[slicer-users] error compiling Slicer-3-6

Dominique Belhachemi domibel at debian.org
Fri Aug 12 16:00:08 EDT 2011


Hi John,

An older discussion on slicer-devel might help.
http://massmail.spl.harvard.edu/public-archives/slicer-devel/2011/006782.html

Dominique


On Fri, Aug 12, 2011 at 3:44 PM, John Drozd <john.drozd at gmail.com> wrote:
> Hi Dominique,
>
> Sorry, I jumped the gun. (It was recompiling things and not getting to the
> new compilations)
>
> After doing the below updates and running ./Slicer3/Scripts/getbuildtest.tcl
> --update, I am getting the same error as before.
>
> John
>
> andy at sandy-desktop:~/Slicer3compiled$ sudo apt-get install subversion cvs
> tcl8.4 gcc g++ libX11-dev
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> cvs is already the newest version.
> g++ is already the newest version.
> gcc is already the newest version.
> libx11-dev is already the newest version.
> tcl8.4 is already the newest version.
> subversion is already the newest version.
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> sandy at sandy-desktop:~/Slicer3compiled$ sudo apt-get install libXt-dev
> libxext-dev libgl1-mesa-dev libglu1-mesa-dev libncurses5-dev
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> libgl1-mesa-dev is already the newest version.
> libglu1-mesa-dev is already the newest version.
> libncurses5-dev is already the newest version.
> libxext-dev is already the newest version.
> libxt-dev is already the newest version.
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> sandy at sandy-desktop:~/Slicer3compiled$ sudo apt-get install
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> sandy at sandy-desktop:~/Slicer3compiled$ sudo apt-get install tcsh
> libosmesa6-dev
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> libosmesa6-dev is already the newest version.
> tcsh is already the newest version.
> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
> sandy at sandy-desktop:~/Slicer3compiled$
>
>
> On Fri, Aug 12, 2011 at 3:24 PM, John Drozd <john.drozd at gmail.com> wrote:
>>
>> Hi Dominique,
>>
>> Thank you.  It is continuing to compile now and not giving the error.
>> I am installing and compiling Slicer on this new computer to see if I can
>> get the EM Segmenter Full Brain Parcellation Working.
>> It had a problem with my video driver on the other computer.  I'll try the
>> commands you suggested and check the driver bug fixes for that computer as
>> well.
>>
>> Thanks,
>> John
>>
>>
>> On Fri, Aug 12, 2011 at 3:10 PM, Dominique Belhachemi <domibel at debian.org>
>> wrote:
>>>
>>> Please try the following:
>>>
>>> $ sudo apt-get install subversion cvs tcl8.4 gcc g++ libX11-dev
>>> libXt-dev libxext-dev libgl1-mesa-dev libglu1-mesa-dev libncurses5-dev
>>> tcsh libosmesa6-dev
>>>
>>> and then compile again
>>>
>>> $ ./Slicer3/Scripts/getbuildtest.tcl --update
>>>
>>> Thanks
>>> Dominique
>>>
>>>
>>> On Fri, Aug 12, 2011 at 3:05 PM, John Drozd <john.drozd at gmail.com> wrote:
>>> > Hi Steve,
>>> >
>>> > It is a brand new computer.
>>> > Sorry, Correction, the OS is Ubuntu 11.0.4 64 bit (not 11.0.3).
>>> >
>>> > John
>>> >
>>> > On Fri, Aug 12, 2011 at 3:03 PM, John Drozd <john.drozd at gmail.com>
>>> > wrote:
>>> >>
>>> >> Hi Steve,
>>> >>
>>> >> It is 64 bit.
>>> >>
>>> >> John
>>> >>
>>> >> On Fri, Aug 12, 2011 at 2:53 PM, John Drozd <john.drozd at gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> Hi Steve,
>>> >>>
>>> >>> I am using Ubuntu linux 11.0.3.
>>> >>>
>>> >>> John
>>> >>>
>>> >>> On Fri, Aug 12, 2011 at 2:50 PM, Steve Pieper <pieper at ibility.net>
>>> >>> wrote:
>>> >>>>
>>> >>>> Hi John -
>>> >>>>
>>> >>>> What OS are you building on?
>>> >>>>
>>> >>>> -Steve
>>> >>>>
>>> >>>> On Fri, Aug 12, 2011 at 2:38 PM, John Drozd <john.drozd at gmail.com>
>>> >>>> wrote:
>>> >>>> > Hi,
>>> >>>> >
>>> >>>> > At the end of this snippet of output, I am getting an error in the
