[Tubetk-developers] runtime error

Wei Liu weiliu620 at gmail.com
Mon Feb 3 18:40:18 EST 2014 

Hi Stephen,

After following your cmake command I am able to configure without the
missing QTWEBKIT error. Although I got one error during the build process
(see the error log at the end of this message), all other tubetk binaries
are built OK. Now when I run the same CropImage command, I got the correct
output. I also tried a few other commands and they all run without the
runtime error that I encountered before. So, as a summary:

-- Build TubeTK without slicer, has the VTK runtime error.
-- Build TubeTK, give the Slicer flag and path at ccmake GUI, got the
missing QTWEBKIT error.
-- Build TubeTK, give the slicer flag and path at cmake command line (as
suggested by Stephen), configure and build good (with one exception of JSON
build error below). Most binaries run without runtime VTK error.

I'm satisfied with the results, especially considering the early
development stage of TubeTK.

Thanks everyone for the help!

Wei


----------------------------------------------------------
Generating TransformTubesCLP.h
Scanning dependencies of target SimulateAcquisitionArtifactsUsingPriorLib
Scanning dependencies of target SubSampleTubesLib
GenerateCLP --logoFiles
/home/sci/weiliu/packages/TubeTK/Base/CLI/TubeTKLogo.h --InputXML
/home/sci/weiliu/packages/TubeTK/Applications/TransformTubes/TransformTubes.xml
--OutputCxx
/home/sci/weiliu/packages/TubeTK-withSlicer/TubeTK-build/Applications/TransformTubes/TransformTubesCLP.h
GenerateCLP: Found 1 parameters groups
GenerateCLP: Group "IO" has 6 parameters
Scanning dependencies of target TransformTubesLib
/usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld:
/home/sci/weiliu/packages/TubeTK-withSlicer/JsonCpp-build/lib/libjsoncpp.a(json_reader.cpp.o):
relocation R_X86_64_32 against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/home/sci/weiliu/packages/TubeTK-withSlicer/JsonCpp-build/lib/libjsoncpp.a:
could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[5]: *** [lib/TubeTK/libRegisterImageToTubesUsingRigidTransformLib.so]
Error 1
make[5]: Target
`Applications/RegisterImageToTubesUsingRigidTransform/CMakeFiles/RegisterImageToTubesUsingRigidTransformLib.dir/build'
not remade because of errors.
make[4]: ***
[Applications/RegisterImageToTubesUsingRigidTransform/CMakeFiles/RegisterImageToTubesUsingRigidTransformLib.dir/all]
Error 2


On Sun, Feb 2, 2014 at 7:35 PM, Stephen Aylward <stephen.aylward at kitware.com
> wrote:

> Hi
>
> From an empty build directory, please set Slicer_DIR and
> QT_QMAKE_EXECUTABLE.  I am doing this from.memory, so the names might be
> slightly off.  The command will be
>
> cmake -DSlicer_DIR:path=<enter path here> -DQT_QMAKE_EXECUTABLE:path=<path
> to your qmake> -DTubeTK_USE_SLICER:bool=ON <path to tubetk source>
>
> Or something close to that.  I can get the specifics when at work later.
>
> S
>
> --
> Sent via phone.  Please excuse the brevity and typos.
>
> --
> Stephen R. Aylward, Ph.D.
> Senior Director of Operations
> Kitware, North Carolina
> On Feb 2, 2014 7:58 PM, "Wei Liu" <weiliu620 at gmail.com> wrote:
>
>> Stephen,
>>
>> My system does have qmake at /usr/bin, as shown by 'which qmake'. When
>> running ccmake the first time for TubeTK, ccmake found this system qmake.
>> Once I choose to build Slicer extension and give the Slicer-build
>> directory, I got the following error:
>>
>>  CMake Error at
>> /home/sci/weiliu/projects/Slicer-SuperBuild-Rel/Slicer-build/SlicerConfig.cmake:547
>> (message):
>>    Variable QT_QMAKE_EXECUTABLE defined prior calling
>> 'find_package(Slicer)'
>>    does NOT match value used to configure Slicer.  It probably means that
>> a
>>    different QT_QMAKE_EXECUTABLE has been used to configure this project
>> and
>>    Slicer.
>>
>>    QT_QMAKE_EXECUTABLE=/usr/bin/qmake
>>
>>
>>
>>  Slicer_QT_QMAKE_EXECUTABLE=/home/sci/weiliu/QtSDK/Desktop/Qt/474/gcc/bin/qmake
>>  Call Stack (most recent call first):
>>
>>  /home/sci/weiliu/projects/Slicer-SuperBuild-Rel/Slicer-build/SlicerConfig.cmake:565
>> (slicer_config_set_ep)
>>    CMakeLists.txt:175 (find_package)
>>
>>
>>
>>
>> To get rid of this error, I have to manually set the qmake to the one in
>> the QtSDK that I downloaded from Slicer website.
>>
>> Wei
>>
>>
>> On Sun, Feb 2, 2014 at 5:47 PM, Stephen Aylward <
>> stephen.aylward at kitware.com> wrote:
>>
>>> Ah.  It shouldn't be asking for qmake.  It should get that from the
>>> slicer build info.
>>>
>>> Perhaps it is mixing a system qt with the version used to build slicer.
>>> We have tested that in the past,  but it might not be working now.
>>>
>>> If you type "which qmake" does it return a path to another qmake?
>>>
>>> S
>>> --
>>> Sent via phone.  Please excuse the brevity and typos.
>>>
>>> --
>>> Stephen R. Aylward, Ph.D.
>>> Senior Director of Operations
>>> Kitware, North Carolina
>>> On Feb 2, 2014 6:42 PM, "Wei Liu" <weiliu620 at gmail.com> wrote:
>>>
>>>> Christopher,
>>>>
>>>> Here is what I found under the QT SDK directory that I downloaded from
>>>> Slicer website:
>>>>
>>>> weiliu at wukong:~/QtSDK/Desktop/Qt/474/gcc/lib> ll libQtWebKit.*
>>>> -rw-r--r-- 1 weiliu sci      934 Jan 22 10:29 libQtWebKit.la
>>>> lrwxrwxrwx 1 weiliu sci       20 Jan 22 10:29 libQtWebKit.so ->
>>>> libQtWebKit.so.4.7.4
>>>> lrwxrwxrwx 1 weiliu sci       20 Jan 22 10:29 libQtWebKit.so.4 ->
>>>> libQtWebKit.so.4.7.4
>>>> lrwxrwxrwx 1 weiliu sci       20 Jan 22 10:29 libQtWebKit.so.4.7 ->
>>>> libQtWebKit.so.4.7.4
>>>> -rwxr-xr-x 1 weiliu sci 22791816 Jan 22 10:29 libQtWebKit.so.4.7.4
>>>>
>>>> In the ccmake of TubeTK, if I just set Slicer build directory in order
