<div dir="ltr">Hi Stephen,<div><br></div><div>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:</div>
<div><br></div><div>-- Build TubeTK without slicer, has the VTK runtime error.</div><div>-- Build TubeTK, give the Slicer flag and path at ccmake GUI, got the missing QTWEBKIT error. </div><div>-- 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. </div>
<div><br></div><div>I'm satisfied with the results, especially considering the early development stage of TubeTK. </div><div><br></div><div>Thanks everyone for the help!</div><div><br></div><div>Wei</div><div><br></div>
<div><br></div><div>----------------------------------------------------------</div><div><div>Generating TransformTubesCLP.h</div><div>Scanning dependencies of target SimulateAcquisitionArtifactsUsingPriorLib</div><div>Scanning dependencies of target SubSampleTubesLib</div>
<div>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</div>
<div>GenerateCLP: Found 1 parameters groups</div><div>GenerateCLP: Group "IO" has 6 parameters</div><div>Scanning dependencies of target TransformTubesLib</div><div>/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</div>
<div>/home/sci/weiliu/packages/TubeTK-withSlicer/JsonCpp-build/lib/libjsoncpp.a: could not read symbols: Bad value</div><div>collect2: error: ld returned 1 exit status</div><div>make[5]: *** [lib/TubeTK/libRegisterImageToTubesUsingRigidTransformLib.so] Error 1</div>
<div>make[5]: Target `Applications/RegisterImageToTubesUsingRigidTransform/CMakeFiles/RegisterImageToTubesUsingRigidTransformLib.dir/build' not remade because of errors.</div><div>make[4]: *** [Applications/RegisterImageToTubesUsingRigidTransform/CMakeFiles/RegisterImageToTubesUsingRigidTransformLib.dir/all] Error 2</div>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Feb 2, 2014 at 7:35 PM, Stephen Aylward <span dir="ltr"><<a href="mailto:stephen.aylward@kitware.com" target="_blank">stephen.aylward@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Hi</p>
<p dir="ltr">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</p>
<p dir="ltr">cmake -DSlicer_DIR:path=<enter path here> -DQT_QMAKE_EXECUTABLE:path=<path to your qmake> -DTubeTK_USE_SLICER:bool=ON <path to tubetk source></p>
<p dir="ltr">Or something close to that. I can get the specifics when at work later.</p><div class="im HOEnZb">
<p dir="ltr">S</p>
<p dir="ltr">--<br>
Sent via phone. Please excuse the brevity and typos.</p>
<p dir="ltr">--<br>
Stephen R. Aylward, Ph.D.<br>
Senior Director of Operations<br>
Kitware, North Carolina</p>
</div><div class="HOEnZb"><div class="h5"><div class="gmail_quote">On Feb 2, 2014 7:58 PM, "Wei Liu" <<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Stephen,<div><br></div><div>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:</div>
<div><br></div><div><div> CMake Error at /home/sci/weiliu/projects/Slicer-SuperBuild-Rel/Slicer-build/SlicerConfig.cmake:547 (message):</div><div> Variable QT_QMAKE_EXECUTABLE defined prior calling 'find_package(Slicer)'</div>
<div> does NOT match value used to configure Slicer. It probably means that a</div><div> different QT_QMAKE_EXECUTABLE has been used to configure this project and</div><div> Slicer.</div><div><br></div><div> QT_QMAKE_EXECUTABLE=/usr/bin/qmake</div>
<div><br></div><div><br></div><div> Slicer_QT_QMAKE_EXECUTABLE=/home/sci/weiliu/QtSDK/Desktop/Qt/474/gcc/bin/qmake</div><div> Call Stack (most recent call first):</div><div> /home/sci/weiliu/projects/Slicer-SuperBuild-Rel/Slicer-build/SlicerConfig.cmake:565 (slicer_config_set_ep)</div>
<div> CMakeLists.txt:175 (find_package)</div></div><div><br></div><div><br></div><div><br></div><div><br></div><div>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.</div>
