dylib, but I think this causing problems too.  This allows the build to continue but not for long.  It fails.  [  3%] Building CXX object Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx: In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*, const Nrrd*, double*)’:
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795: error: ‘BIFF_STRLEN’ was not declared in this scope
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802: error: ‘err’ was not declared in this scope
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806: error: ‘err’ was not declared in this scope
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810: error: ‘err’ was not declared in this scope
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815: error: ‘err’ was not declared in this scope
>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824: error: ‘err’ was not declared in this scope
>>>>>>> make[2]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
>>>>>>> make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
>>>>>>> make: *** [all] Error 2
>>>>>>>
>>>>>>> I did a quick google search to find where the declaration of BIFF_STRLEN, but wasn't able to find anything too useful.  My configuration is Darwin 10.2.0
>>>>>>> cmake 2.8.0
>>>>>>> tcl/tk 8.5 (from os x)
>>>>>>> incrTcl 3.3 (from macports)
>>>>>>> vtk 5.4.2 itk 3.16.0
>>>>>>> kwwidgets 1.0.0
>>>>>>> teem 1.11.0
>>>>>>> SlicerLibCurl 7.12.1
>>>>>>> Slicer3 3.4
>>>>>>>
>>>>>>> In summary.  I would like to find a solution to the cmake configure error, as I believe that is causing problems in addition to the build error.  If anyone has pointers, please let me know.  Thanks.
>>>>>>>
>>>>>>> Chris Gorman
>>>>> ------------------------------------------------------------------------
>>>>> _______________________________________________
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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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>>> [hidden email]
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Re: building Slicer3 3.4

pieper
Administrator
Hi Chris -

Thanks for the extra info - I agree with your analysis.  Slicer 3.4 was
cut before mac os 10.6 came out(*) so it doesn't have the patches needed
to build there while the current 3.5 development trunk of slicer does.

We do build our releases and nightlies on older machines to avoid these
kinds of issues, although eventually we move forward.  Katie has the
current OSes for the nightly builds documented on the wiki somewhere.

But thanks for passing on the build logs - based on that info I realized
that one of the modules that had recently been backported to 3.4 was
missing the .xml file needed to build, and that's why your build and
tests were failing.  3.4 might work now if you svn update.

But snowleopard and the trunk should be working pretty well.  I have a
nightly build ("common.bwh.harvard.edu" on the dashboard) that does a
clean build of everything each night.

What's the data that doesn't load on slicer 3.5 but does in 3.4?

-Steve


(*) thanks for the explanation of the darwin kernel number 10.2 versus
the OS number 10.6 - odd indeed...

Chris Gorman wrote:
> Hello again.
>
> Per Steve's suggestion I've attached a two build.logs.  I need to include 2 because the build fails half way through with the python issue and I needed to apply some patches.  As to the gcc error, apparently it is a gcc 3 switch that has been deprecated.  At least it is as of gcc 4.2 which is the default compiler from XCode 3.2.1.  As to the os versions I believe I unintentionally misled Steve.  Darwin is the kernel and is not the same version as the operating system.  Darwin 10.2.0 is actually OS X 10.6.2.  Who knows why versioning was done this way but it is.    So it appears that building on 10.6.2 won't work for 3.4 but it does mostly for 3.5 alpha.  It is likely that your builds  are built on 10.5 with XCode 3.1.3 or something like that.  I made the jump to 10.6, but am actually regretting it.  Hopefully in a few months more things will build properly on 10.6.  I would consider that it may not be a good use of time to debug why the build for Slicer 3.4 doesn't work, si
nce an Intel binary is available if needed, and instead to target efforts to why the 3.5 alpha build doesn't display some of the loaded data.  Thanks for all the help.

