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[Seg3D] Re: Announcing Seg3D 2.1


Chronological Thread 
  • From: Ramón Casero Cañas <rcasero@gmail.com>
  • To: seg3d@sci.utah.edu
  • Subject: [Seg3D] Re: Announcing Seg3D 2.1
  • Date: Thu, 15 Sep 2011 19:20:01 +0100
On 07/09/11 21:09, Jeroen Stinstra wrote:
Dear Seg3D users,

We are pleased to announce Seg3D version 2.1.

This new version introduces many new features such as :
        * provenance tracking and playback of provenance trails
        * a speedline tool for tracing the contours
        * 3D picking for improved navigation
        * a measurement tool for measuring distances
        * and many bug fixes to improve stability

The new version is available at http://software.sci.utah.edu/

We hope you enjoy the new version,


Hi,

I'm trying it for Ubuntu Natty Linux 64 bit. I have 2 comments and a compilation error.


* QT 4.7 is available with the current Ubuntu Natty, so Install.txt is misleading in saying

"For Linux Qt is available in most package managers. Most likely Qt was already installed on your system, however it is likely to be an older version than Qt 4.7. Hence download and compile the Qt 4.7 development package using your favorite package manager if you wish to install Seg3D on your Linux system."

It's simpler just to install package libqt4-dev.

If QT 3 is also installed in the system, then

$ cd bin
$ cmake ../src

will give an error saying that QT >= 4.6.0 is not installed. In my case, I had to remove package libqt3-mt-dev



* Configuration of ITK gives some warnings

<SCREEN>

-- Configuring insight toolkit
CMake Warning (dev) at Externals/itk/CMakeLists.txt:147 (LINK_DIRECTORIES):
  This command specifies the relative path

    .

  as a link directory.

Policy CMP0015 is not set: link_directories() treats paths relative to the
source dir. Run "cmake --help-policy CMP0015" for policy details. Use the
  cmake_policy command to set the policy and suppress this warning.
This warning is for project developers.  Use -Wno-dev to suppress it.

Attention: You have chosen to use the new statistics framework instead of the existing framework. The statistics classes have been re-designed/refactored and in several cases do not conform to the API of the older framework. You may need to change your code to use the new API.
Attention: You have chosen to use the files in the Review directory. The Copyright of these files has not been cleared up, and the coding style and API of the classes in the Review directory may change drastically as it get code reviews from the developers. Please set ITK_USE_REVIEW to OFF if you don't want to use these files.

</SCREEN>


* The compilation error is

<SCREEN>

[ 64%] Building C object Externals/python/CMakeFiles/python.dir/Modules/_multiprocessing/semaphore.c.o
cd /home/ramc/secure_data/comlab/Seg3D_2.1.0-code/bin/Externals/python && /usr/bin/gcc -DSCI_64BITS -DGLEW_STATIC -DTEEM_STATIC -DLIBXML_STATIC -DTINYXML_STATIC -DBOOST_ALL_NO_LIB -DQT_NO_KEYWORDS -DTIXML_USE_STL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DBUILD_WITH_PYTHON -DPy_NO_ENABLE_SHARED -DBOOST_PYTHON_STATIC_MODULE -DBOOST_PYTHON_STATIC_LIB -DPy_BUILD_CORE -DPy_NO_ENABLE_SHARED -DZ_PREFIX -I/usr/include/qt4 -I/usr/include/qt4/QtOpenGL -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtCore -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/gdcm/Source/Common -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/bin/Externals/gdcm/Source/Common -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/gdcm/Source/DataStructureAndEncodingDefinition -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/gdcm/Source/MediaStorageAndFileFormat -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/gdcm/Source/DataDictionary -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/gdcm/Source/InformationObjectDefinition -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/zlib -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Include -I/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/bin/Externals/python -o CMakeFiles/python.dir/Modules/_multiprocessing/semaphore.c.o -c /home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:15:5: error: expected specifier-qualifier-list before ‘SEM_HANDLE’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:208:26: error: expected ‘)’ before ‘*’ token
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_acquire’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:283:13: error: ‘SemLockObject’ has no member named ‘kind’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:283:42: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:283:42: error: ‘SemLockObject’ has no member named ‘last_tid’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:284:15: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:310:32: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:312:35: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:314:19: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:329:11: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:330:9: error: ‘SemLockObject’ has no member named ‘last_tid’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_release’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:338:13: error: ‘SemLockObject’ has no member named ‘kind’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:339:14: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:339:14: error: ‘SemLockObject’ has no member named ‘last_tid’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:345:17: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:346:19: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:349:9: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:353:17: error: ‘SemLockObject’ has no member named ‘maxvalue’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:355:33: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:363:34: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:388:22: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:391:11: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: At top level:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:402:38: error: expected declaration specifiers or ‘...’ before ‘SEM_HANDLE’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘newsemlockobject’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:409:9: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:409:20: error: ‘handle’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:409:20: note: each undeclared identifier is reported only once for each function it appears in
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:410:9: error: ‘SemLockObject’ has no member named ‘kind’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:411:9: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:412:9: error: ‘SemLockObject’ has no member named ‘last_tid’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:413:9: error: ‘SemLockObject’ has no member named ‘maxvalue’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_new’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:421:5: error: ‘SEM_HANDLE’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:421:16: error: expected ‘;’ before ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:439:5: error: ‘handle’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:441:19: error: ‘SEM_FAILED’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:447:5: error: too many arguments to function ‘newsemlockobject’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:402:1: note: declared here
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_rebuild’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:463:5: error: ‘SEM_HANDLE’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:463:16: error: expected ‘;’ before ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:467:28: error: ‘handle’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:470:5: error: too many arguments to function ‘newsemlockobject’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:402:1: note: declared here
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_dealloc’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:476:13: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:476:25: error: ‘SEM_FAILED’ undeclared (first use in this function)
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:477:9: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_count’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:484:37: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_ismine’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:491:28: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:491:28: error: ‘SemLockObject’ has no member named ‘last_tid’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_iszero’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:516:25: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:521:26: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: In function ‘semlock_afterfork’:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:536:9: error: ‘SemLockObject’ has no member named ‘count’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c: At top level:
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:573:30: error: ‘SemLockObject’ has no member named ‘handle’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:575:21: error: ‘SemLockObject’ has no member named ‘kind’
/home/ramc/secure_data/comlab/Seg3D_2.1.0-code/src/Externals/python/Modules/_multiprocessing/semaphore.c:577:25: error: ‘SemLockObject’ has no member named ‘maxvalue’
make[2]: *** [Externals/python/CMakeFiles/python.dir/Modules/_multiprocessing/semaphore.c.o] Error 1
make[2]: Leaving directory `/home/scratch/ramc/comlab/Seg3D_2.1.0-code/bin'
make[1]: *** [Externals/python/CMakeFiles/python.dir/all] Error 2
make[1]: Leaving directory `/home/scratch/ramc/comlab/Seg3D_2.1.0-code/bin'
make: *** [all] Error 2


</SCREEN>

--
Dr. Ramón Casero Cañas

Computational Biology
Department of Computer Science
University of Oxford
Wolfson Building, Parks Rd
Oxford OX1 3QD

tlf     +44 (0) 1865 610737
web     http://web.comlab.ox.ac.uk/people/Ramon.CaseroCanas
photos  http://www.flickr.com/photos/rcasero/

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