>>>> to build Slicer extension, I got error that says qmake should be same with
>>>> the one that is used to build Slicer. So I point the qmake to the one under
>>>> QT SDK. The configuration then goes through, so I suppose the setting is
>>>> correct.
>>>>
>>>> Wei
>>>>
>>>>
>>>> On Sun, Feb 2, 2014 at 4:32 PM, Christopher Mullins <
>>>> christopher.mullins at kitware.com> wrote:
>>>>
>>>>> Can you confirm that you built or installed Qt with webkit?  You
>>>>> should have the file libQtWebKit.so somewhere in the build tree or
>>>>> installation directory.  Also make sure your QT_QMAKE_EXECUTABLE is set
>>>>> correctly.
>>>>>
>>>>>
>>>>> On Sun, Feb 2, 2014 at 5:40 PM, Wei Liu <weiliu620 at gmail.com> wrote:
>>>>>
>>>>>> Stephen,
>>>>>>
>>>>>> I did what you suggested. However, after step 3) and choose
>>>>>> 'configure' in ccmake, I got the same error message that I reported to you
>>>>>> in a different email thread.  The error is:
>>>>>>
>>>>>>  CMake Error at
>>>>>> /home/sci/weiliu/packages/Slicer/CMake/SlicerBlockFindQtAndCheckVersion.cmake:43
>>>>>> (message):
>>>>>>    error: Missing Qt module QTWEBKIT
>>>>>>  Call Stack (most recent call first):
>>>>>>
>>>>>>  /home/sci/weiliu/packages/Slicer/CMake/SlicerBlockFindQtAndCheckVersion.cmake:72
>>>>>> (__SlicerBlockFindQtAndCheckVersion_find_qt)
>>>>>>
>>>>>>  /home/sci/weiliu/projects/Slicer-SuperBuild-Rel/Slicer-build/SlicerConfig.cmake:760
>>>>>> (include)
>>>>>>    CMakeLists.txt:175 (find_package)
>>>>>>
>>>>>>
>>>>>> I've made sure that I start from an empty build directory. By the
>>>>>> way, my Slicer build is a good one. I used a customized QT SDK (version
>>>>>> 474) from [1].
>>>>>>
>>>>>> [1]
>>>>>> http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_Instructions/Prerequisites/Qt#Download_Qt:_Source_and_Binaries
>>>>>>
>>>>>> Wei
>>>>>>
>>>>>>
>>>>>> On Sun, Feb 2, 2014 at 1:40 PM, Stephen Aylward <
>>>>>> stephen.aylward at kitware.com> wrote:
>>>>>>
>>>>>>> Only options to change are
>>>>>>>
>>>>>>> 1) TubeTK_BUILD_SLICER_EXTENSION = ON
>>>>>>> 2) TubeTK_USE_SLICER = ON
>>>>>>>
>>>>>>> Then type [c] to configure.  This will produce an error message if
>>>>>>> Slicer isn't automatically found...so
>>>>>>>
>>>>>>> 3) Slicer_DIR = <YourPathToSlicerBuild>/Slicer-build
>>>>>>> -- Yes, point it to the Slicer-build subdir that is within the
>>>>>>> top-level directory in which Slicer was built.
>>>>>>>
>>>>>>> Do not change any other options.
>>>>>>>
>>>>>>> You should do this in an empty build directory.  There are likely to
>>>>>>> be problems if you try to switch a current build from being a
>>>>>>> stand-alone build to being a Slicer-dependent build.
>>>>>>>
>>>>>>> s
>>>>>>>
>>>>>>>
>>>>>>> On Sun, Feb 2, 2014 at 2:49 PM, Wei Liu <weiliu620 at gmail.com> wrote:
>>>>>>> > Thanks, Matt and Stephen. I checked the CmakeOutput.log file under
>>>>>>> VTK-build
>>>>>>> > and didn't find any errors. Is that the best way to check build
>>>>>>> logs?
>>>>>>> >
>>>>>>> > I do have a recent Slicer build that includes VTK. Let me try to
>>>>>>> point
>>>>>>> > TubeTK to it and see what happens.
>>>>>>> >
>>>>>>> > Wei
>>>>>>> >
>>>>>>> >
>>>>>>> > On Sun, Feb 2, 2014 at 12:34 PM, Stephen Aylward