>
> Chris Gorman
>
>
> ------------------------------------------------------------------------
>
>
>
> On 2009-12-15, at 8:03 PM, Steve Pieper wrote:
>
>> Hi Chris -
>>
>> Yes, sometimes it is threading the needle to get all the right versions of the OS, python, tcl, etc building with the right flags.  I believe the --Wno-long-double was introduced for compatibility with OSX 10.6 so I'm not sure about 10.2.  Also we typically build our own tcl/tk 8.4 so I don't know if it's possible to build with the OS's 10.5 (I'm guissing not).  If you could generate a build log for your system that might help track down the remaining issues.
>>
>> Regarding your earlier question, you can run 'make package' in the Slicer3-build directory to get a tar.gz of an installable slicer (or specify --pack argument to getbuildtest).  Essentially you will get a directory tree that you can copy to wherever you want it.  As long as the contents are in the same relative locations everything should work.
>>
>> Best,
>> Steve
>>
>> Chris Gorman wrote:
>>> Hello again.
>>> I have some updates on this.  First off I cannot reproduce the problems with errors caused by the tcl.h header, so you may want to disregard them.  I have disabled some macports ports which may have allowed me to bypass this problem.
>>> The first problem I have building slicer3.4 with xcode 3.2.1 and darwin 10.2.0 is python2.5 it fails as gcc cannot find the switch -Wno-long-double.  Thanks to the macports folks (http://trac.macports.org/browser/trunk/dports/lang/python25/Portfile) I have some patches that get around this.  I applied ./patch-64bit.diff ./patch-configure-arch_only.diff ./patch-configure-badcflags.diff ./patch-Lib-cgi.py.diff ./patch-Lib-distutils-dist.py.diff ./patch-Makefile.pre.in.diff ./patch-setup.py.diff.  In my haste, I applied a few extra patches which I will try reverting to see if this gets the build to work they are ./not_used_in_macports/patch-FSIORefNum.diff ./not_used_in_macports/patch-Misc-setuid-prog.c.diff ./not_used_in_macports/patch-Modules-posixmodule.c.diff ./not_used_in_macports/patch-pyconfig.h.in.diff.
>>> The build still fails although much further along.  There is no Slicer-real built, so it will not run.  Unfortunately I didn't do a build.log, but I can if anyone's interested. running: sh /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Scripts/versioner.tcl
>>> Slicer3_HOME is /Users/chrisgorman/src/medical-imaging/slicer/Slicer3
>>> running: make Experimental
>>>   Site: Macintosh.local
>>>   Build name: Darwin-g++
>>> Create new tag: 20091215-1938 - Experimental
>>> Start processing tests
>>> Configure project
>>>   Each . represents 1024 bytes of output
>>>    . Size of output: 0K
>>> Build project
>>>   Each symbol represents 1024 bytes of output.
>>>   '!' represents an error and '*' a warning.
>>>    ...! Size of output: 3K
>>> Error(s) when building project
>>>   3 Compiler errors
>>>   1 Compiler warnings
>>> Test project /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build
>>>  1/ 95 Testing Parser1Test1                     Passed
>>>  2/ 95 Testing Parser1Test2                     Passed
>>>  3/ 95 Testing ModuleFactoryTest                Passed
>>>  4/ 95 Testing Slicer3CLPExample1               Passed
>>>  5/ 95 Testing Slicer3CLPExample2               Passed
>>>  6/ 95 Testing Slicer3CLPExample3               Passed
>>>  7/ 95 Testing LMParser1Test1                   Passed
>>>  8/ 95 Testing LMParser1Test2                   Passed
>>>  9/ 95 Testing VTKITKVectorReader               Passed
>>> 10/ 95 Testing VTKITKBSplineTransform           Passed
>>> 11/ 95 Testing Slicer3GUITest1               ***Failed  12/ 95 Testing Slicer3GUITest2               ***Failed  13/ 95 Testing Slicer3FiducialsTest1         ***Failed  14/ 95 Testing Slicer3FiducialsTest2         ***Failed  15/ 95 Testing QdecModuleLibs                ***Failed  16/ 95 Testing TractographyTestGlyphs        ***Failed  17/ 95 Testing ChangeTrackerCL_Help             Passed
>>> 18/ 95 Testing ChangeTrackerCL_TestGlobalReg ***Failed  19/ 95 Testing ChangeTrackerCL_TestFull_Inten***Failed  20/ 95 Testing DiffusionEditorTest           ***Failed  21/ 95 Testing DiffusionEditorGradients      ***Failed  22/ 95 Testing DiffusionEditorGlyphsTracts   ***Failed  23/ 95 Testing DiffusionEditorTensor         ***Failed  24/ 95 Testing vtkEMSegmentMRMLManagerTest      Passed
