[Insight-developers] Slicer ITKv4 team status update
Williams, Norman K
norman-k-williams at uiowa.edu
Thu Jan 24 14:55:21 EST 2013
So, I just spent a few hours on fixing the FindDCMTK.cmake from CTK to
work with ITK.
It worked, pretty much, as long as you only ever pointed CMake at an
INSTALLED version of DCMTK. It didn't work to point it at a DCMTK build
directory.
So to fix this, I had to go looking in the build directory for a
CMakeDirectoryInformation.cmake file, and include that to pickup the
source directory. This is required for an uninstalled build, because the
headers are all in the source directory.
Here's a fun fact: There are 4 versions of FindDCMTK.cmake in the ITK
source directory:
./Modules/ThirdParty/DCMTK/CMake/FindDCMTK.cmake
./Modules/ThirdParty/GDCM/src/gdcm/CMake/FindDCMTK.cmake
./Modules/ThirdParty/VNL/src/vxl/config/cmake/Modules/FindDCMTK.cmake
./Modules/ThirdParty/VNL/src/vxl/config/cmake/Modules/NewCMake/FindDCMTK.cm
ake
What's hilarious is that they're all different! To be fair one of the
files in VNL includes the other. The one in GDCM seems to have something
to do with making sure GDCM and DCMTK are inter-operable.
On 1/24/13 10:08 AM, "Jean-Christophe Fillion-Robin"
<jchris.fillionr at kitware.com> wrote:
>Hi Kent,
>
>
>Agree on all point :). Shortly, I will send an email to discuss an action
>plan with all the involved people / toolkit.
>
>
>In the mean time, would be great if the find module within ITKv4 could be
>fixed.
>
>
>@Brad: We could workaround the issue doing what you suggest .. but it
>will complexity things even more.
>
>
>Thanks again for your help,
>Jc
>
>
>
>On Thu, Jan 24, 2013 at 11:01 AM, Williams, Norman K
><norman-k-williams at uiowa.edu> wrote:
>
>The 'stock' FindDCMTK.cmake is broken, and the version in
>ITK/Modules/ThirdParty/DCMTK/CMake is patched to add these libraries.
>
>I have a build going to try and incorporate the CTK version into ITK; see
>my previous E-mail. This is kind of a mess, and it's complicated by
>several factors in DCMTK.
>
>1. There are 2 different build systems being maintained in DCMTK
>2. the FindDCMTK.cmake distributed in CMake can only successfully
>configure in an installed version created with the Autoconf build system.
>3. The CMake build of DCMTK doesn't generate config files to mesh with
>CMakes find_package cleanly.
>4. No current version of FindDCMTK.cmake can successfully set up building
>against a DCMTK build directory (as opposed to an installed DCMTK)
>
>Fixing all this involves coordination between the DCMTK, ITK, Slicer, and
>CMake developer teams.
>
>--
>Kent Williams norman-k-williams at uiowa.edu
>
>
>
>
>
>
>On 1/24/13 12:22 AM, "Jean-Christophe Fillion-Robin"
><jchris.fillionr at kitware.com> wrote:
>
>>Hi Brad,
>>
>>
>>I also tried using CMake 2.8.10 and the error still occurs. Looking at
>>the link line reported below [1], we can see that the path to the library
>>"liboflog.a" and "libofstd.a" are incompelete. Indeed, these ones are
>>referenced as:
>>
>>
>> /lib/liboflog.a
>>and
>> /lib/libofstd.a
>>
>>
>>If I manually "fix" the command, the library "libITKIODCMTK-4.4.dylib" is
>>successfully linked.
>>
>>
>>There is probably an issue in either FindDCMTK.cmake, DCMTKConfig.cmake
>>or in the way ITKv4 link the library libITKIODCMTK.
>>
>>
>>Adding some message statement in the FindDCMTK.cmake bundled with ITKv4,
>>it turns out that the library are incorrectly discovered at that level.
>>Since on the system I am building, the following library exists:
>>
>>
>> $ ls -als /lib
>>1504 -rw-r--r-- 1 kitware admin 769104 May 14 2012 /lib/liboflog.a
>> 792 -rw-r--r-- 1 kitware admin 405336 May 14 2012 /lib/libofstd.a
>>
>>
>>
>>
>>
>>This folder only contains these two libraries, I suspect that this folder
>>has been created by mistake almost a year ago ... I just deleted the
>>folder and the build seems to be continuing as expected.
>>
>>
>>The problem didn't occur because the FindDCMTK.cmake available within CTK
>>doesn't search that location. See
>>https://github.com/commontk/CTK/blob/master/Utilities/CMake/FindDCMTK.cma
>>k
>>e#L69-79
>>
>>
>>I would recommend that the version available in CTK is used in ITKv4 ...
>>it has been fixed and optimized for now few years. DCMTK maintainers even
>>contributed. See
>>https://github.com/commontk/CTK/commits/master/Utilities/CMake/FindDCMTK.
>>c
>>make
>>
>>
>>@Steve: You have probably a similar issue on your workstation.
