[Vv] Problems installing CLITK via vv superbuild file
Bilal Tahir
b.tahir at sheffield.ac.uk
Fri Feb 22 23:58:25 CET 2013
Dear All,
I am trying to install CLITK by adding the relevant =ON options on the
CMakeLists.txt file (attached edited version in this email) found in the
following link
https://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=blob;f=superbuild/CMakeLists.txt
I then run the following two commands:
cmake superbuild-file-directorymake
However, after running 'make' it started installing the programs (ITK, QT
and VTK) one after the other for several hours until it reached 60% of the
last program 'VV' where it gave the following errors and stopped:
collect2: ld returned 1 exit status
make[5]: *** [bin/vv] Error 1
make[4]: *** [vv/CMakeFiles/vv.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [Stamp/VV/VV-build] Error 2
make[1]: *** [CMakeFiles/VV.dir/all] Error 2
make: *** [all] Error 2
I've copied and posted some of the last few lines up till the point that
the error came.
The 'make' command created several folders in my home folder
(/home/md1bat/) including 'Source' and 'Build'. It appears that ITK, QT and
VTK (not VV) completed as you can see from the /home/md1bat/CMakeFiles/
folder.
[image: Inline images 1]
Within the 'Build' folder, each of the four programs, ITK, VTK, QT and VV
have at least a bin and/or lib folder. This is not the case in the 'Source'
folder. Therefore, I have added the paths of the respective bin and lib
folders from the 'Build' folder (not Source) to my .bashrc file (attached
in this email). However, none of the programs (including the completed ITK,
QT and VTK) seem to work even if I want to check which version I have
installed using the command e.g itk --version. I have now deleted the
precompiled 'VV' Oct 2012 version which used to work with the command vv.
However, the command vv now gives the output 'command not found'.
I'm not sure if I have done the export path correctly on my .bashrc as I
have referenced it to the 'Build' folder and not the 'Source' folder as
there was no bin or lib folders within that. Furthermore, I have no idea
why the errors occurred.
Please let me know if you have any suggestions.
Best wishes,
Bilal Tahir,
James Morrison Researcher in Radiotherapy Imaging,
University of Sheffield/Weston Park Cancer Hospital
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cmake_minimum_required(VERSION 2.8)
cmake_policy(VERSION 2.8)
# set a default build type if it is undefined, then make sure it goes in the cache
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()
set(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Build configuration type" FORCE)
set(build_type ${CMAKE_BUILD_TYPE})
#=========================================================
MACRO (DD in)
MESSAGE(${in}=${${in}})
ENDMACRO(DD)
#=========================================================
project(SuperBuild_VV)
if(MSVC)
set(CMAKE_C_FLAGS_DEBUG "/D_DEBUG /MTd /Zi /Ob0 /Od /RTC1" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_MINSIZEREL "/MT /O1 /Ob1 /D NDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "/MT /O2 /Ob2 /D NDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "/MT /Zi /O2 /Ob1 /D NDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "/D_DEBUG /MTd /Zi /Ob0 /Od /RTC1" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_MINSIZEREL "/MT /O1 /Ob1 /D NDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "/MT /O2 /Ob2 /D NDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/MT /Zi /O2 /Ob1 /D NDEBUG" CACHE STRING "" FORCE)
endif(MSVC)
include(ExternalProject)
set(base "${CMAKE_BINARY_DIR}")
set_property(DIRECTORY PROPERTY EP_BASE ${base})
set(source_prefix ${base}/Source)