>>> 25/ 95 Testing vtkEMSegmentPreprocessingManag   Passed
>>> 26/ 95 Testing vtkEMSegmentBlackBoxSegmentati   Passed
>>> 27/ 95 Testing vtkEMSegmentBuildAndRunNewSegm   Passed
>>> 28/ 95 Testing EMSegCL_Help                     Passed
>>> 29/ 95 Testing EMSegCL_Version                  Passed
>>> 30/ 95 Testing EMSegCL_RunDefaultNodes          Passed
>>> 31/ 95 Testing EMSegCL_RunNormalize             Passed
>>> 32/ 95 Testing EMSegCL_RunSetEverything         Passed
>>> 33/ 95 Testing EMSegCL_DisableMultithreading    Passed
>>> 34/ 95 Testing EMSegCL_EFBogusParameterNode     Passed
>>> 35/ 95 Testing EMSegCL_EFBogusMRMLScene         Passed
>>> 36/ 95 Testing EMSegCL_EFBogusTargetImages      Passed
>>> 37/ 95 Testing EMSegCL_EFTooManyImages          Passed
>>> 38/ 95 Testing EMSegCL_EFTooFewImages           Passed
>>> 39/ 95 Testing EMSegCL_EFBogusResultStandardI   Passed
>>> 40/ 95 Testing ModelIntoLabelVolumeTest      ***Failed  41/ 95 Testing OrientImageTest1              ***Failed  42/ 95 Testing OrientImageTest2              ***Failed  43/ 95 Testing OrientImageTest3              ***Failed  44/ 95 Testing AddTest                       ***Failed  45/ 95 Testing ThresholdTest                 ***Failed  46/ 95 Testing CheckerBoardTest              ***Failed  47/ 95 Testing MedianImageFilterTest         ***Failed  48/ 95 Testing GaussianBlurImageFilterTest   ***Failed  49/ 95 Testing LinearRegistrationTest00      ***Failed  50/ 95 Testing LinearRegistrationTest01      ***Failed  51/ 95 Testing LinearRegistrationTest02      ***Failed  52/ 95 Testing LinearRegistrationTest03      ***Failed  53/ 95 Testing LinearRegistrationTest04      ***Failed  54/ 95 Testing BSplineRegistrationTest00     ***Failed  55/ 95 Testing TestGridTransformRegistrationT***Failed  56/ 95 Testing AffineRegistrationTest        ***Failed  57/ 95 Testing ConfidenceConnected
Test       ***Failed  58/ 95 Testing CurvatureAnisotropicDiffusionT***Failed  59/ 95 Testing DicomToNrrdConverterTest      ***Failed  60/ 95 Testing DiffusionTensorEstimationTest ***Failed  61/ 95 Testing DiffusionTensorMathematicsTest***Failed  62/ 95 Testing DiffusionTensorTestTest       ***Failed  63/ 95 Testing DiffusionWeightedTestTest     ***Failed  64/ 95 Testing DWIDicomLoadTest              ***Failed  65/ 95 Testing ExecutionModelTourTest        ***Failed  66/ 95 Testing FreesurferSurfaceSectionExtrac***Failed  67/ 95 Testing GradientAnisotropicDiffusionTe***Failed  68/ 95 Testing GrayscaleFillHoleImageFilterTe***Failed  69/ 95 Testing GrayscaleGrindPeakImageFilterT***Failed  70/ 95 Testing GrayscaleModelMakerTest       ***Failed  71/ 95 Testing HistogramMatchingTest         ***Failed  72/ 95 Testing ImageLabelCombineTest         ***Failed  73/ 95 Testing ImageReadDicomWriteTest       ***Failed  74/ 95 Testing LabelMapSmoothingTest         ***Failed  75/ 95 Testing M
odelMakerTest                ***Failed  76/ 95 Testing MultipleModelsExampleTest     ***Failed  77/ 95 Testing OtsuThresholdImageFilterTest  ***Failed  78/ 95 Testing OtsuThresholdSegmentationTest ***Failed  79/ 95 Testing ResampleVolume2Test           ***Failed  80/ 95 Testing ResampleVolumeTest            ***Failed  81/ 95 Testing RigidRegistrationTest01       ***Failed  82/ 95 Testing SubtractTest                  ***Failed  83/ 95 Testing VotingBinaryHoleFillingImageFi***Failed  84/ 95 Testing ZeroCrossingBasedEdgeDetection***Failed  85/ 95 Testing Slicer3CLTest1                ***Failed  86/ 95 Testing Slicer3CLTest2                ***Failed  87/ 95 Testing Slicer3CLTest3                ***Failed  88/ 95 Testing Slicer3CLTest4                ***Failed  89/ 95 Testing Slicer3CLTest5                ***Failed  90/ 95 Testing Slicer3CLTest6                ***Failed  91/ 95 Testing Slicer3CLTest7                ***Failed  92/ 95 Testing Slicer3ScrollTest             ***Failed
  93/ 95 Testing Slicer3MRMLUndo               ***Failed  94/ 95 Testing Slicer3MRMLVolume             ***Failed  95/ 95 Testing EventBrokerTest               ***Failed 28% tests passed, 68 tests failed out of 95