>>
>>
>>Hth
>>Jc
>>
>>
>>
>>
>>
>>
>>[1] $ make ITKIODCMTK/fast VERBOSE=1
>>make -f Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/build.make
>>Modules/IO/DCMTK/src/CMakeFiles/ITKIODCMTK.dir/build
>>Linking CXX shared library ../../../../lib/libITKIODCMTK-4.4.dylib
>>cd
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/ITKv4-build/Modules/IO/DCMTK/src &&
>>"/Users/kitware/Dashboards/Support/CMake 2.8-10.app/Contents/bin/cmake"
>>-E cmake_link_script
>> CMakeFiles/ITKIODCMTK.dir/link.txt --verbose=1
>>/usr/bin/c++ -Wall -Wcast-align -Wdisabled-optimization -Wextra
>>-Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow
>>-Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow
>>-Wno-deprecated
>> -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -O3
>>-DNDEBUG -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk
>>-mmacosx-version-min=10.6 -dynamiclib -Wl,-headerpad_max_install_names
>>-compatibility_version 1.0.0 -current_version 1.0.0
>> -o ../../../../lib/libITKIODCMTK-4.4.1.dylib -install_name
>
>
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/ITKv4-build/lib/libITKIODCMTK-4.4.1.dylib
>>CMakeFiles/ITKIODCMTK.dir/itkDCMTKImageIO.cxx.o
>>CMakeFiles/ITKIODCMTK.dir/itkDCMTKFileReader.cxx.o
>> CMakeFiles/ITKIODCMTK.dir/itkDCMTKImageIOFactory.cxx.o
>>CMakeFiles/ITKIODCMTK.dir/itkDCMTKSeriesFileNames.cxx.o
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmdata.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmimage.a
>>
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmimgle.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmjpeg.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmnet.a
>>
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmpstat.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmqrdb.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmsr.a
>>
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libdcmtls.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libijg12.a
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libijg16.a
>>
>>/Users/kitware/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.
>>8
>>.10.2-ITKv4/DCMTK-install/lib/libijg8.a
>
>
>>/lib/liboflog.a /lib/libofstd.a
>>../../../../lib/libITKIOImageBase-4.4.1.dylib
>>../../../../lib/libITKCommon-4.4.1.dylib
>>../../../../lib/libitksys-4.4.1.dylib
>>../../../../lib/libITKVNLInstantiation-4.4.1.dylib
>>../../../../lib/libitkvnl_algo-4.4.1.dylib
>> ../../../../lib/libitkv3p_lsqr-4.4.1.dylib
>>../../../../lib/libitkvnl-4.4.1.dylib
>>../../../../lib/libitkvcl-4.4.1.dylib
>>../../../../lib/libitkv3p_netlib-4.4.1.dylib -lm -lm
>>
>>
>>
>>
>>
>>
>>On Wed, Jan 23, 2013 at 11:34 PM, Bradley Lowekamp
>><blowekamp at mail.nih.gov> wrote:
>>
>>Removing the ccache front end still produced a successful build.
>>http://slicer.cdash.org/buildSummary.php?buildid=58957
>>
>>
>>I am going to upgrade to cmake 2.8.8 and rebuild.
>>
>>
>>Brad
>>
>>On Jan 23, 2013, at 9:12 PM, Jean-Christophe Fillion-Robin
>><jchris.fillionr at kitware.com> wrote:
>>
>>
>>I don't think so, the only two available frameworks are 10.7 and 10.8.
>>
>>
>>$ ls
>>/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Deve
>>l
>>oper/SDKs/
>>MacOSX10.7.sdkMacOSX10.8.sdk
>>
>>
>>Jc
>>
>>
>>
>>
>>On Wed, Jan 23, 2013 at 8:39 PM, Bradley Lowekamp
>><blowekamp at mail.nih.gov> wrote:
>>
>>JC,
>>
>>
>>Are you able to Target OS 10.6, and run it there?
>>
>>
>>Brad
>>
>>On Jan 23, 2013, at 8:30 PM, Jean-Christophe Fillion-Robin
>><jchris.fillionr at kitware.com> wrote:
>>
>>
>>Hi Folks,
>>
>>
>>On Mountain Lion, I was able to build without any issue :)
>>
>>
>>$ uname -a
>>Darwin factory-south 12.2.0 Darwin Kernel Version 12.2.0: Sat Aug 25
>>00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64 x86_64
>>
>>
>>$ g++ --version
>>i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build
>>5658) (LLVM build 2336.11.00)
>>[...]
>>
>>
>>$ xcodebuild -version
>>Xcode 4.5.2
>>Build version 4G2008a
>>
>>
>>That said, I see the following warning at startup ... any idea what could
>>be done to avoid this ?