set(build_prefix ${base}/Build)
set(install_prefix ${base}/Install)
find_package(Git REQUIRED)
#=========================================================
# QT
SET(QtWinSpecFiles "${source_prefix}/qt/mkspecs/win32-msvc2003/qmake.conf";
"${source_prefix}/qt/mkspecs/win32-msvc2005/qmake.conf";
"${source_prefix}/qt/mkspecs/win32-msvc2008/qmake.conf";
"${source_prefix}/qt/mkspecs/win32-msvc2010/qmake.conf")
ExternalProject_Add(
QT
SOURCE_DIR ${source_prefix}/qt
GIT_REPOSITORY git://gitorious.org/qt/qt.git
GIT_TAG v4.8.3
PATCH_COMMAND sed -i "s/\\-MD/-MT/g" ${QtWinSpecFiles}
CONFIGURE_COMMAND ${source_prefix}/qt/configure -confirm-license
-static
-fast
-opensource
-release
-prefix ${build_prefix}/QT
-nomake examples
-nomake demos
-qt-libpng
-no-libtiff
-no-libjpeg
-no-libmng
INSTALL_COMMAND ""
)
SET(qmake_executable "${build_prefix}/QT/bin/qmake")
#=========================================================
#=========================================================
# VTK
SET(VTK_CMAKE_CXX_STANDARD_LIBRARIES "${CMAKE_CXX_STANDARD_LIBRARIES}")
IF(MSVC)
SET(VTK_CMAKE_CXX_STANDARD_LIBRARIES "${VTK_CMAKE_CXX_STANDARD_LIBRARIES} Imm32.lib Winmm.lib Ws2_32.lib")
ENDIF(MSVC)
ExternalProject_Add(
VTK
DEPENDS QT
SOURCE_DIR ${source_prefix}/vtk
GIT_REPOSITORY git://vtk.org/VTK.git
GIT_TAG v5.10.0
INSTALL_COMMAND ""
CMAKE_ARGS
-DQT_QMAKE_EXECUTABLE:FILEPATH=${qmake_executable}
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
-DCMAKE_C_FLAGS_MINSIZEREL:STRING=${CMAKE_C_FLAGS_MINSIZEREL}
-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
-DCMAKE_CXX_FLAGS_MINSIZEREL:STRING=${CMAKE_CXX_FLAGS_MINSIZEREL}
-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}/${proj}
-DCMAKE_BUILD_TYPE:STRING=${build_type}
-DBUILD_SHARED_LIBS:BOOL=OFF
-DBUILD_EXAMPLES:BOOL=OFF
-DBUILD_TESTING:BOOL=OFF
-DVTK_USE_QT:BOOL=ON
-DVTK_USE_QVTK_QTOPENGL:BOOL=ON
-DCMAKE_CXX_STANDARD_LIBRARIES:STRING=${VTK_CMAKE_CXX_STANDARD_LIBRARIES}
)
SET(VTK_DIR ${build_prefix}/VTK)
#=========================================================
#=========================================================
# ITK
ExternalProject_Add(
ITK
SOURCE_DIR ${source_prefix}/itk
GIT_REPOSITORY git://itk.org/ITK.git
GIT_TAG v4.2.0
INSTALL_COMMAND ""
CMAKE_ARGS
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
-DCMAKE_C_FLAGS_MINSIZEREL:STRING=${CMAKE_C_FLAGS_MINSIZEREL}
-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
-DCMAKE_CXX_FLAGS_MINSIZEREL:STRING=${CMAKE_CXX_FLAGS_MINSIZEREL}
-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}/${proj}
-DCMAKE_BUILD_TYPE:STRING=${build_type}
-DBUILD_SHARED_LIBS:BOOL=OFF
-DBUILD_EXAMPLES:BOOL=OFF
-DBUILD_TESTING:BOOL=OFF
)
SET(ITK_DIR ${build_prefix}/ITK)
#=========================================================
#=========================================================
# VV
SET(VV_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
if(MSVC)
SET(VV_CMAKE_CXX_FLAGS "${VV_CMAKE_CXX_FLAGS} /bigobj")
endif(MSVC)
SET(VV_CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS})
if(CMAKE_COMPILER_IS_GNUCXX)
SET(VV_CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
endif(CMAKE_COMPILER_IS_GNUCXX)
SET(MAKE_COMMAND "make")
if(MSVC)
SET(MAKE_COMMAND "nmake")
endif(MSVC)
ExternalProject_Add(
VV
DEPENDS QT VTK ITK
SOURCE_DIR ${source_prefix}/vv
GIT_REPOSITORY git://git.creatis.insa-lyon.fr/clitk
INSTALL_COMMAND ${MAKE_COMMAND} package
CMAKE_ARGS
-DQT_QMAKE_EXECUTABLE:FILEPATH=${qmake_executable}
-DITK_DIR:PATH=${ITK_DIR}
-DVTK_DIR:PATH=${VTK_DIR}
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
-DCMAKE_C_FLAGS_MINSIZEREL:STRING=${CMAKE_C_FLAGS_MINSIZEREL}
-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
-DCMAKE_CXX_FLAGS_MINSIZEREL:STRING=${CMAKE_CXX_FLAGS_MINSIZEREL}