>>> The following tests FAILED:
>>> 11 - Slicer3GUITest1 (Failed)
>>> 12 - Slicer3GUITest2 (Failed)
>>> 13 - Slicer3FiducialsTest1 (Failed)
>>> 14 - Slicer3FiducialsTest2 (Failed)
>>> 15 - QdecModuleLibs (Failed)
>>> 16 - TractographyTestGlyphs (Failed)
>>> 18 - ChangeTrackerCL_TestGlobalReg (Failed)
>>> 19 - ChangeTrackerCL_TestFull_Intensity (Failed)
>>> 20 - DiffusionEditorTest (Failed)
>>> 21 - DiffusionEditorGradients (Failed)
>>> 22 - DiffusionEditorGlyphsTracts (Failed)
>>> 23 - DiffusionEditorTensor (Failed)
>>> 40 - ModelIntoLabelVolumeTest (Failed)
>>> 41 - OrientImageTest1 (Failed)
>>> 42 - OrientImageTest2 (Failed)
>>> 43 - OrientImageTest3 (Failed)
>>> 44 - AddTest (Failed)
>>> 45 - ThresholdTest (Failed)
>>> 46 - CheckerBoardTest (Failed)
>>> 47 - MedianImageFilterTest (Failed)
>>> 48 - GaussianBlurImageFilterTest (Failed)
>>> 49 - LinearRegistrationTest00 (Failed)
>>> 50 - LinearRegistrationTest01 (Failed)
>>> 51 - LinearRegistrationTest02 (Failed)
>>> 52 - LinearRegistrationTest03 (Failed)
>>> 53 - LinearRegistrationTest04 (Failed)
>>> 54 - BSplineRegistrationTest00 (Failed)
>>> 55 - TestGridTransformRegistrationTest00 (Failed)
>>> 56 - AffineRegistrationTest (Failed)
>>> 57 - ConfidenceConnectedTest (Failed)
>>> 58 - CurvatureAnisotropicDiffusionTest (Failed)
>>> 59 - DicomToNrrdConverterTest (Failed)
>>> 60 - DiffusionTensorEstimationTest (Failed)
>>> 61 - DiffusionTensorMathematicsTest (Failed)
>>> 62 - DiffusionTensorTestTest (Failed)
>>> 63 - DiffusionWeightedTestTest (Failed)
>>> 64 - DWIDicomLoadTest (Failed)
>>> 65 - ExecutionModelTourTest (Failed)
>>> 66 - FreesurferSurfaceSectionExtractionTest (Failed)
>>> 67 - GradientAnisotropicDiffusionTest (Failed)
>>> 68 - GrayscaleFillHoleImageFilterTest (Failed)
>>> 69 - GrayscaleGrindPeakImageFilterTest (Failed)
>>> 70 - GrayscaleModelMakerTest (Failed)
>>> 71 - HistogramMatchingTest (Failed)
>>> 72 - ImageLabelCombineTest (Failed)
>>> 73 - ImageReadDicomWriteTest (Failed)
>>> 74 - LabelMapSmoothingTest (Failed)
>>> 75 - ModelMakerTest (Failed)
>>> 76 - MultipleModelsExampleTest (Failed)
>>> 77 - OtsuThresholdImageFilterTest (Failed)
>>> 78 - OtsuThresholdSegmentationTest (Failed)
>>> 79 - ResampleVolume2Test (Failed)
>>> 80 - ResampleVolumeTest (Failed)
>>> 81 - RigidRegistrationTest01 (Failed)
>>> 82 - SubtractTest (Failed)
>>> 83 - VotingBinaryHoleFillingImageFilterTest (Failed)
>>> 84 - ZeroCrossingBasedEdgeDetectionImageFilterTest (Failed)
>>> 85 - Slicer3CLTest1 (Failed)
>>> 86 - Slicer3CLTest2 (Failed)
>>> 87 - Slicer3CLTest3 (Failed)
>>> 88 - Slicer3CLTest4 (Failed)
>>> 89 - Slicer3CLTest5 (Failed)
>>> 90 - Slicer3CLTest6 (Failed)
>>> 91 - Slicer3CLTest7 (Failed)
>>> 92 - Slicer3ScrollTest (Failed)
>>> 93 - Slicer3MRMLUndo (Failed)
>>> 94 - Slicer3MRMLVolume (Failed)
>>> 95 - EventBrokerTest (Failed)
>>> Performing coverage
>>> Cannot find any coverage files. Ignoring Coverage request.
>>> Submit files (using http)
>>>   Using HTTP submit method
>>>   Drop site: http://www.cdash.org/CDash/submit.php?project=Slicer3
>>>   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Build.xml
>>>   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Configure.xml
>>>   Uploaded: /Users/chrisgorman/src/medical-imaging/slicer/Slicer3-build/Testing/20091215-1938/Test.xml
>>>   Submission successful
>>> Errors while running CTest
>>> make[3]: *** [CMakeFiles/Experimental] Error 8
>>> make[2]: *** [CMakeFiles/Experimental.dir/all] Error 2
>>> make[1]: *** [CMakeFiles/Experimental.dir/rule] Error 2
>>> make: *** [Experimental] Error 2
>>> child process exited abnormally
>>> Results: build of "Experimental" failed  As to the Slicer3.5 alpha build, it will build and run on my system, but some problems occur.  Trying out the Slicer3Minute tutorial, the display shows no change on the once the dataset is loaded.  The Slicer3Visualization tutorial the volume loads and is displayed, but some of the other effects don't work, for example loading the label map (tutorial page 38 part 2) shows no change on the images.  I haven't tried anything else yet.  Chris Gorman
>>> Macports patches.
>>> ------------------------------------------------------------------------
>>> In my patches directory and applied in haste, no longer part of the macports python 2.5 build.
>>> ------------------------------------------------------------------------
>>> On 2009-12-15, at 9:07 AM, Chris Gorman wrote:
>>>> Hello,
>>>>
>>>> First off thank you for the pointer on teem 1.10 Steve.  It resolved the error that was occurring regarding BIFF_STRLEN.  My build went a bit further after that.  My next problem was the inability for the cmake command to find a TCL_LIBRARY.  Inspection of the build scripts indicated it was set as a tcl variable and passed to cmake.  I ran a grep through the source code and found a reference to it appeared to be used only in Applications/GUI/Slicer3.cxx amongst a few references in the .svn directories.  I then edited Applications/GUI/Slicer3.cxx and hard coded my tcl library in place of the build one.  Next I commented out the check for TCL_LIBRARY in Libs/SlicerIO/CMakeLists.txt and tried to build again.  I got a bit further but it still failed to build.
>>>>
>>>> Linking C executable ../../bin/scat
>>>> cd /Users/chrisgorman/src/medical-imaging/slicer/bingcc/Libs/SlicerIO && /opt/local/bin/cmake -E cmake_link_script CMakeFiles/scat.dir/link.txt --verbose=1
>>>> /usr/bin/gcc   -mmacosx-version-min=10.6   -Wall -Wno-uninitialized -Wno-unused-parameter -no-cpp-precomp    -Wl,-search_paths_first -headerpad_max_install_names -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib     CMakeFiles/scat.dir/scat.c.o  -o ../../bin/scat  -L/usr/local/lib/InsightToolkit -L/usr/local/lib/KWWidgets -L/usr/local/lib/vtk-5.4 -L/usr/local/lib -L/Users/chrisgorman/src/medical-imaging/curl/bingcc/bin ../../lib/libslicerio.a Undefined symbols:
>>>> "_Tcl_DStringInit", referenced from:
>>>>     _slicerFgets in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_CreateInterp", referenced from:
>>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Gets", referenced from:
>>>>     _slicerFgets in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Tell", referenced from:
>>>>     _slicerFtell in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Flush", referenced from:
>>>>     _slicerFflush in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_ErrnoMsg", referenced from:
>>>>     _slicerFseek in libslicerio.a(slicerio.c.o)
>>>>     _slicerFtell in libslicerio.a(slicerio.c.o)
>>>>     _slicerUngetc in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Seek", referenced from:
>>>>     _slicerFseek in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Eof", referenced from:
>>>>     _slicerFeof in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_DStringFree", referenced from:
>>>>     _slicerFgets in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_OpenCommandChannel", referenced from:
>>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Read", referenced from:
>>>>     _slicerFread in libslicerio.a(slicerio.c.o)
>>>>     _slicerFgetc in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Ungets", referenced from:
>>>>     _slicerUngetc in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Free", referenced from:
>>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>>>     _slicerFprintf in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Write", referenced from:
>>>>     _slicerFwrite in libslicerio.a(slicerio.c.o)
>>>>     _slicerFputc in libslicerio.a(slicerio.c.o)
>>>>     _slicerFprintf in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_GetErrno", referenced from:
>>>>     _slicerFseek in libslicerio.a(slicerio.c.o)
>>>>     _slicerFtell in libslicerio.a(slicerio.c.o)
>>>>     _slicerUngetc in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Close", referenced from:
>>>>     _slicerFclose in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_Alloc", referenced from:
>>>>     _slicerFprintf in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_GetStdChannel", referenced from:
>>>>     _slicerFwrite in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_SplitList", referenced from:
>>>>     _slicerFopen in libslicerio.a(slicerio.c.o)
>>>> "_Tcl_DeleteInterp", referenced from:
>>>>     _slicerFclose in libslicerio.a(slicerio.c.o)
>>>> ld: symbol(s) not found
>>>> collect2: ld returned 1 exit status
>>>>
>>>> My original reason for doing the manual build was an error with one of the build steps trying to load a header from my system, tcl.h I think, and failing because it needed tcl.h from the build tree instead.  Unfortunately I didn't save any output.  So, I tried going around my system and hiding tcl/tk libraries and headers and tried the regular build process with getbuildtest.tcl and it worked.  I ended up with an alpha version, but otherwise what I wanted.  My next question is how do I install the build?  It seems that if I move anything around it can no longer find the libraries.  (This is not a big deal, I don't mind running it in place.)  It's too bad the manual build failed.  It would have been nice to be able to contribute the notes to the wiki.
>>>>
>>>> Chris Gorman
>>>>
>>>> On 2009-12-13, at 9:06 PM, Steve Pieper wrote:
>>>>
>>>>> Hi Chris -
>>>>>
>>>>> I added the note about VTK_USE_COCOA to the wiki page - thanks for the feedback.  In general those pages about the manual configuration get out of sync - if you run into problems you can compare your steps the ones performed by the genlib script (it basically just automates the various checkouts and cmake configures and builds).  If you want, feel free to update the wiki with the latest info based on your experiences.
>>>>>
>>>>> One thing I do know from recent experience is that you'll need to use teem 1.10 with slicer 3.4 (in teem 1.11 the BIFF_STRLEN was removed).
>>>>>
>>>>> -Steve
>>>>>
>>>>> Chris Gorman wrote:
>>>>>> On 2009-12-13, at 4:49 PM, Chris Gorman wrote:
>>>>>>> Hello,
>>>>>>>
>>>>>>> This didn't post properly.  Trying again.
>>>>>>>
>>>>>>> On 2009-12-13, at 3:13 PM, Chris Gorman wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> VTK_USE_COCOA needs to be disabled in order to get the VTK_USE_TK option presented.  From VTK/CMakeLists.txt
>>>>>>>>
>>>>>>>> SET(VTK_CAN_USE_TK)
>>>>>>>> IF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>>>>> IF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>>>>  SET(VTK_CAN_USE_TK 1)
>>>>>>>> ENDIF(NOT VTK_USE_COCOA  AND NOT  VTK_DISABLE_TK_INIT)
>>>>>>>> ENDIF(VTK_WRAP_PYTHON OR VTK_WRAP_TCL)
>>>>>>>> VTK_DEPENDENT_OPTION(VTK_USE_TK "Build VTK with Tk support" ON
>>>>>>>>                   "VTK_CAN_USE_TK" OFF)
>>>>>>>>
>>>>>>>> The web page http://www.slicer.org/slicerWiki/index.php/Slicer3:Manual_Build needs to be updated to inform users about this as it only mentions disabling VTK_USE_CARBON.   Which, if I recall correctly, is disabled by default now.  (At least it was on vtk 5.4.2.)
>>>>>>>>
>>>>>>>> The next issue is building slicer3.  During configure I get CMake Error at Libs/SlicerIO/CMakeLists.txt:17 (message):
>>>>>>>> Could not find tcl
>>>>>>>>
>>>>>>>> I tried to hack in the value from my VTK configure, but this doesn't seem to be work, probably due to my lack of understanding of cmake grammar.  Setting it by SET(TCL_LIBRARY "/System/Library/Frameworks/tcl.framework")
>>>>>>>>
>>>>>>>> in Libs/SlicerIO/CMakeLists.txt just before the tests, as it was set for vtk.  I also tried to set TCL_LIBRARY to point to the libtcl.dylib, but I think this causing problems too.  This allows the build to continue but not for long.  It fails.  [  3%] Building CXX object Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx: In member function ‘int vtkNRRDReader::tenSpaceDirectionReduce(Nrrd*, const Nrrd*, double*)’:
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:795: error: ‘BIFF_STRLEN’ was not declared in this scope
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:802: error: ‘err’ was not declared in this scope
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:806: error: ‘err’ was not declared in this scope
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:810: error: ‘err’ was not declared in this scope
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:815: error: ‘err’ was not declared in this scope
>>>>>>>> /Users/chrisgorman/src/medical-imaging/slicer/Slicer3/Libs/vtkTeem/vtkNRRDReader.cxx:824: error: ‘err’ was not declared in this scope
>>>>>>>> make[2]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/vtkNRRDReader.cxx.o] Error 1
>>>>>>>> make[1]: *** [Libs/vtkTeem/CMakeFiles/vtkTeem.dir/all] Error 2
>>>>>>>> make: *** [all] Error 2
>>>>>>>>
>>>>>>>> I did a quick google search to find where the declaration of BIFF_STRLEN, but wasn't able to find anything too useful.  My configuration is Darwin 10.2.0
>>>>>>>> cmake 2.8.0
>>>>>>>> tcl/tk 8.5 (from os x)
>>>>>>>> incrTcl 3.3 (from macports)
>>>>>>>> vtk 5.4.2 itk 3.16.0
>>>>>>>> kwwidgets 1.0.0
>>>>>>>> teem 1.11.0
>>>>>>>> SlicerLibCurl 7.12.1
>>>>>>>> Slicer3 3.4
>>>>>>>>
>>>>>>>> In summary.  I would like to find a solution to the cmake configure error, as I believe that is causing problems in addition to the build error.  If anyone has pointers, please let me know.  Thanks.
>>>>>>>>
>>>>>>>> Chris Gorman
>>>>>> ------------------------------------------------------------------------
>>>>>> _______________________________________________
>>>>>> slicer-devel mailing list
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>>>>>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
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Re: building Slicer3 3.4