>>> >>>> > compilation process for Slicer-3-6.
>>> >>>> >
>>> >>>> > Could anyone help me.
>>> >>>> >
>>> >>>> > Thank you,
>>> >>>> > John
>>> >>>> >
>>> >>>> > Built target vtkGeovisTCL
>>> >>>> > make -f Wrapping/Tcl/CMakeFiles/vtk.dir/build.make
>>> >>>> > Wrapping/Tcl/CMakeFiles/vtk.dir/depend
>>> >>>> > make[2]: Entering directory
>>> >>>> > `/home/sandy/Slicer3compiled/Slicer3-lib/VTK-build'
>>> >>>> > cd /home/sandy/Slicer3compiled/Slicer3-lib/VTK-build &&
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/CMake-build/bin/cmake -E
>>> >>>> > cmake_depends "Unix Makefiles"
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/VTK
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/VTK/Wrapping/Tcl
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/VTK-build
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/VTK-build/Wrapping/Tcl
>>> >>>> >
>>> >>>> >
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/VTK-build/Wrapping/Tcl/CMakeFiles/vtk.dir/DependInfo.cmake
>>> >>>> > --color=
>>> >>>> > make[2]: Leaving directory
>>> >>>> > `/home/sandy/Slicer3compiled/Slicer3-lib/VTK-build'
>>> >>>> > make -f Wrapping/Tcl/CMakeFiles/vtk.dir/build.make
>>> >>>> > Wrapping/Tcl/CMakeFiles/vtk.dir/build
>>> >>>> > make[2]: Entering directory
>>> >>>> > `/home/sandy/Slicer3compiled/Slicer3-lib/VTK-build'
>>> >>>> > Linking CXX executable ../../bin/vtk
>>> >>>> > cd /home/sandy/Slicer3compiled/Slicer3-lib/VTK-build/Wrapping/Tcl
>>> >>>> > &&
>>> >>>> > /home/sandy/Slicer3compiled/Slicer3-lib/CMake-build/bin/cmake -E
>>> >>>> > cmake_link_script CMakeFiles/vtk.dir/link.txt --verbose=1
>>> >>>> > /usr/bin/g++     -Wno-deprecated -g
>>> >>>> >
>>> >>>> > -L/home/sandy/Slicer3compiled/Slicer-3-6/../Slicer3-lib/tcl-build/lib
>>> >>>> > CMakeFiles/vtk.dir/vtkTkAppInit.cxx.o  -o ../../bin/vtk -rdynamic
>>> >>>> >
>>> >>>> > -L/home/sandy/Slicer3compiled/Slicer-3-6/../Slicer3-lib/tcl-build/lib
>>> >>>> > ../../bin/libvtkCommonTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkFilteringTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkGraphicsTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkImagingTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkIOTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkRenderingTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkVolumeRenderingTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkHybridTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkWidgetsTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkParallelTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkGeovisTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkInfovisTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkViewsTCL.so.5.6.0
>>> >>>> > -ltk8.4 -ltcl8.4 -lm ../../bin/libvtkVolumeRendering.so.5.6.0
>>> >>>> > ../../bin/libvtkInfovisTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkWidgetsTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkHybridTCL.so.5.6.0 ../../bin/libvtkIOTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkRenderingTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkGraphicsTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkImagingTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkFilteringTCL.so.5.6.0
>>> >>>> > ../../bin/libvtkCommonTCL.so.5.6.0 -ltk8.4 -ltcl8.4 -lm
>>> >>>> > ../../bin/libvtkGeovis.so.5.6.0 ../../bin/libvtkViews.so.5.6.0
>>> >>>> > ../../bin/libvtkInfovis.so.5.6.0 ../../bin/libvtkWidgets.so.5.6.0
>>> >>>> > ../../bin/libvtkHybrid.so.5.6.0 ../../bin/libvtkParallel.so.5.6.0
>>> >>>> > ../../bin/libvtkRendering.so.5.6.0
>>> >>>> > ../../bin/libvtkGraphics.so.5.6.0
>>> >>>> > ../../bin/libvtkImaging.so.5.6.0 ../../bin/libvtkIO.so.5.6.0
>>> >>>> > ../../bin/libvtkFiltering.so.5.6.0 ../../bin/libvtkCommon.so.5.6.0
>>> >>>> > -lm
>>> >>>> > ../../bin/libvtksys.so.5.6.0 -ldl
>>> >>>> >
>>> >>>> > -Wl,-rpath-link,/home/sandy/Slicer3compiled/Slicer3-lib/VTK-build/bin
