[Insight-developers] Slicer4 and ITKv4 packaging
Bill Lorensen
bill.lorensen at gmail.com
Sun Feb 26 08:15:30 EST 2012
I renamed the tree and ran the generated dog. It worked well.
On Sat, Feb 25, 2012 at 7:15 PM, Jean-Christophe Fillion-Robin
<jchris.fillionr at kitware.com> wrote:
> Hi Bill,
>
> This is good news :)
>
> On mac, could you make sure to rename your build tree before you try to
> run/install the generated dmg ?
> You can rename your build tree back to its original name afterward.
>
> I just want to make sure that the library bundled in the packages are all
> properly "fixedup" and are not
> referencing anything in the build tree.
>
> Thanks
> Jc
>
>
> On Sat, Feb 25, 2012 at 7:08 PM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>>
>> Great news.
>>
>> 1) linux packaging of Slicer4/ITKv4 works
>> 2) mac packaging of Slicer4/ITKv4 works
>>
>> I need to check in changes to Slicer4, but I will wait until the
>> dashboard madness subsides.
>>
>> After that, I'll be looking for someone to verify the packaging for
>> windows.
>>
>> Thanks to Jc for all of his help,
>>
>> Bill
>>
>> On Sat, Feb 25, 2012 at 11:04 AM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>> > Hans,
>> >
>> > The Slicer dashboard looks pretty bad today. I'll wait until it clears
>> > up before checking my changes.
>> >
>> > I'm verifying the Mac package now.
>> >
>> > Bill
>> >
>> > On Sat, Feb 25, 2012 at 10:22 AM, Johnson, Hans J
>> > <hans-johnson at uiowa.edu> wrote:
>> >> Bill,
>> >>
>> >> THANK YOU, THANK YOU, THANK YOU!
>> >>
>> >> I am extremely appreciative of your efforts in getting this issue
>> >> resolved. Please let me know when you feel the ITKv4 packaging is
>> >> working
>> >> and committed for Slicer so that I can start on the todo list that has
>> >> been waiting on this.
>> >>
>> >> Thanks,
>> >> Hans
>> >>
>> >> On 2/25/12 7:25 AM, "Bill Lorensen" <bill.lorensen at gmail.com> wrote:
>> >>
>> >>>Yes, I made both changes and the linux package works great. I ran the
>> >>>tests and several fail but I think that most are failing on ITKv3
>> >>>(although tray's Slicer dashboard has problems).
>> >>>
>> >>>Now I'm trying the Mac packaging.
>> >>>
>> >>>On Sat, Feb 25, 2012 at 12:54 AM, Jean-Christophe Fillion-Robin
>> >>><jchris.fillionr at kitware.com> wrote:
>> >>>> Excellent
>> >>>>
>> >>>> Just to make sure there are no confusion, both changes are required.
>> >>>>This is
>> >>>> particularly important for the Mac packaging. Do you think you could
>> >>>>give a
>> >>>> try ?
>> >>>>
>> >>>> Note also that installing all components of ITKv4 is a workaround. I
>> >>>>just
>> >>>> created an entry in Jira https://issues.itk.org/jira/browse/ITK-2893
>> >>>>
>> >>>> Thanks
>> >>>> Jc
>> >>>>
>> >>>>
>> >>>> On Fri, Feb 24, 2012 at 11:39 PM, Bill Lorensen
>> >>>><bill.lorensen at gmail.com>
>> >>>> wrote:
>> >>>>>
>> >>>>> Jc,
>> >>>>>
>> >>>>> Thanks. I had tried 1) before without success. After doing 2)
>> >>>>> everything installs fine and runs fine.
>> >>>>>
>> >>>>> Thanks again. I'll check in the changes over the weekend.