Chris Gorman
Hello Steve,

Slicer 3.5 won't render some of the tutorials properly.  The Slicer3Minute tutorial, the 3d viewer and 2d slice viewers don't change once the dataset is loaded.  The Slicer3Visualization tutorial the volume loads and is displayed, but some of the other effects don't work, for example loading the label map (tutorial page 38 part 2) shows no change on the images.  I don't yet know that 3.4 will render this properly, I only assume it does because of the screenshots in the tutorial. Also now for some reason post 'make package' slicer3.5 now dies while loading with a SIGFPE {floating-point exception}.  

Macintosh:bin chrisgorman$ Slicer3
Setting up launch environment...
Starting Slicer: /usr/local/Slicer3-3.5-alpha-2009-12-14-darwin-x86

child killed: floating-point exception
 
CHILDKILLED 23536 SIGFPE {floating-point exception}

And something is wrong with the orientation.  The splash screen used to appear in the middle of the screen with loading information, pre SIGFPE and now it appears in the top left corner with and nothing is displayed on it.  

Based on your information Steve, I'll try a build of 3.4 and if that fails a new checkout of 3.5.  Do you want to analyze another build log, this time for 3.5?  Thanks for all the help.

Chris Gorman

On 2009-12-16, at 12:06 AM, Steve Pieper wrote:

> Hi Chris -
>
> Thanks for the extra info - I agree with your analysis.  Slicer 3.4 was cut before mac os 10.6 came out(*) so it doesn't have the patches needed to build there while the current 3.5 development trunk of slicer does.
>
> We do build our releases and nightlies on older machines to avoid these kinds of issues, although eventually we move forward.  Katie has the current OSes for the nightly builds documented on the wiki somewhere.
>
> But thanks for passing on the build logs - based on that info I realized that one of the modules that had recently been backported to 3.4 was missing the .xml file needed to build, and that's why your build and tests were failing.  3.4 might work now if you svn update.
>
> But snowleopard and the trunk should be working pretty well.  I have a nightly build ("common.bwh.harvard.edu" on the dashboard) that does a clean build of everything each night.
>
> What's the data that doesn't load on slicer 3.5 but does in 3.4?
>
> -Steve
>
>
> (*) thanks for the explanation of the darwin kernel number 10.2 versus the OS number 10.6 - odd indeed...
>
> Chris Gorman wrote:
>> Hello again.
>> Per Steve's suggestion I've attached a two build.logs.  I need to include 2 because the build fails half way through with the python issue and I needed to apply some patches.  As to the gcc error, apparently it is a gcc 3 switch that has been deprecated.  At least it is as of gcc 4.2 which is the default compiler from XCode 3.2.1.  As to the os versions I believe I unintentionally misled Steve.  Darwin is the kernel and is not the same version as the operating system.  Darwin 10.2.0 is actually OS X 10.6.2.  Who knows why versioning was done this way but it is.    So it appears that building on 10.6.2 won't work for 3.4 but it does mostly for 3.5 alpha.  It is likely that your builds  are built on 10.5 with XCode 3.1.3 or something like that.  I made the jump to 10.6, but am actually regretting it.  Hopefully in a few months more things will build properly on 10.6.  I would consider that it may not be a good use of time to debug why the build for Slicer 3.4 doesn't work, !
 si