>>
>>
>>
>>factory-south:Slicer-build kitware$ ./Slicer
>>WARNING: In
>
>
>>/Volumes/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.8.10.2
>>0
>>130121-g92bd8-ITKv4/ITKv4/Modules/Core/Common/src/itkObjectFactoryBase.cx
>>x
>>, line 514
>>/Volumes/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.8.10.2
>>0
>>130121-g92bd8-ITKv4/Slicer-build/lib/Slicer-4.2/ITKFactories/libMGHIOPlug
>>i
>
>>n.so is already loaded
>>
>>
>>WARNING: In
>
>>/Volumes/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.8.10.2
>>0
>>130121-g92bd8-ITKv4/ITKv4/Modules/Core/Common/src/itkObjectFactoryBase.cx
>>x
>>, line 514
>>/Volumes/Dashboards/Experimental/Slicer-Superbuild-Release-cmake-2.8.10.2
>>0
>>130121-g92bd8-ITKv4/Slicer-build/lib/Slicer-4.2/ITKFactories/libMRMLIDIOP
>>l
>
>>ugin.so is already loaded
>>
>>
>>
>>Thanks
>>Jc
>>
>>
>>
>>
>>On Wed, Jan 23, 2013 at 6:50 PM, Bradley Lowekamp
>><blowekamp at mail.nih.gov> wrote:
>>
>>Hans,
>>
>>
>>I am going to have to dis-agree with you on several points.
>>
>>
>>It is not a custom build compiler. It just the ccache front end to the
>>system compiler as reported. I have the Intel Compiler and CCache
>>installed. I don't have any custom built compilers or Mac Port tools etc
>>install on the system. The information I reported
>> about the compiler is accurate.
>>
>>
>>I did intent t o run the with the raw system compiler though; me culpa.
>>I'll re-run with the raw system then, with the suggested CMake upgrade
>>later.
>>
>>
>>The compiler work just fine for SimpleITK. The Mac Pro workstation was my
>>primary system up until 3 months ago for years. I developed most of
>>SimpleITK with that compiler. So it works to my knowledge.
>>
>>
>>I don't have too much experience with OpenMP, but we did run into an
>>issue when trying to abuse it with the ITK threading model.
>>
>>
>>I have compiled OpenCV many time with that compiler as well.
>>
>>
>>
>>
>>However, the later versions for the Apple compiler the ones where llvm is
>>masquerading as gcc are un-usable in my opinion. Only the most recent
>>ones seems OK. As long as "llvm" in not contained in the output of" gcc
>>--version" I would expect that things
>> should build OK.
>>
>>
>>Has as I recall you began switching more to Macs when Lion came out? Is
>>that correct?
>>
>>
>>Brad
>>
>>On Jan 23, 2013, at 6:01 PM, "Johnson, Hans J" <hans-johnson at uiowa.edu>
>>wrote:
>>
>>
>>I'm now confused about what we are trying to accomplish. We are stuck
>>because we need features of DCMTK that don't build on an old compiler
>>that has known issues. That compiler will also not compile SimpleITK,
>>and it does not work with openmp directives,
>> and it has failures with other applications (we had troubles with OpenCV
>>compiling on that compiler, and quickly moved to internal build or clang
>>compilers). At one point in time we were not getting valid builds of
>>BRAINSStand alone as well (due to the openmp
>> bug).
>>
>>
>>Hans
>>=================================================================
>>Hans J. Johnson, Ph.D.
>>Assistant Professor, Department of Psychiatry
>>
>>
>>Mailing Address:
>>W274 GH Email:
>hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>
>>200 Hawkins Drive Phone:
>
>
>>(319) 353 8587 <tel:%28319%29%20353%208587> <tel:%28319%29%20353%208587>
>>The University of Iowa
>>Iowa City, IA 52242
>>
>>
>>
>>
>>
>>
>>
>>From: Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com>
>>Date: Wednesday, January 23, 2013 4:52 PM
>>To: Hans Johnson <hans-johnson at uiowa.edu>
>>Cc: Bradley Lowekamp <blowekamp at mail.nih.gov>, "pieper at bwh.harvard.edu"
>><pieper at bwh.harvard.edu>,
>> "Miller, James V (GE Global Research)" <millerjv at ge.com>, Luis Ibanez
>><luis.ibanez at kitware.com>, Matt McCormick <matt.mccormick at kitware.com>,
>> Bill Lorensen <bill.lorensen at gmail.com>, Stephen Aylward
>><Stephen.Aylward at kitware.com>, Kent Williams
>><norman-k-williams at uiowa.edu>,
>> Ron Kikinis <kikinis at bwh.harvard.edu>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>Brad,
>>That explain the issue. Could you try to build with the compiler provided
>>on your machine ? I expect it also fails ...
>>Thanks
>>Jc
>>
>>
>>
>>On Wed, Jan 23, 2013 at 5:47 PM, Johnson, Hans J
>><hans-johnson at uiowa.edu> wrote:
>>
>>Brad was using a custom built compiler on that computer, and not the
>>default system compilers. This may not have been as good of a test as we
>>thought.
>>
>>
>>/nfs/Users/blowekamp/local/bin/g++-4.2
>>
>>
>>Hans
>>
>>
>>=================================================================
>>Hans J. Johnson, Ph.D.