>>>>>>> > <stephen.aylward at kitware.com> wrote:
>>>>>>> >>
>>>>>>> >> Also, Ricardo is building it on opensuse.   It seems to be
>>>>>>> failing on the
>>>>>>> >> vtk build.  Perhaps try building vtk on its own via vtk.org or
>>>>>>> build slicer
>>>>>>> >> and point tubetk to it...see slicer.org
>>>>>>> >>
>>>>>>> >> S
>>>>>>> >>
>>>>>>> >> --
>>>>>>> >> Sent via phone.  Please excuse the brevity and typos.
>>>>>>> >>
>>>>>>> >> --
>>>>>>> >> Stephen R. Aylward, Ph.D.
>>>>>>> >> Senior Director of Operations
>>>>>>> >> Kitware, North Carolina
>>>>>>> >>
>>>>>>> >> On Feb 2, 2014 2:31 PM, "Matt McCormick" <
>>>>>>> matt.mccormick at kitware.com>
>>>>>>> >> wrote:
>>>>>>> >>>
>>>>>>> >>> Hi Wei,
>>>>>>> >>>
>>>>>>> >>> Builds reporting to the dashboard should be reproducible (there
>>>>>>> is
>>>>>>> >>> Debian Stable and Ubuntu 12.04 and 13.04 reporting):
>>>>>>> >>>
>>>>>>> >>>   http://open.cdash.org/index.php?project=TubeTK
>>>>>>> >>>
>>>>>>> >>> If further help is needed, we can give personalized attention
>>>>>>> with a
>>>>>>> >>> support contract:
>>>>>>> >>>
>>>>>>> >>>   http://www.kitware.com/products/support.html
>>>>>>> >>>
>>>>>>> >>> Thanks,
>>>>>>> >>> Matt
>>>>>>> >>>
>>>>>>> >>> On Sun, Feb 2, 2014 at 11:51 AM, Wei Liu <weiliu620 at gmail.com>
>>>>>>> wrote:
>>>>>>> >>> > Oops, I sent previous email before finishing it.
>>>>>>> >>> >
>>>>>>> >>> > Yes Matt, I meant TubeTK_USE_VTK.  So, I started a clean
>>>>>>> build, with
>>>>>>> >>> > all
>>>>>>> >>> > cmake options set to default (the UtbeT_USE_VTK = ON). Now I
>>>>>>> have
>>>>>>> >>> > different
>>>>>>> >>> > errors:
>>>>>>> >>> >
>>>>>>> >>> > ./CropImage: symbol lookup error:
>>>>>>> >>> >
>>>>>>> >>> >
>>>>>>> /home/sci/weiliu/packages/TubeTK-Release/VTK-build/bin/libvtkInfovis.so.5.10:
>>>>>>> >>> > undefined symbol: _ZTI8vtkArray
>>>>>>> >>> >
>>>>>>> >>> > I don't remember the exact difference between this build and
>>>>>>> the
>>>>>>> >>> > previous
>>>>>>> >>> > one. The difference may be some Cmake options.
>>>>>>> >>> >
>>>>>>> >>> > Do you suggest me to use another OS, like ubuntu or
>>>>>>> Redhat-based OS?
>>>>>>> >>> >
>>>>>>> >>> > Wei
>>>>>>> >>> >
>>>>>>> >>> >
>>>>>>> >>> >
>>>>>>> >>> > On Fri, Jan 31, 2014 at 5:46 PM, Matt McCormick
>>>>>>> >>> > <matt.mccormick at kitware.com>
>>>>>>> >>> > wrote:
>>>>>>> >>> >>
>>>>>>> >>> >> Hmm, the only variable that should be adjusted should be
>>>>>>> called
>>>>>>> >>> >> TubeTK_USE_VTK.
>>>>>>> >>> >>
>>>>>>> >>> >> Starting a clean build with the defaults is good first step.
>>>>>>> >>> >>
>>>>>>> >>> >> Thanks,
>>>>>>> >>> >> Matt
>>>>>>> >>> >>
>>>>>>> >>> >> On Fri, Jan 31, 2014 at 7:35 PM, Wei Liu <weiliu620 at gmail.com>
>>>>>>> wrote:
>>>>>>> >>> >> > Matt,
>>>>>>> >>> >> >
>>>>>>> >>> >> > I didn't install VTK in the system, and I double checked the
>>>>>>> >>> >> > /usr/lib
>>>>>>> >>> >> > and
>>>>>>> >>> >> > lib64 directory.
>>>>>>> >>> >> >
>>>>>>> >>> >> > I built with the USE_VTK set to off. Is that a possible
>>>>>>> reason? I'm
>>>>>>> >>> >> > re-building TubeTK with it on now.
>>>>>>> >>> >> >
>>>>>>> >>> >> > Wei
>>>>>>> >>> >> >
>>>>>>> >>> >> >
