[Tubetk-developers] runtime error

Stephen Aylward stephen.aylward at kitware.com
Mon Feb 3 20:44:44 EST 2014 

Outstanding!

We continue to make rapid progress on TubeTK,  Right now the
priorities are vessel-based registrations and vessel extractions -
they are works in progress.

Functioning tools include sliding registration, mergeAdjacent images,
and various other segmentation and registration methods.

s

On Mon, Feb 3, 2014 at 6:40 PM, Wei Liu <weiliu620 at gmail.com> wrote:
> 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
>>>>>
>>>>>
>>>
>



-- 
====================================================
Stephen R. Aylward, Ph.D.
Senior Director of Operations, North Carolina, Kitware, Inc.
http://www.kitware.com and http://www.aylward.org
(919) 969-6990 x300
====================================================

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