>>Assistant Professor, Department of Psychiatry
>>
>>
>>Mailing Address:
>>W274 GH Email:
>hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>
>>200 Hawkins Drive Phone:
>
>
>>(319) 353 8587 <tel:%28319%29%20353%208587> <tel:%28319%29%20353%208587>
>>The University of Iowa
>>Iowa City, IA 52242
>>
>>
>>
>>
>>
>>
>>
>>
>>From: Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com>
>>Date: Wednesday, January 23, 2013 3:59 PM
>>To: Bradley Lowekamp <blowekamp at mail.nih.gov>
>>Cc: Hans Johnson <hans-johnson at uiowa.edu>, "pieper at bwh.harvard.edu"
>><pieper at bwh.harvard.edu>,
>> "Miller, James V (GE Global Research)" <millerjv at ge.com>, Luis Ibanez
>><luis.ibanez at kitware.com>, Matt McCormick <matt.mccormick at kitware.com>,
>> Bill Lorensen <bill.lorensen at gmail.com>, Stephen Aylward
>><Stephen.Aylward at kitware.com>, Kent Williams
>><norman-k-williams at uiowa.edu>,
>> Ron Kikinis <kikinis at bwh.harvard.edu>
>>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>
>>
>>Hi Brad,
>>
>>
>>This is good news. Your config is exactly the same as
>
>>"factory.kitware.com <http://factory.kitware.com>
>><http://factory.kitware.com/>" where it fails to
>>build.
>>
>>
>>It seems you are currently using CMake 2.8.8rc1, could you try with CMake
>>2.8.8. This is the version currently installed on the factory.
>>
>>
>>Thanks for your help,
>>Jc
>>
>>
>>
>>On Wed, Jan 23, 2013 at 11:51 AM, Bradley Lowekamp
>><blowekamp at mail.nih.gov> wrote:
>>
>>Here is my build:
>>
>>
>>http://slicer.cdash.org/buildSummary.php?buildid=58791
>>
>>On Jan 23, 2013, at 8:37 AM, "Johnson, Hans J" <hans-johnson at uiowa.edu>
>>wrote:
>>
>>
>>JC,
>>
>>
>>From my reading of the wiki page, it appears that Xcode 3.2.6 is not
>>supported or compatible with 10.8. As of 10.8, Xcode is a free
>>download again from the App store.
>>
>>
>>Xcode is not part of the software update until you install a version
>>newer than 4.3 (The first application bundle that is downloaded from the
>>App Store and using the App Store updating mechanisms). Xcode 3.2.6
>>will not be updated by "sudo softwareupdate
>> -l"
>>
>>
>>Hans
>>
>>
>>From: <Johnson>, Hans Johnson <hans-johnson at uiowa.edu>
>>Date: Wednesday, January 23, 2013 7:25 AM
>>To: "pieper at bwh.harvard.edu" <pieper at bwh.harvard.edu>, Jean-Christophe
>>Fillion-Robin <jchris.fillionr at kitware.com>
>>Cc: "Miller, James V (GE Global Research)" <millerjv at ge.com>, Bradley
>>Lowekamp <blowekamp at mail.nih.gov>, Luis
>> Ibanez <luis.ibanez at kitware.com>, Matt McCormick
>><matt.mccormick at kitware.com>, Bill Lorensen <bill.lorensen at gmail.com>,
>> Stephen Aylward <Stephen.Aylward at kitware.com>, Kent Williams
>><norman-k-williams at uiowa.edu>, Ron Kikinis <kikinis at bwh.harvard.edu>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>JC,
>>
>>
>>I agree that we need to support 10.6 for the binary distribution, but do
>>we need to support it for the build environment? The newer versions of
>>Xcode have fixed many of these strange errors. That was one of the very
>>first gcc/llvm mashup compilers, and
>> it has many strange behaviors.
>>
>>
>>http://en.wikipedia.org/wiki/Xcode
>>
>>
>>The Xcode version 4 as been available since June 2010.
>>
>>
>>Hans
>>
>>
>>From: Steve Pieper <pieper at ibility.net>
>>Reply-To: "pieper at bwh.harvard.edu" <pieper at bwh.harvard.edu>
>>Date: Wednesday, January 23, 2013 6:17 AM
>>To: Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com>
>>Cc: Hans Johnson <hans-johnson at uiowa.edu>, "Miller, James V (GE Global
>>Research)" <millerjv at ge.com>, Bradley
>> Lowekamp <blowekamp at mail.nih.gov>, Luis Ibanez
>><luis.ibanez at kitware.com>, Matt McCormick <matt.mccormick at kitware.com>,
>> Bill Lorensen <bill.lorensen at gmail.com>, Stephen Aylward
>><Stephen.Aylward at kitware.com>, Kent Williams
>><norman-k-williams at uiowa.edu>,
>> Ron Kikinis <kikinis at bwh.harvard.edu>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>Here's the version info on the machine where I get link errors:
>>
>>
>>#1 ~ $ xcodebuild -version
>>Xcode 3.2.6
>>Component versions: DevToolsCore-1809.0; DevToolsSupport-1806.0
>>BuildVersion: 10M2518
>>
>>
>>#2 ~ $ g++ -version
>>i686-apple-darwin11-llvm-g++-4.2: no input files
>>
>>
>>#3 ~ $ uname -a
>
>
>>Darwin common.bwh.harvard.edu <http://common.bwh.harvard.edu>
>><http://common.bwh.harvard.edu/> 11.4.2
>>Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012;
>>root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
>>
>>
>>#5 ~ $ sudo softwareupdate -l
>>Password:
>>Software Update Tool
>>Copyright 2002-2010 Apple
>>
>>
>>No new software available.