>> >>>>>
>> >>>>> Bill
>> >>>>>
>> >>>>> On Fri, Feb 24, 2012 at 10:18 PM, Jean-Christophe Fillion-Robin
>> >>>>> <jchris.fillionr at kitware.com> wrote:
>> >>>>> > Bill,
>> >>>>> >
>> >>>>> > Please consider the solution I discussed in my previous email and
>> >>>>>things
>> >>>>> > should work better :)
>> >>>>> >
>> >>>>> > To summarise:
>> >>>>> >
>> >>>>> > 1) In External_ITKv4.cmake
>> >>>>> >
>> >>>>> >
>> >>>>> > -DITK_INSTALL_INSTALL_LIBRARY_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
>> >>>>> > -DITK_INSTALL_INSTALL_ARCHIVE_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
>> >>>>> >
>> >>>>> > => This is something that should be documented in the migration
>> >>>>>guide if
>> >>>>> > ITKv4.
>> >>>>> > The variable ITK_INSTALL_LIB_DIR isn't valid anymore.
>> >>>>> >
>> >>>>> >
>> >>>>> > 2) Around line 9 of CMake/SlicerBlockInstallCMakeProjects.cmake,
>> >>>>>add
>> >>>>> > the
>> >>>>> > following:
>> >>>>> >
>> >>>>> >
>> >>>>> > set(component ALL)
>> >>>>> > if(${ITK_VERSION_MAJOR} STREQUAL "3")
>> >>>>> > set(component RuntimeLibraries)
>> >>>>> > endif()
>> >>>>> > set(CPACK_INSTALL_CMAKE_PROJECTS
>> >>>>> > "${CPACK_INSTALL_CMAKE_PROJECTS};${ITK_DIR};ITK;${component};/")
>> >>>>> >
>> >>>>> > Hth
>> >>>>> > Jc
>> >>>>> >
>> >>>>> >
>> >>>>> > On Fri, Feb 24, 2012 at 8:23 PM, Bill Lorensen
>> >>>>><bill.lorensen at gmail.com>
>> >>>>> > wrote:
>> >>>>> >>
>> >>>>> >> I've have seen the same issues that you see. I have tried
>> >>>>> >> specifying
>> >>>>> >> -DITK_INSTALL_LIB_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
>> >>>>> >> and it does not seem to change anything.
>> >>>>> >>
>> >>>>> >> What puzzles me is that a make package for ITKv4 (outside of
>> >>>>> >> slicer)
>> >>>>> >> produces a valid package.
>> >>>>> >>
>> >>>>> >> Bill
>> >>>>> >>
>> >>>>> >> On Fri, Feb 24, 2012 at 6:14 PM, Jean-Christophe Fillion-Robin
>> >>>>> >> <jchris.fillionr at kitware.com> wrote:
>> >>>>> >> > Hi Bill,
>> >>>>> >> >
>> >>>>> >> > Thanks for working on the ITKv4 integration. I will try to
>> >>>>> >> > provide
>> >>>>> >> > additional details and guidance below.
>> >>>>> >> >
>> >>>>> >> > Slicer packaging system install its dependent project using
>> >>>>>cmake by
>> >>>>> >> > specifying explicitly which components should be installed in
>> >>>>> >> > the
>> >>>>> >> > Slicer
>> >>>>> >> > install tree.
>> >>>>> >> >
>> >>>>> >> > I just run a "make package" in a Slicer-ITKv4 build tree, and
>> >>>>> >> > I
>> >>>>> >> > notice
>> >>>>> >> > that
>> >>>>> >> > only the following libraries are installed:
>> >>>>> >> >
>> >>>>> >> > libITKDICOMParser-4.1.so
>> >>>>> >> > libITKEXPAT-4.1.so
>> >>>>> >> > libITKgiftiio-4.1.so
>> >>>>> >> > libitkjpeg-4.1.so
>> >>>>> >> > libITKMetaIO-4.1.so
>> >>>>> >> > libitkNetlibSlatec-4.1.so
>> >>>>> >> > libITKniftiio-4.1.so
>> >>>>> >> > libITKNrrdIO-4.1.so
>> >>>>> >> > libitkopenjpeg-4.1.so
>> >>>>> >> > libitkpng-4.1.so
>> >>>>> >> > libitktiff-4.1.so
>> >>>>> >> > libitkv3p_lsqr-4.1.so
>> >>>>> >> > libitkv3p_netlib-4.1.so
>> >>>>> >> > libitkvcl-4.1.so
>> >>>>> >> > libitkvnl-4.1.so
>> >>>>> >> > libitkvnl_algo-4.1.so
>> >>>>> >> > libitkzlib-4.1.so
>> >>>>> >> > libITKznz-4.1.so
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > 1) There libraries are located in ./lib folder whereas they are
>> >>>>> >> > expected
>> >>>>> >> > in
>> >>>>> >> > "./lib/Slicer-4.0". Looking at ITKv3 external project. The
>> >>>>> >> > option
>> >>>>> >> >
>> >>>>> >> > -DITK_INSTALL_LIB_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
>> >>>>> >> >
>> >>>>> >> > is passed.