> nce an Intel binary is available if needed, and instead to target efforts to why the 3.5 alpha build doesn't display some of the loaded data.  Thanks for all the help.
>> Chris Gorman
>> ------------------------------------------------------------------------
>> On 2009-12-15, at 8:03 PM, Steve Pieper wrote:
>>> Hi Chris -
>>>
>>> Yes, sometimes it is threading the needle to get all the right versions of the OS, python, tcl, etc building with the right flags.  I believe the --Wno-long-double was introduced for compatibility with OSX 10.6 so I'm not sure about 10.2.  Also we typically build our own tcl/tk 8.4 so I don't know if it's possible to build with the OS's 10.5 (I'm guissing not).  If you could generate a build log for your system that might help track down the remaining issues.
>>>
>>> Regarding your earlier question, you can run 'make package' in the Slicer3-build directory to get a tar.gz of an installable slicer (or specify --pack argument to getbuildtest).  Essentially you will get a directory tree that you can copy to wherever you want it.  As long as the contents are in the same relative locations everything should work.
>>>
>>> Best,
>>> Steve

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Re: building Slicer3 3.4

pieper
Administrator
Hi Chris -

Hmmm... regarding tutorials: that's definitely buggy behavior -- yes,
3.4 was used to make (and teach) those tutorials so it should work.  We
also want them to work the same on 3.5 and now that I test I see that
some bug has crept into the trunk recently.  We'll need to hunt that
down on this end -- several active developments are going on in the
trunk and I'm not sure what caused this breakage.

-Steve

Chris Gorman wrote:

> Hello Steve,
>
> Slicer 3.5 won't render some of the tutorials properly.  The Slicer3Minute tutorial, the 3d viewer and 2d slice viewers don't change once the dataset is loaded.  The Slicer3Visualization tutorial the volume loads and is displayed, but some of the other effects don't work, for example loading the label map (tutorial page 38 part 2) shows no change on the images.  I don't yet know that 3.4 will render this properly, I only assume it does because of the screenshots in the tutorial. Also now for some reason post 'make package' slicer3.5 now dies while loading with a SIGFPE {floating-point exception}.  
>
> Macintosh:bin chrisgorman$ Slicer3
> Setting up launch environment...
> Starting Slicer: /usr/local/Slicer3-3.5-alpha-2009-12-14-darwin-x86
>
> child killed: floating-point exception
>  
> CHILDKILLED 23536 SIGFPE {floating-point exception}
>
> And something is wrong with the orientation.  The splash screen used to appear in the middle of the screen with loading information, pre SIGFPE and now it appears in the top left corner with and nothing is displayed on it.  
>
> Based on your information Steve, I'll try a build of 3.4 and if that fails a new checkout of 3.5.  Do you want to analyze another build log, this time for 3.5?  Thanks for all the help.
>
> Chris Gorman
>
> On 2009-12-16, at 12:06 AM, Steve Pieper wrote:
>
>> Hi Chris -
>>
>> Thanks for the extra info - I agree with your analysis.  Slicer 3.4 was cut before mac os 10.6 came out(*) so it doesn't have the patches needed to build there while the current 3.5 development trunk of slicer does.
>>
>> We do build our releases and nightlies on older machines to avoid these kinds of issues, although eventually we move forward.  Katie has the current OSes for the nightly builds documented on the wiki somewhere.
>>
>> But thanks for passing on the build logs - based on that info I realized that one of the modules that had recently been backported to 3.4 was missing the .xml file needed to build, and that's why your build and tests were failing.  3.4 might work now if you svn update.
>>
>> But snowleopard and the trunk should be working pretty well.  I have a nightly build ("common.bwh.harvard.edu" on the dashboard) that does a clean build of everything each night.
>>
>> What's the data that doesn't load on slicer 3.5 but does in 3.4?
>>
>> -Steve
>>
>>
>> (*) thanks for the explanation of the darwin kernel number 10.2 versus the OS number 10.6 - odd indeed...
>>
>> Chris Gorman wrote:
>>> Hello again.
>>> Per Steve's suggestion I've attached a two build.logs.  I need to include 2 because the build fails half way through with the python issue and I needed to apply some patches.  As to the gcc error, apparently it is a gcc 3 switch that has been deprecated.  At least it is as of gcc 4.2 which is the default compiler from XCode 3.2.1.  As to the os versions I believe I unintentionally misled Steve.  Darwin is the kernel and is not the same version as the operating system.  Darwin 10.2.0 is actually OS X 10.6.2.  Who knows why versioning was done this way but it is.    So it appears that building on 10.6.2 won't work for 3.4 but it does mostly for 3.5 alpha.  It is likely that your builds  are built on 10.5 with XCode 3.1.3 or something like that.  I made the jump to 10.6, but am actually regretting it.  Hopefully in a few months more things will build properly on 10.6.  I would consider that it may not be a good use of time to debug why the build for Slicer 3.4 doesn't work,
!

>  si
>> nce an Intel binary is available if needed, and instead to target efforts to why the 3.5 alpha build doesn't display some of the loaded data.  Thanks for all the help.
>>> Chris Gorman
>>> ------------------------------------------------------------------------
>>> On 2009-12-15, at 8:03 PM, Steve Pieper wrote:
>>>> Hi Chris -
>>>>
>>>> Yes, sometimes it is threading the needle to get all the right versions of the OS, python, tcl, etc building with the right flags.  I believe the --Wno-long-double was introduced for compatibility with OSX 10.6 so I'm not sure about 10.2.  Also we typically build our own tcl/tk 8.4 so I don't know if it's possible to build with the OS's 10.5 (I'm guissing not).  If you could generate a build log for your system that might help track down the remaining issues.
>>>>
>>>> Regarding your earlier question, you can run 'make package' in the Slicer3-build directory to get a tar.gz of an installable slicer (or specify --pack argument to getbuildtest).  Essentially you will get a directory tree that you can copy to wherever you want it.  As long as the contents are in the same relative locations everything should work.
>>>>
>>>> Best,
>>>> Steve
>
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Re: building Slicer3 3.4

Chris Gorman
In reply to this post by pieper
Hello Steve,

Per your suggestion I've tried to check out a new svn of slicer 3.4 and build it.  Here are my notes.