<div><br></div><div>Wei</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Feb 2, 2014 at 5:47 PM, Stephen Aylward <span dir="ltr"><<a href="mailto:stephen.aylward@kitware.com" target="_blank">stephen.aylward@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Ah. It shouldn't be asking for qmake. It should get that from the slicer build info.</p>
<p dir="ltr">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.</p>
<p dir="ltr">If you type "which qmake" does it return a path to another qmake?</p><div>
<p dir="ltr">S<br>
--<br>
Sent via phone. Please excuse the brevity and typos.</p>
<p dir="ltr">--<br>
Stephen R. Aylward, Ph.D.<br>
Senior Director of Operations<br>
Kitware, North Carolina</p>
</div><div><div><div class="gmail_quote">On Feb 2, 2014 6:42 PM, "Wei Liu" <<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Christopher,<div><br></div><div>Here is what I found under the QT SDK directory that I downloaded from Slicer website: </div><div><br></div><div><div>weiliu@wukong:~/QtSDK/Desktop/Qt/474/gcc/lib> ll libQtWebKit.*</div>
<div>-rw-r--r-- 1 weiliu sci 934 Jan 22 10:29 libQtWebKit.la</div><div>lrwxrwxrwx 1 weiliu sci 20 Jan 22 10:29 libQtWebKit.so -> libQtWebKit.so.4.7.4</div><div>lrwxrwxrwx 1 weiliu sci 20 Jan 22 10:29 libQtWebKit.so.4 -> libQtWebKit.so.4.7.4</div>
<div>lrwxrwxrwx 1 weiliu sci 20 Jan 22 10:29 libQtWebKit.so.4.7 -> libQtWebKit.so.4.7.4</div><div>-rwxr-xr-x 1 weiliu sci 22791816 Jan 22 10:29 libQtWebKit.so.4.7.4</div></div><div><br></div><div>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. </div>
<div><br></div><div>Wei</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Feb 2, 2014 at 4:32 PM, Christopher Mullins <span dir="ltr"><<a href="mailto:christopher.mullins@kitware.com" target="_blank">christopher.mullins@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.</div>
<div class="gmail_extra"><div><div><br><br><div class="gmail_quote">On Sun, Feb 2, 2014 at 5:40 PM, Wei Liu <span dir="ltr"><<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Stephen,<div><br></div><div>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: </div>
<div><br></div><div><div> CMake Error at /home/sci/weiliu/packages/Slicer/CMake/SlicerBlockFindQtAndCheckVersion.cmake:43 (message):</div><div> error: Missing Qt module QTWEBKIT</div><div> Call Stack (most recent call first):</div>
<div> /home/sci/weiliu/packages/Slicer/CMake/SlicerBlockFindQtAndCheckVersion.cmake:72 (__SlicerBlockFindQtAndCheckVersion_find_qt)</div><div> /home/sci/weiliu/projects/Slicer-SuperBuild-Rel/Slicer-build/SlicerConfig.cmake:760 (include)</div>
<div> CMakeLists.txt:175 (find_package)</div></div><div><br></div><div><br></div><div>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]. </div>
<div><br></div><div>[1] <a href="http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_Instructions/Prerequisites/Qt#Download_Qt:_Source_and_Binaries" target="_blank">http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_Instructions/Prerequisites/Qt#Download_Qt:_Source_and_Binaries</a><span><font color="#888888"><br>
</font></span></div><span><font color="#888888"><div><br></div><div>Wei</div></font></span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Feb 2, 2014 at 1:40 PM, Stephen Aylward <span dir="ltr"><<a href="mailto:stephen.aylward@kitware.com" target="_blank">stephen.aylward@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Only options to change are<br>
<br>
1) TubeTK_BUILD_SLICER_EXTENSION = ON<br>
2) TubeTK_USE_SLICER = ON<br>
<br>
Then type [c] to configure. This will produce an error message if<br>
Slicer isn't automatically found...so<br>
<br>
3) Slicer_DIR = <YourPathToSlicerBuild>/Slicer-build<br>
-- Yes, point it to the Slicer-build subdir that is within the<br>
top-level directory in which Slicer was built.<br>
<br>