>> >>>>> >> >
>> >>>>> >> > See
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>>
>> >>>>> >>>>>https://github.com/Slicer/Slicer/blob/master/SuperBuild/External_ITKv3.c
>> >>>>>make#L52
>> >>>>> >> >
>> >>>>> >> > It means the same thing should probably be done for ITKv4
>> >>>>> >> > external
>> >>>>> >> > project.
>> >>>>> >> >
>> >>>>> >> > Looking at the CMakeLists.txt, there is indeed a variables
>> >>>>> >> > named
>> >>>>> >> > ITK_INSTALL_LIBRARY_DIR, ITK_INSTALL_ARCHIVE_DIR, ...
>> >>>>> >> > See
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>>
>> >>>>> >>>>>http://itk.org/gitweb?p=ITK.git;a=blob;f=CMakeLists.txt;h=d9ac50f81439c1
>> >>>>>7f490d1cd8fb00f07afc861015;hb=HEAD#l50
>> >>>>> >> >
>> >>>>> >> > In the case of ITKv4, we should probably set the following:
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > -DITK_INSTALL_INSTALL_LIBRARY_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > -DITK_INSTALL_INSTALL_ARCHIVE_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
>> >>>>> >> >
>> >>>>> >> > => This is something that should be documented in the migration
>> >>>>>guide
>> >>>>> >> > if
>> >>>>> >> > ITKv4.
>> >>>>> >> > The variable ITK_INSTALL_LIB_DIR isn't valid anymore.
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > 2) The question regarding the components.
>> >>>>> >> >
>> >>>>> >> > Within ITKv4 source code, the "itk_module_target_install" macro
>> >>>>>seems
>> >>>>> >> > to
>> >>>>> >> > responsible of installing the target.
>> >>>>> >> >
>> >>>>> >> > Seems no Component is specified in the install rule. It means
>> >>>>> >> > it's
>> >>>>> >> > not
>> >>>>> >> > possible to do a component based installation :( . It means
>> >>>>> >> > that
>> >>>>>when
>> >>>>> >> > ITKv4
>> >>>>> >> > is packaged by an other project all the headers, doc, etc ...
>> >>>>>will be
>> >>>>> >> > installed even if not needed. This something we would like to
>> >>>>>avoid
>> >>>>> >> > in
>> >>>>> >> > Slicer.
>> >>>>> >> >
>> >>>>> >> > See
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>>
>> >>>>> >>>>>http://itk.org/gitweb?p=ITK.git;a=blob;f=CMake/ITKModuleMacros.cmake;h=b
>> >>>>>9458d73e2f2df2bf85220da7ad09d2934d78be5;hb=HEAD#l194
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > Within ITKv3, a component was specified.