Eureka, it works osx 10.6.2 xcode 3.2.1 (gcc / g++ 4.2)!

I have installed on my system tcl/tk from macports and have set the CPPFLAGS environment variable to try to include headers from macports.  This combination causes the tcl/tk portion of the build to fail as it grabs a header from my 8.5 rather than the build tree's 8.4 and errors.  My solution was to temporarily "deactivate" the tcl/tk from macports, which allowed the build to continue.  Unsetting the variable may also have positive results, but I did not test this.

Next problem becomes python.  This was already mentioned in this thread, but I'm mentioning it again to be comprehensive.  There is a deprecated gcc switch that is being passed and gcc-4.2 doesn't like this, and throws an error.  The solution I had was to apply the patches the folks at macports.org used to get their build to work.  See earlier in the thread if you want the patches.

After this I get one test error
15/ 95 Testing QdecModuleLibs                ***Failed
I think this is something related to qt and I only have qt-4.5.3-mac installed, which may not be compatible with the qt from Slicer3.

The final "error" get is after make package.  Running Slicer3 from the installed tar ball I get notification of a missing Slicer3Version.txt.  A quick copy of Slicer3-build/lib/Slicer3/Slicer3Version.txt to Slicer3-3.4.1-2009-12-16-darwin-x86/lib/Slicer3/ and the "error message" dissapears.

Thanks to Steve for his time and for debugging the .xml file error.  Now on to the tutorials.

Steve, It wouldn't be too difficult for me to run a trunk build and create a log file, if you think that it would be useful to help track down the errors 3.5 does when trying to run the tutorials.  As I recall there were a few tests that failed  not just the one as with 3.4.

Chris Gorman

On 2009-12-16, at 12:06 AM, Steve Pieper wrote:

>
> But thanks for passing on the build logs - based on that info I realized that one of the modules that had recently been backported to 3.4 was missing the .xml file needed to build, and that's why your build and tests were failing.  3.4 might work now if you svn update.
>
>


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Re: building Slicer3 3.4

pieper
Administrator
Hi Chris -

Thanks for posting your notes - that's a help for folks following in
your footsteps.  The 3.4 Qdec failing test might be due to the BLT
extension to tk - it has always been a bit problematic on mac.

On the tutorial dataset, I was able to confirm that it's not loading
right on the trunk.  I did discover that switching to a different layout
fixes the problem (use menu button on the right side at the top).
Hopefully that will be tracked down soon.

There are a couple other failing tests in the trunk right now (for
shame, everyone!) but hopefully they won't get in your way.

Best,
Steve

Chris Gorman wrote:

> Hello Steve,
>
> Per your suggestion I've tried to check out a new svn of slicer 3.4 and build it.  Here are my notes.
>
> Eureka, it works osx 10.6.2 xcode 3.2.1 (gcc / g++ 4.2)!
>
> I have installed on my system tcl/tk from macports and have set the CPPFLAGS environment variable to try to include headers from macports.  This combination causes the tcl/tk portion of the build to fail as it grabs a header from my 8.5 rather than the build tree's 8.4 and errors.  My solution was to temporarily "deactivate" the tcl/tk from macports, which allowed the build to continue.  Unsetting the variable may also have positive results, but I did not test this.
>
> Next problem becomes python.  This was already mentioned in this thread, but I'm mentioning it again to be comprehensive.  There is a deprecated gcc switch that is being passed and gcc-4.2 doesn't like this, and throws an error.  The solution I had was to apply the patches the folks at macports.org used to get their build to work.  See earlier in the thread if you want the patches.
>
> After this I get one test error
> 15/ 95 Testing QdecModuleLibs                ***Failed
> I think this is something related to qt and I only have qt-4.5.3-mac installed, which may not be compatible with the qt from Slicer3.
>
> The final "error" get is after make package.  Running Slicer3 from the installed tar ball I get notification of a missing Slicer3Version.txt.  A quick copy of Slicer3-build/lib/Slicer3/Slicer3Version.txt to Slicer3-3.4.1-2009-12-16-darwin-x86/lib/Slicer3/ and the "error message" dissapears.
>
> Thanks to Steve for his time and for debugging the .xml file error.  Now on to the tutorials.
>
> Steve, It wouldn't be too difficult for me to run a trunk build and create a log file, if you think that it would be useful to help track down the errors 3.5 does when trying to run the tutorials.  As I recall there were a few tests that failed  not just the one as with 3.4.
>
> Chris Gorman
>
> On 2009-12-16, at 12:06 AM, Steve Pieper wrote:
>
>> But thanks for passing on the build logs - based on that info I realized that one of the modules that had recently been backported to 3.4 was missing the .xml file needed to build, and that's why your build and tests were failing.  3.4 might work now if you svn update.
>>
>>
>
>
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> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
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