>>> >>>> > ../../bin/libvtkRenderingTCL.so.5.6.0: undefined reference to
>>> >>>> > `vtkXOpenGLRenderWindow::SetDisplayId(_XDisplay*)'
>>> >>>> > ../../bin/libvtkRendering.so.5.6.0: undefined reference to
>>> >>>> > `vtkXOpenGLRenderWindow::New()'
>>> >>>> > ../../bin/libvtkRendering.so.5.6.0: undefined reference to
>>> >>>> > `vtkXRenderWindowInteractor::New()'
>>> >>>> > ../../bin/libvtkRenderingTCL.so.5.6.0: undefined reference to
>>> >>>> > `vtkXOpenGLRenderWindow::SetParentId(unsigned long)'
>>> >>>> > ../../bin/libvtkRenderingTCL.so.5.6.0: undefined reference to
>>> >>>> > `vtkXOpenGLRenderWindow::GetWindowId()'
>>> >>>> > collect2: ld returned 1 exit status
>>> >>>> > make[2]: *** [bin/vtk] Error 1
>>> >>>> > make[2]: Leaving directory
>>> >>>> > `/home/sandy/Slicer3compiled/Slicer3-lib/VTK-build'
>>> >>>> > make[1]: *** [Wrapping/Tcl/CMakeFiles/vtk.dir/all] Error 2
>>> >>>> > make[1]: Leaving directory
>>> >>>> > `/home/sandy/Slicer3compiled/Slicer3-lib/VTK-build'
>>> >>>> > make: *** [all] Error 2
>>> >>>> >
>>> >>>> > child process exited abnormally
>>> >>>> > 1
>>> >>>> >     while executing
>>> >>>> > "error $ret"
>>> >>>> >     (procedure "runcmd" line 23)
>>> >>>> >     invoked from within
>>> >>>> > "runcmd make -j 8"
>>> >>>> >     ("eval" body line 1)
>>> >>>> >     invoked from within
>>> >>>> > "eval runcmd $::MAKE "
>>> >>>> >     invoked from within
>>> >>>> > "if { [BuildThis $::VTK_TEST_FILE "vtk"] == 1 } {
>>> >>>> >     cd $Slicer3_LIB
>>> >>>> >
>>> >>>> >     runcmd $::SVN co $::VTK_TAG VTK
>>> >>>> > #    if { ![file exists VTK] } {
>>> >>>> > #        ev..."
>>> >>>> >     (file "./Scripts/genlib.tcl" line 921)
>>> >>>> >
>>> >>>> > child process exited abnormally
>>> >>>> > ERROR: failed to run getbuildtest: sh ./Scripts/genlib.tcl
>>> >>>> > /home/sandy/Slicer3compiled/Slicer-3-6/../Slicer3-lib -64
>>> >>>> > --test-type
>>> >>>> > Experimental
>>> >>>> > sandy at sandy-desktop:~/Slicer3compiled$
>>> >>>> >
>>> >>>> >
>>> >>>> > --
>>> >>>> > John Drozd
>>> >>>> > Post-Doctoral Fellow, Robarts Research Institute
>>> >>>> > The University of Western Ontario
>>> >>>> > London, ON, Canada
>>> >>>> > http://publish.uwo.ca/~jdrozd2
>>> >>>> >
>>> >>>> >
>>> >>>> > _______________________________________________
>>> >>>> > slicer-users mailing list
>>> >>>> > slicer-users at bwh.harvard.edu
>>> >>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>> >>>> > To unsubscribe: send email to
>>> >>>> > slicer-users-request at massmail.spl.harvard.edu
>>> >>>> > with unsubscribe as the subject
>>> >>>> >
>>> >>>
>>> >>>
>>> >>>
>>> >>> --
>>> >>> John Drozd
>>> >>> Post-Doctoral Fellow, Robarts Research Institute
>>> >>> The University of Western Ontario
>>> >>> London, ON, Canada
>>> >>> http://publish.uwo.ca/~jdrozd2
>>> >>>
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> John Drozd
>>> >> Post-Doctoral Fellow, Robarts Research Institute
>>> >> The University of Western Ontario
>>> >> London, ON, Canada
>>> >> http://publish.uwo.ca/~jdrozd2
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > John Drozd
>>> > Post-Doctoral Fellow, Robarts Research Institute
>>> > The University of Western Ontario
>>> > London, ON, Canada
>>> > http://publish.uwo.ca/~jdrozd2
>>> >
>>> >
>>> > _______________________________________________
>>> > slicer-users mailing list
>>> > slicer-users at bwh.harvard.edu
>>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>>> > To unsubscribe: send email to
>>> > slicer-users-request at massmail.spl.harvard.edu
>>> > with unsubscribe as the subject
>>> >
>>
>>
>>
>> --
>> John Drozd
>> Post-Doctoral Fellow, Robarts Research Institute
>> The University of Western Ontario
>> London, ON, Canada
>> http://publish.uwo.ca/~jdrozd2
>>
>
>
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2
>
>



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