>> >>>>> >> >
>> >>>>> >> > IF(NOT ITK_INSTALL_NO_LIBRARIES)
>> >>>>> >> > INSTALL(TARGETS ITKCommon itkvnl_inst
>> >>>>> >> > RUNTIME DESTINATION ${ITK_INSTALL_BIN_DIR_CM24} COMPONENT
>> >>>>> >> > RuntimeLibraries
>> >>>>> >> > LIBRARY DESTINATION ${ITK_INSTALL_LIB_DIR_CM24} COMPONENT
>> >>>>> >> > RuntimeLibraries
>> >>>>> >> > ARCHIVE DESTINATION ${ITK_INSTALL_LIB_DIR_CM24} COMPONENT
>> >>>>> >> > Development)
>> >>>>> >> > ENDIF(NOT ITK_INSTALL_NO_LIBRARIES)
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > See
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>>
>> >>>>> >>>>>http://itk.org/gitweb?p=ITK.git;a=blob;f=Code/Common/CMakeLists.txt;h=55
>>
>> >>>>> >>>>>749ea90e6d8d253d882b5a9cf7524cd92bcf7c;hb=389c62087f77cf116cf53039f4d667
>> >>>>>a544c824bc#l168
>> >>>>> >> >
>> >>>>> >> > The workaround the component issue would be to add the
>> >>>>> >> > following
>> >>>>>line
>> >>>>> >> > in
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>>
>> >>>>> >>>>>https://github.com/Slicer/Slicer/blob/master/CMake/SlicerBlockInstallCMa
>> >>>>>keProjects.cmake#L9
>> >>>>> >> >
>> >>>>> >> > // --------------
>> >>>>> >> > set(component ALL)
>> >>>>> >> > if(${ITK_VERSION_MAJOR} STREQUAL "3")
>> >>>>> >> > set(component RuntimeLibraries)
>> >>>>> >> > endif()
>> >>>>> >> > set(CPACK_INSTALL_CMAKE_PROJECTS
>> >>>>> >> >
>> >>>>> >> > "${CPACK_INSTALL_CMAKE_PROJECTS};${ITK_DIR};ITK;${component};/")
>> >>>>> >> > // --------------
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > After applying this two fixes, let me know how it goes.
>> >>>>> >> > Thanks
>> >>>>> >> > Jc
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > Ps: Documentation about CPACK_INSTALL_CMAKE_PROJECTS is here:
>> >>>>> >> > http://www.cmake.org/Wiki/CMake:CPackConfiguration
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> > On Fri, Feb 24, 2012 at 4:56 PM, Bill Lorensen
>> >>>>> >> > <bill.lorensen at gmail.com>
>> >>>>> >> > wrote:
>> >>>>> >> >>
>> >>>>> >> >> Jc,
>> >>>>> >> >>
>> >>>>> >> >> Please consider me a newbie regarding packaging. And, I have
>> >>>>> >> >> not
>> >>>>> >> >> read/analyzed your e-mail. ITKv4, make package, creates a
>> >>>>> >> >> valid
>> >>>>>and
>> >>>>> >> >> usable package. Why is that not sufficient for Slicer4?
>> >>>>> >> >>
>> >>>>> >> >> Bill
>> >>>>> >> >>
>> >>>>> >> >> On Fri, Feb 24, 2012 at 4:42 PM, Jean-Christophe Fillion-Robin
>> >>>>> >> >> <jchris.fillionr at kitware.com> wrote:
>> >>>>> >> >> > Hi Bill,
>> >>>>> >> >> >
>> >>>>> >> >> > Are you packaging on linux or mac ?
>> >>>>> >> >> >
>> >>>>> >> >> > //-----------------------------------
>> >>>>> >> >> > Linux / Windows:
>> >>>>> >> >> >
>> >>>>> >> >> > Within Slicer, ITK is told to installed itself in the file
>> >>>>> >> >> > SlicerBlockInstallCMakeProject
>> >>>>> >> >> > s.cmake
>> >>>>> >> >> >
>> >>>>> >> >> > See
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>>
>> >>>>> >>>>>https://github.com/Slicer/Slicer/blob/master/CMake/SlicerBlockInstallCMa
>> >>>>>keProjects.cmake#L9
>> >>>>> >> >> >
>> >>>>> >> >> > You can see that the current system expects the ITK
>> >>>>> >> >> > libraries
>> >>>>>to
>> >>>>> >> >> > be
>> >>>>> >> >> > associated with the RuntimeLibraries component.