Do not change any other options.<br>
<br>
You should do this in an empty build directory. There are likely to<br>
be problems if you try to switch a current build from being a<br>
stand-alone build to being a Slicer-dependent build.<br>
<br>
s<br>
<div><div><br>
<br>
On Sun, Feb 2, 2014 at 2:49 PM, Wei Liu <<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>> wrote:<br>
> Thanks, Matt and Stephen. I checked the CmakeOutput.log file under VTK-build<br>
> and didn't find any errors. Is that the best way to check build logs?<br>
><br>
> I do have a recent Slicer build that includes VTK. Let me try to point<br>
> TubeTK to it and see what happens.<br>
><br>
> Wei<br>
><br>
><br>
> On Sun, Feb 2, 2014 at 12:34 PM, Stephen Aylward<br>
> <<a href="mailto:stephen.aylward@kitware.com" target="_blank">stephen.aylward@kitware.com</a>> wrote:<br>
>><br>
>> Also, Ricardo is building it on opensuse. It seems to be failing on the<br>
>> vtk build. Perhaps try building vtk on its own via <a href="http://vtk.org" target="_blank">vtk.org</a> or build slicer<br>
>> and point tubetk to it...see <a href="http://slicer.org" target="_blank">slicer.org</a><br>
>><br>
>> S<br>
>><br>
>> --<br>
>> Sent via phone. Please excuse the brevity and typos.<br>
>><br>
>> --<br>
>> Stephen R. Aylward, Ph.D.<br>
>> Senior Director of Operations<br>
>> Kitware, North Carolina<br>
>><br>
>> On Feb 2, 2014 2:31 PM, "Matt McCormick" <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>><br>
>> wrote:<br>
>>><br>
>>> Hi Wei,<br>
>>><br>
>>> Builds reporting to the dashboard should be reproducible (there is<br>
>>> Debian Stable and Ubuntu 12.04 and 13.04 reporting):<br>
>>><br>
>>> <a href="http://open.cdash.org/index.php?project=TubeTK" target="_blank">http://open.cdash.org/index.php?project=TubeTK</a><br>
>>><br>
>>> If further help is needed, we can give personalized attention with a<br>
>>> support contract:<br>
>>><br>
>>> <a href="http://www.kitware.com/products/support.html" target="_blank">http://www.kitware.com/products/support.html</a><br>
>>><br>
>>> Thanks,<br>
>>> Matt<br>
>>><br>
>>> On Sun, Feb 2, 2014 at 11:51 AM, Wei Liu <<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>> wrote:<br>
>>> > Oops, I sent previous email before finishing it.<br>
>>> ><br>
>>> > Yes Matt, I meant TubeTK_USE_VTK. So, I started a clean build, with<br>
>>> > all<br>
>>> > cmake options set to default (the UtbeT_USE_VTK = ON). Now I have<br>
>>> > different<br>
>>> > errors:<br>
>>> ><br>
>>> > ./CropImage: symbol lookup error:<br>
>>> ><br>
>>> > /home/sci/weiliu/packages/TubeTK-Release/VTK-build/bin/libvtkInfovis.so.5.10:<br>
>>> > undefined symbol: _ZTI8vtkArray<br>
>>> ><br>
>>> > I don't remember the exact difference between this build and the<br>
>>> > previous<br>
>>> > one. The difference may be some Cmake options.<br>
>>> ><br>
>>> > Do you suggest me to use another OS, like ubuntu or Redhat-based OS?<br>
>>> ><br>
>>> > Wei<br>
>>> ><br>
>>> ><br>
>>> ><br>
>>> > On Fri, Jan 31, 2014 at 5:46 PM, Matt McCormick<br>
>>> > <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>><br>
>>> > wrote:<br>
>>> >><br>
>>> >> Hmm, the only variable that should be adjusted should be called<br>
>>> >> TubeTK_USE_VTK.<br>
>>> >><br>
>>> >> Starting a clean build with the defaults is good first step.<br>
>>> >><br>
>>> >> Thanks,<br>
>>> >> Matt<br>
>>> >><br>
>>> >> On Fri, Jan 31, 2014 at 7:35 PM, Wei Liu <<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>> wrote:<br>
>>> >> > Matt,<br>
>>> >> ><br>
>>> >> > I didn't install VTK in the system, and I double checked the<br>
>>> >> > /usr/lib<br>
>>> >> > and<br>
>>> >> > lib64 directory.<br>
>>> >> ><br>
>>> >> > I built with the USE_VTK set to off. Is that a possible reason? I'm<br>
