[Insight-developers] Slicer4 and ITKv4 packaging
Johnson, Hans J
hans-johnson at uiowa.edu
Sat Feb 25 10:22:14 EST 2012
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
>>> >> >> >
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> Unpaid intern in BillsBasement at noware dot com
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > --
>>> >> > +1 919 869 8849
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >> Unpaid intern in BillsBasement at noware dot com
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > +1 919 869 8849
>>> >
>>>
>>>
>>>
>>> --
>>> Unpaid intern in BillsBasement at noware dot com
>>
>>
>>
>>
>> --
>> +1 919 869 8849
>>
>
>
>
>--
>Unpaid intern in BillsBasement at noware dot com
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