>> >>>>> >> >> >
>> >>>>> >> >> > => Is it still the case with ITKv4 ?
>> >>>>> >> >> >
>> >>>>> >> >> > This file is itself included from here:
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>>
>> >>>>> >>>>>https://github.com/Slicer/Slicer/blob/master/CMake/SlicerCPack.cmake#L32
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> > //-----------------------------------
>> >>>>> >> >> > MacOSX:
>> >>>>> >> >> >
>> >>>>> >> >> > The fixup bundle mechanism expects the libraries to exist in
>> >>>>> >> >> > ITK_LIBRARY_DIRS
>> >>>>> >> >> > See
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>>
>> >>>>> >>>>>https://github.com/Slicer/Slicer/blob/master/Utilities/LastConfigureStep
>> >>>>>/SlicerCompleteBundles.cmake.in#L201
>> >>>>> >> >> >
>> >>>>> >> >> > Is ITK_LIBRARY_DIRS properly set with ITKConfig.cmake ?
>> >>>>> >> >> >
>> >>>>> >> >> > Hth
>> >>>>> >> >> > Jc
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> > On Fri, Feb 24, 2012 at 4:11 PM, Bill Lorensen
>> >>>>> >> >> > <bill.lorensen at gmail.com>
>> >>>>> >> >> > wrote:
>> >>>>> >> >> >>
>> >>>>> >> >> >> Folks,
>> >>>>> >> >> >>
>> >>>>> >> >> >> I'm trying to package Slicer4 with ITKv4.
>> >>>>> >> >> >>
>> >>>>> >> >> >> 1) for ITKv4, make package produces a proper tarball that I
>> >>>>>can
>> >>>>> >> >> >> untar
>> >>>>> >> >> >> and
>> >>>>> >> >> >> use.
>> >>>>> >> >> >> 2) for Sllicer4, make package does not contain the ITKv4
>> >>>>> >> >> >> includes.
>> >>>>> >> >> >> Also, the package contains ITKv4's ThirdParty libraries,
>> >>>>> >> >> >> but
>> >>>>>none
>> >>>>> >> >> >> of
>> >>>>> >> >> >> the other ITK libraries.
>> >>>>> >> >> >>
>> >>>>> >> >> >> So, is there some special requirement in Slicer4 that must
>> >>>>> >> >> >> be
>> >>>>> >> >> >> present
>> >>>>> >> >> >> to achieve a proper package?
>> >>>>> >> >> >>
>> >>>>> >> >> >> Bill
>> >>>>> >> >> >> _______________________________________________
>> >>>>> >> >> >> Powered by www.kitware.com
>> >>>>> >> >> >>
>> >>>>> >> >> >> Visit other Kitware open-source projects at
>> >>>>> >> >> >> http://www.kitware.com/opensource/opensource.html
>> >>>>> >> >> >>
>> >>>>> >> >> >> Kitware offers ITK Training Courses, for more information
>> >>>>>visit:
>> >>>>> >> >> >> http://kitware.com/products/protraining.html
>> >>>>> >> >> >>
>> >>>>> >> >> >> Please keep messages on-topic and check the ITK FAQ at:
>> >>>>> >> >> >> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>> >> >> >>
>> >>>>> >> >> >> Follow this link to subscribe/unsubscribe:
>> >>>>> >> >> >> http://www.itk.org/mailman/listinfo/insight-developers
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> >
>> >>>>> >> >> > --
>> >>>>> >> >> > +1 919 869 8849
>> >>>>> >> >> >
>> >>>>> >> >>
>> >>>>> >> >>
>> >>>>> >> >>
>> >>>>> >> >> --
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>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
>> >>>>> >> >
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>> >>>>> >>
>> >>>>> >>
>> >>>>> >>
>> >>>>> >> --
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>> >>>>> >
>> >>>>> >
>> >>>>> >
>> >>>>> >
>> >>>>> > --
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>> >>>>> >
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
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>> >>>>
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>> >>>
>> >>>
>> >>>
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>> >>>
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>> >>>http://www.itk.org/Wiki/ITK_FAQ
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