>>
>>
>>
>>
>>
>>
>>On Tue, Jan 22, 2013 at 11:26 PM, Jean-Christophe Fillion-Robin
>><jchris.fillionr at kitware.com> wrote:
>>
>
>>On that system [factory.kitwarein.com <http://factory.kitwarein.com>
>><http://factory.kitwarein.com/>],
>>the only available update seems to be ITunesX. See below.
>>
>>
>>Let's also note that since the reported kernel is 10.8, the corresponding
>>MacOSX release is 10.6.8. See
>>http://en.wikipedia.org/wiki/Darwin_(operating_system)#Release_history
>>and
>http://en.wikipedia.org/wiki/Mac_OS_X_Snow_Leopard#Release_history
><http://en.wikipedia.org/wiki/Mac_OS_X_Snow_Leopard#Release_history>
>>
>>
>>I believe a lot of people are still using this version of MacOSX (Snow
>>Leopard) and we should make sure to support it.
>>
>>
>>
>>$ softwareupdate -l
>>Software Update Tool
>>Copyright 2002-2009 Apple
>>
>>
>>Software Update found the following new or updated software:
>> * iTunesX-11.0.1
>>iTunes (11.0.1), 193391K [recommended]
>>
>>
>>
>>
>>On Tue, Jan 22, 2013 at 11:16 PM, Jean-Christophe Fillion-Robin
>><jchris.fillionr at kitware.com> wrote:
>>
>>Hi Hans,
>>
>>
>
>>On the machine [factory.kitware.com <http://factory.kitware.com>
>><http://factory.kitware.com/>] where
>>it fails to compile, here are the complete stats:
>>
>>
>>$ xcodebuild -version
>>Xcode 3.2.6
>>Component versions: DevToolsCore-1809.0; DevToolsSupport-1806.0
>>BuildVersion: 10M2518
>>
>>
>>
>>$ g++ --version
>>i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
>>
>>
>>
>>
>>$ uname -a
>
>>Darwin factory.kitwarein.com <http://factory.kitwarein.com>
>><http://factory.kitwarein.com/> 10.8.0
>>Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011;
>>root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
>>
>>
>>
>>
>>I will look if XCode can be updated.
>>
>>
>>@Steve: What are the details of your MacOSX system where it also fails ?
>>
>>
>>Thanks
>>Jc
>>
>>
>>
>>On Tue, Jan 22, 2013 at 10:29 PM, Johnson, Hans J
>><hans-johnson at uiowa.edu> wrote:
>>
>>JC,
>>
>>
>>Is that a pre-release compiler? On all my 10.8 computers the version of
>>gcc is
>>i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build
>>5658)
>>
>> ^^
>> ^^^^
>>
>>
>>i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
>>
>> ^^
>> ^^^^^^^^^^
>>
>>
>>I don't have that combination anywhere on my computers. I think it is
>>odd that you OS is 10.8 (I.e. Darwin 11), but the compiler is stated to
>>be darwin10.
>>
>>
>>==================
>>xcodebuild -version
>>Xcode 4.5.2
>>Build version 4G2008a
>>
>>
>>
>>
>>
>>Hans
>>
>>
>>
>>From: Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com>
>>Date: Tuesday, January 22, 2013 8:20 PM
>>
>>To: Hans Johnson <hans-johnson at uiowa.edu>
>>Cc: "Miller, James V (GE Global Research)" <millerjv at ge.com>, Bradley
>>Lowekamp <blowekamp at mail.nih.gov>, Steve
>> Pieper <pieper at bwh.harvard.edu>, Luis Ibanez <luis.ibanez at kitware.com>,
>>Matt McCormick <matt.mccormick at kitware.com>,
>> Bill Lorensen <bill.lorensen at gmail.com>, Stephen Aylward
>><Stephen.Aylward at kitware.com>, Kent Williams
>><norman-k-williams at uiowa.edu>,
>> Ron Kikinis <kikinis at bwh.harvard.edu>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>
>>
>>Hi Hans,
>>
>>
>>Looking more carefully, the build errors occured on "factory" and not
>>"factory-south" [newest machine], the following compilers are used on
>>that machine:
>>
>>
>>factory at kitware:/Users/kitware> gcc --version
>>i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
>>Copyright (C) 2007 Free Software Foundation, Inc.
>>This is free software; see the source for copying conditions. There is
>>NO
>>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>PURPOSE.