>>> >> > re-building TubeTK with it on now.<br>
>>> >> ><br>
>>> >> > Wei<br>
>>> >> ><br>
>>> >> ><br>
>>> >> ><br>
>>> >> ><br>
>>> >> > On Fri, Jan 31, 2014 at 4:08 PM, Matt McCormick<br>
>>> >> > <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>><br>
>>> >> > wrote:<br>
>>> >> >><br>
>>> >> >> Hi Wei,<br>
>>> >> >><br>
>>> >> >> This is not expected. Is a system VTK installed?<br>
>>> >> >><br>
>>> >> >> Thanks,<br>
>>> >> >> Matt<br>
>>> >> >><br>
>>> >> >><br>
>>> >> >><br>
>>> >> >> On Fri, Jan 31, 2014 at 5:58 PM, Wei Liu <<a href="mailto:weiliu620@gmail.com" target="_blank">weiliu620@gmail.com</a>><br>
>>> >> >> wrote:<br>
>>> >> >> > Dear TubeTK developers,<br>
>>> >> >> ><br>
>>> >> >> > I've successfully built TubeTK in release mode. But when I try to<br>
>>> >> >> > run<br>
>>> >> >> > one of<br>
>>> >> >> > the commands in TubeTK-build/bin/ I got the following error:<br>
>>> >> >> ><br>
>>> >> >> > ./CropImage: symbol lookup error:<br>
>>> >> >> ><br>
>>> >> >> ><br>
>>> >> >> ><br>
>>> >> >> > /home/sci/weiliu/packages/TubeTK-Release/VTK-build/bin/libvtkInfovis.so.5.10:<br>
>>> >> >> > undefined symbol: _ZTI21vtkArrayDataAlgorithm<br>
>>> >> >> ><br>
>>> >> >> > I'm using gcc 4.7.1 under opensuse 12.2 64 bit. And I just let<br>
>>> >> >> > tubetk<br>
>>> >> >> > to<br>
>>> >> >> > build everything including ITK and VTK. Actually I got the same<br>
>>> >> >> > error<br>
>>> >> >> > when<br>
>>> >> >> > trying to run other commands.<br>
>>> >> >> ><br>
>>> >> >> > Is this error expected at this stage of development?<br>
>>> >> >> ><br>
>>> >> >> > Thanks,<br>
>>> >> >> > Wei<br>
>>> >> >> ><br>
>>> >> >> > _______________________________________________<br>
>>> >> >> > Tubetk-developers mailing list<br>
>>> >> >> > <a href="mailto:Tubetk-developers@tubetk.org" target="_blank">Tubetk-developers@tubetk.org</a><br>
>>> >> >> ><br>
>>> >> >> > <a href="http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers" target="_blank">http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers</a><br>
>>> >> >> ><br>
>>> >> ><br>
>>> >> ><br>
>>> ><br>
>>> ><br>
>>> _______________________________________________<br>
>>> Tubetk-developers mailing list<br>
>>> <a href="mailto:Tubetk-developers@tubetk.org" target="_blank">Tubetk-developers@tubetk.org</a><br>
>>> <a href="http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers" target="_blank">http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers</a><br>
><br>
><br>
<br>
<br>
<br>
</div></div><span><font color="#888888">--<br>
<br>
====================================================<br>
Stephen R. Aylward, Ph.D.<br>
Senior Director of Operations, North Carolina, Kitware, Inc.<br>
<a href="http://www.kitware.com" target="_blank">http://www.kitware.com</a><br>
<a href="http://www.aylward.org" target="_blank">http://www.aylward.org</a><br>
<a href="tel:%28919%29%20969-6990%20x300" value="+19199696990" target="_blank">(919) 969-6990 x300</a><br>
====================================================<br>
</font></span></blockquote></div><br></div>
</div></div><br>_______________________________________________<br>
Tubetk-developers mailing list<br>
<a href="mailto:Tubetk-developers@tubetk.org" target="_blank">Tubetk-developers@tubetk.org</a><br>
<a href="http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers" target="_blank">http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br></div></div><span><font color="#888888">Christopher Mullins<div>R&D Engineer</div><div>Kitware Inc.,</div><div><a href="tel:919.869.8871" value="+19198698871" target="_blank">919.869.8871</a></div>
</font></span></div>
</blockquote></div><br></div>
</blockquote></div>
</div></div></blockquote></div><br></div>
</blockquote></div>
</div></div></blockquote></div><br></div>