>>>>>>> >>> >> >
>>>>>>> >>> >> >
>>>>>>> >>> >> > On Fri, Jan 31, 2014 at 4:08 PM, Matt McCormick
>>>>>>> >>> >> > <matt.mccormick at kitware.com>
>>>>>>> >>> >> > wrote:
>>>>>>> >>> >> >>
>>>>>>> >>> >> >> Hi Wei,
>>>>>>> >>> >> >>
>>>>>>> >>> >> >> This is not expected.  Is a system VTK installed?
>>>>>>> >>> >> >>
>>>>>>> >>> >> >> Thanks,
>>>>>>> >>> >> >> Matt
>>>>>>> >>> >> >>
>>>>>>> >>> >> >>
>>>>>>> >>> >> >>
>>>>>>> >>> >> >> On Fri, Jan 31, 2014 at 5:58 PM, Wei Liu <
>>>>>>> weiliu620 at gmail.com>
>>>>>>> >>> >> >> wrote:
>>>>>>> >>> >> >> > Dear TubeTK developers,
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> > I've successfully built TubeTK in release mode. But when
>>>>>>> I try to
>>>>>>> >>> >> >> > run
>>>>>>> >>> >> >> > one of
>>>>>>> >>> >> >> > the commands in TubeTK-build/bin/ I got the following
>>>>>>> error:
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> > ./CropImage: symbol lookup error:
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> >
>>>>>>> /home/sci/weiliu/packages/TubeTK-Release/VTK-build/bin/libvtkInfovis.so.5.10:
>>>>>>> >>> >> >> > undefined symbol: _ZTI21vtkArrayDataAlgorithm
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> > I'm using gcc 4.7.1 under opensuse 12.2 64 bit. And I
>>>>>>> just let
>>>>>>> >>> >> >> > tubetk
>>>>>>> >>> >> >> > to
>>>>>>> >>> >> >> > build everything including ITK and VTK. Actually I got
>>>>>>> the same
>>>>>>> >>> >> >> > error
>>>>>>> >>> >> >> > when
>>>>>>> >>> >> >> > trying to run other commands.
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> > Is this error expected at this stage of development?
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> > Thanks,
>>>>>>> >>> >> >> > Wei
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> > _______________________________________________
>>>>>>> >>> >> >> > Tubetk-developers mailing list
>>>>>>> >>> >> >> > Tubetk-developers at tubetk.org
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >> >
>>>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers
>>>>>>> >>> >> >> >
>>>>>>> >>> >> >
>>>>>>> >>> >> >
>>>>>>> >>> >
>>>>>>> >>> >
>>>>>>> >>> _______________________________________________
>>>>>>> >>> Tubetk-developers mailing list
>>>>>>> >>> Tubetk-developers at tubetk.org
>>>>>>> >>>
>>>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers
>>>>>>> >
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> ====================================================
>>>>>>> Stephen R. Aylward, Ph.D.
>>>>>>> Senior Director of Operations, North Carolina, Kitware, Inc.
>>>>>>> http://www.kitware.com
>>>>>>> http://www.aylward.org
>>>>>>> (919) 969-6990 x300
>>>>>>> ====================================================
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Tubetk-developers mailing list
>>>>>> Tubetk-developers at tubetk.org
>>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Christopher Mullins
>>>>> R&D Engineer
>>>>> Kitware Inc.,
>>>>> 919.869.8871
>>>>>
>>>>
>>>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/tubetk-developers/attachments/20140203/ec28bac2/attachment-0002.html>

More information about the Tubetk-developers mailing list