>>
>>
>>factory at kitware:/Users/kitware> g++ --version
>>i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
>>Copyright (C) 2007 Free Software Foundation, Inc.
>>This is free software; see the source for copying conditions. There is
>>NO
>>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>PURPOSE.
>>
>>
>>factory at kitware:/Users/kitware> uname -a
>
>
>>Darwin factory.kitwarein.com <http://factory.kitwarein.com>
>><http://factory.kitwarein.com/> 10.8.0
>>Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011;
>>root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
>>
>>
>>
>>
>>I do a clean build to confirm there is an issue.
>>
>>
>>I will also do a clean build on "factory-south" where the most recent
>>compilers are installed.
>>
>>
>>Thanks
>>Jc
>>
>>
>>
>>On Tue, Jan 22, 2013 at 9:04 PM, Johnson, Hans J
>><hans-johnson at uiowa.edu> wrote:
>>
>>I just did a clean build:
>>
>>
>>johnsonhj at neuron$ CC=/usr/bin/gcc CXX=/usr/bin/g++ ccmake ../Slicer
>>
>>
>>
>>
>>[100%] Built target Slicer
>>/scratch/johnsonhj/src/Slicer-gcc
>>
>>
>>johnsonhj at neuron$ /usr//bin/gcc --version
>>i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build
>>5658) (LLVM build 2336.11.00)
>>Copyright (C) 2007 Free Software Foundation, Inc.
>>This is free software; see the source for copying conditions. There is
>>NO
>>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>PURPOSE.
>>
>>
>>/scratch/johnsonhj/src/Slicer-gcc
>>johnsonhj at neuron$ /usr/bin/g++ --version
>>i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 (Based on Apple Inc. build
>>5658) (LLVM build 2336.11.00)
>>Copyright (C) 2007 Free Software Foundation, Inc.
>>This is free software; see the source for copying conditions. There is
>>NO
>>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>PURPOSE.
>>
>>
>>/scratch/johnsonhj/src/Slicer-gcc
>>johnsonhj at neuron$ uname -a
>
>
>>Darwin neuron.psychiatry.uiowa.edu <http://neuron.psychiatry.uiowa.edu>
>><http://neuron.psychiatry.uiowa.edu/>
>>11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012;
>>root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
>>
>>
>>
>>================
>>I'll try the 10.8 version next.
>>
>>
>>Hans
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>=================================================================
>>Hans J. Johnson, Ph.D.
>>Assistant Professor, Department of Psychiatry
>>
>>
>>Mailing Address:
>>W274 GH Email:
>hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>
>>200 Hawkins Drive Phone:
>
>>(319) 353 8587 <tel:%28319%29%20353%208587> <tel:%28319%29%20353%208587>
>>The University of Iowa
>>Iowa City, IA 52242
>>
>>
>>
>>
>>
>>
>>
>>From: Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com>
>>Date: Tuesday, January 22, 2013 5:46 PM
>>To: Hans Johnson <hans-johnson at uiowa.edu>
>>Cc: "Miller, James V (GE Global Research)" <millerjv at ge.com>, Bradley
>>Lowekamp <blowekamp at mail.nih.gov>, Steve
>> Pieper <pieper at bwh.harvard.edu>, Luis Ibanez <luis.ibanez at kitware.com>,
>>Matt McCormick <matt.mccormick at kitware.com>,
>> Bill Lorensen <bill.lorensen at gmail.com>, Stephen Aylward
>><Stephen.Aylward at kitware.com>, Kent Williams
>><norman-k-williams at uiowa.edu>,
>> Ron Kikinis <kikinis at bwh.harvard.edu>
>>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>
>>
>>Dashboard machine is building with a gcc provided by the latest XCode on
>>the latest MacOSX. I didn't install any gcc with homebrew or similar.
>>Given the fact it is a nightly dashboard, a clean build is redone every
>>night.
>>Jc
>>
>>
>>
>>
>>On Tue, Jan 22, 2013 at 6:39 PM, Johnson, Hans J
>><hans-johnson at uiowa.edu> wrote:
>>
>>JC,,
>>
>>
>>I've not been able to reproduce that error. I'll start another clean
>>build, but could it be that the dashboard machine just needs a fresh
>>clean build?
>>
>>
>>Hans
>>
>>
>>
>>
>>From: Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com>
>>Date: Tuesday, January 22, 2013 4:40 PM
>>To: "Miller, James V (GE Global Research)" <millerjv at ge.com>
>>Cc: Bradley Lowekamp <blowekamp at mail.nih.gov>, Steve Pieper
>><pieper at bwh.harvard.edu>, Luis Ibanez <luis.ibanez at kitware.com>,
>> Matt McCormick <matt.mccormick at kitware.com>, Bill Lorensen
>><bill.lorensen at gmail.com>, Stephen Aylward <Stephen.Aylward at kitware.com>,
>> Hans Johnson <hans-johnson at uiowa.edu>, Kent Williams
>><norman-k-williams at uiowa.edu>, Ron Kikinis <kikinis at bwh.harvard.edu>
>>Subject: Re: Slicer ITKv4 team status update
>>
>>
>>
>>Hi Folks,
>>
>>
>>Steve and myself discussed an approach that will probably help us address
>>the windows problem.
>>
>>
>>In the mean time, is there any update regarding the DCMTK build error ?
>>See details below.
>>
>>
>>Thanks for your help,
>>Jc
>>
>>
>>On Thu, Jan 17, 2013 at 3:05 PM, Jean-Christophe Fillion-Robin
>><jchris.fillionr at kitware.com> wrote:
>>
>>Hi Folks,
>>
>>
>>Adding Kent to the thread since they is some issue with ITKIODCMTK on
>>MacOSX 10.8 using . See
>>http://slicer.cdash.org/viewBuildError.php?buildid=56825
>>
>>
>>Any idea how to fix this ?
>>
>>
>>Regarding the
>>windows build error
>
>
>><http://slicer.cdash.org/viewBuildError.php?buildid=56862> not related to
>>ITKIODCMTK, I just pushed
>>a commit
>
>><http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21610
>>>
>>that should help.
>>
>>
>>Thanks for your help,
>>Jc
>>
>>
>>
>>On Mon, Jan 14, 2013 at 10:47 AM, Miller, James V (GE Global Research)
>><millerjv at ge.com> wrote:
>>
>>Ahh man. That is pants!
>>
>>I liked being able to have downloads on project github pages....
>>
>>Jim
>>
>>Jim Miller
>>Senior Scientist
>>GE Research
>>Interventional and Therapy
>>
>>GE imagination at work
>>
>>
>>
>>On Jan 14, 2013, at 10:39 AM, Jean-Christophe Fillion-Robin wrote:
>>
>>
>>@jim: Github deprecated his download/upload api few days ago. That is why
>>I moved the AppLauncher packages on
>>packages.kitware.com <http://packages.kitware.com>
>
>><http://packages.kitware.com/><http://packages.kitware.com/>. We should
>>probably do the same for the simple itk packages. [[ Check slicer devel
>>archive
>> ]]
>>
>>I can provide you with the script I used to upload all the AppLauncher
>>packages on midas.
>>
>>Hth
>>Jc
>>
>>--
>>Sent from my mobile device
>>
>>
>>On Jan 14, 2013 6:45 AM, "Bradley Lowekamp"
>><blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
>>Luis,
>>
>>What is the version of VS8 reported in the About dialog?
>>
>>SP1 is required for SimpleITK and I believe Slicer also. While the TR1
>>bonus pack was originally an extra download is should be included is SP1.
>>
>>However, I don't think that is the problem, as there are two locations
>>that are searched for for these tr1 files, and only one is reporting an
>>error below.
>>
>>If either of these try includes are producing and error is should print a
>>link to the FAQ for more information the relevant entries are around
>>here:
>>
>>http://www.itk.org/Wiki/ITK/Release_4/SimpleITK/FAQ#Do_I_need_to_download
>>_
>>an_option_package_for_TR1_support.3F
>>
>>Please feel free to edit it, if it needs to be clarified.
>>
>>
>>
>>I think your problem is likely the C99 stdint.h. The currently
>>recommendation is to download the file and place it into the compiler.
>>This is pretty ugly and I was never very happy with it, but with it
>>mostly being built on my robots, it seemed passable at
>> the time. As Slicer is adopting it I don't think it's a sensible option
>>any more. So I will look into adding a header to include my version or
>>the system.
>>
>>The unfortunate problem with this is that it is bad practice to add these
>>typedefs into the global namespace as it may introduce problems and
>>naming conflicts. While ITK does provide these typedefs in it's own
>>namespace, it is an ITK header, and there is not
>> a single ITK header in the public SimpleITK interface, so that is not an
>>options. Additionally, I think there are some specific SWIG binding that
>>will get more complicated when there is not stdints in the expected
>>global namespace. Despite the problems of
>> dumping these symbols into the global namespace I think it may be the
>>best option. If anyone else has other thoughts or concerns on this issue
>>please share.
>>
>>I do consider this a significant issue, and I will work on it to get in
>>into the 0.6.0 release.
>>
>>Brad
>>
>>
>>
>>
>>
>>On Jan 14, 2013, at 7:42 AM, Luis Ibanez
>><luis.ibanez at kitware.com<mailto:luis.ibanez at kitware.com>> wrote:
>>
>>Hi Brad,
>>
>>Please find attached the files:
>>
>>
>>
>> * CMakeError.log
>> * CMakeOuput.log
>>
>>taken from the directory
>>
>>
>> * /c/S43X/SimpleITK-build/CMakeFiles
>>
>>Common messages are:
>>
>>1>.\CheckIncludeFile.cxx(1) : fatal error C1083: Cannot open include
>>file: 'tr1/type_traits': No such file or directory
>>
>>1>.\CheckIncludeFile.cxx(1) : fatal error C1083: Cannot open include
>>file: 'tr1/unordered_map': No such file or directory
>>
>>1>.\CheckIncludeFile.cxx(1) : fatal error C1083: Cannot open include
>>file: 'stdint.h': No such file or directory
>>
>>
>>It looks like my VS 2008 does not have installed support for TR1...
>>
>>Could you please advise on what I should do to
>>get my VS 2008 Express installation to support TR1 ?
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>>--------------------------------------------------------------
>>
>>On Mon, Jan 14, 2013 at 7:25 AM, Luis Ibanez
>><luis.ibanez at kitware.com<mailto:luis.ibanez at kitware.com>> wrote:
>>Brad,
>>
>>
>>On Sun, Jan 13, 2013 at 10:11 PM, Bradley Lowekamp
>><blowekamp at mail.nih.gov<mailto:blowekamp at mail.nih.gov>> wrote:
>>Luis,
>>
>>It appears that the windows binary MD5 did not get upgraded the last
>>time, the SWIG version was updated. So the MD5 change should be correct.
>>It's unfortunate that the SimpleiTK version of these file and the Slicer
>>version has diverged. I hope that these can
>> be resolved so that the Slicer version is just a matter of copying the
>>one maintained in SimpleITK.
>>
>>Ok, this item should be no problem.
>>
>>
>>Even with the correct MD5 we are going about 5% download failure rate
>>from Source Forge. Is is likely going to be unacceptable for Slicer. So
>>the source and binary downloads will likely need to be move to the more
>>reliable Midas system.
>>
>>That sounds like a good plan.
>>
>>Do we have already any SimpleITK folder in MIDAS ?
>>
>>Otherwise, we can create one today.
>>
>>
>>To really have a clue about the error you are getting, I would need to
>>see the actually CMake configuration error that cause the error reported
>>by the super build.
>>
>>
>>Yeap,
>>I'll dig it out of the Windows build and send it out later today.
>>
>>
>> Luis
>>
>><CMakeError.log><CMakeOutput.log>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>
>
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>________________________________________
>>Notice: This UI Health Care e-mail (including attachments) is covered by
>>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>confidential and may be legally privileged. If you are not the intended
>>recipient, you are hereby notified that any
>> retention, dissemination, distribution, or copying of this communication
>>is strictly prohibited. Please reply to the sender that you have
>>received the message in error, then delete it. Thank you.
>
>>________________________________________
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>________________________________________
>>Notice: This UI Health Care e-mail (including attachments) is covered by
>>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>confidential and may be legally privileged. If you are not the intended
>>recipient, you are hereby notified that any
>> retention, dissemination, distribution, or copying of this communication
>>is strictly prohibited. Please reply to the sender that you have
>>received the message in error, then delete it. Thank you.
>
>>________________________________________
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>________________________________________
>>Notice: This UI Health Care e-mail (including attachments) is covered by
>>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>confidential and may be legally privileged. If you are not the intended
>>recipient, you are hereby notified that any
>> retention, dissemination, distribution, or copying of this communication
>>is strictly prohibited. Please reply to the sender that you have
>>received the message in error, then delete it. Thank you.
>
>>________________________________________
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>________________________________________
>>Notice: This UI Health Care e-mail (including attachments) is covered by
>>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>confidential and may be legally privileged. If you are not the intended
>>recipient, you are hereby notified that any
>> retention, dissemination, distribution, or copying of this communication
>>is strictly prohibited. Please reply to the sender that you have
>>received the message in error, then delete it. Thank you.
>
>>________________________________________
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>________________________________________
>>Notice: This UI Health Care e-mail (including attachments) is covered by
>>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>confidential and may be legally privileged. If you are not the intended
>>recipient, you are hereby notified that any
>> retention, dissemination, distribution, or copying of this communication
>>is strictly prohibited. Please reply to the sender that you have
>>received the message in error, then delete it. Thank you.
>
>>________________________________________
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>________________________________________
>>Notice: This UI Health Care e-mail (including attachments) is covered by
>>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>>confidential and may be legally privileged. If you are not the intended
>>recipient, you are hereby notified that any
>> retention, dissemination, distribution, or copying of this communication
>>is strictly prohibited. Please reply to the sender that you have
>>received the message in error, then delete it. Thank you.
>
>>________________________________________
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>><tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849 <tel:%2B1%20919%20869%208849>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>--
>>+1 919 869 8849
>>
>
>
>
>________________________________
>Notice: This UI Health Care e-mail (including attachments) is covered by
>the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
>confidential and may be legally privileged. If you are not the intended
>recipient, you are hereby notified that any
> retention, dissemination, distribution, or copying of this communication
>is strictly prohibited. Please reply to the sender that you have
>received the message in error, then delete it. Thank you.
>________________________________
>
>
>
>
>
>
>
>
>
>--
>+1 919 869 8849
>
________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.
________________________________
-------------- next part --------------
A non-text attachment was scrubbed...
Name: FindDCMTK.cmake
Type: application/octet-stream
Size: 6220 bytes
Desc: FindDCMTK.cmake
URL: <http://www.itk.org/pipermail/insight-developers/attachments/20130124/7be8be36/attachment.obj>
More information about the Insight-developers
mailing list