-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_CXX_FLAGS:STRING=${VV_CMAKE_CXX_FLAGS}
-DCMAKE_EXE_LINKER_FLAGS:STRING=${VV_CMAKE_EXE_LINKER_FLAGS}
-DCMAKE_INSTALL_PREFIX:PATH=${install_prefix}/${proj}
-DCMAKE_BUILD_TYPE:STRING=${build_type}
-DBUILD_SHARED_LIBS:BOOL=OFF
-DBUILD_TESTING:BOOL=OFF
-DCLITK_BUILD_REGISTRATION:BOOL=ON
-DCLITK_BUILD_SEGMENTATION:BOOL=ON
-DCLITK_BUILD_TOOLS:BOOL=ON
-DCLITK_EXPERIMENTAL:BOOL=ON
)
#=========================================================
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[ 54%] Building CXX object vv/CMakeFiles/vvLib.dir/vvOverlayPanel.o
/home/md1bat/Source/vv/vv/vvOverlayPanel.cxx: In member function 'void vvOverlayPanel
::setFusionSpinProperty()':
/home/md1bat/Source/vv/vv/vvOverlayPanel.cxx:245: warning: passing 'double' for argum
ent 1 to 'void QAbstractSlider::setValue(int)'
/home/md1bat/Source/vv/vv/vvOverlayPanel.cxx:246: warning: passing 'double' for argum
ent 1 to 'void QAbstractSlider::setValue(int)'
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/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx: In member function 'void vvSegmen
tationDialog::SetImage(itk::SmartPointer<vvImage>)':
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:184: warning: passing 'double' for
argument 1 to 'void QAbstractSlider::setMinimum(int)'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:185: warning: passing 'double' for
argument 1 to 'void QAbstractSlider::setMaximum(int)'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:186: warning: passing 'double' for
argument 1 to 'void QAbstractSlider::setMinimum(int)'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:187: warning: passing 'double' for
argument 1 to 'void QAbstractSlider::setMaximum(int)'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:188: warning: passing 'double' for
argument 1 to 'void QAbstractSlider::setValue(int)'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:189: warning: passing 'double' for
argument 1 to 'void QAbstractSlider::setValue(int)'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx: In member function 'void vvSegmen
tationDialog::InsertSeed()':
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:408: warning: converting to 'int'
from 'float'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:410: warning: converting to 'int'
from 'float'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:412: warning: converting to 'int'
from 'float'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:414: warning: converting to 'int'
from 'float'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:416: warning: converting to 'int'
from 'double'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:417: warning: converting to 'int'
from 'double'
/home/md1bat/Source/vv/vv/vvSegmentationDialog.cxx:418: warning: converting to 'int'
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/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx: In member function 'void vvInte
nsityValueSlider::valueChangedFromSpinBox(double)':
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx:82: warning: passing 'double' fo
r argument 1 to 'void QAbstractSlider::setValue(int)'
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx: In member function 'void vvInte
nsityValueSlider::SetMaximum(double)':
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx:140: warning: passing 'double' f
or argument 1 to 'void QAbstractSlider::setMaximum(int)'
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx: In member function 'void vvInte
nsityValueSlider::SetMinimum(double)':
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx:162: warning: passing 'double' f
or argument 1 to 'void QAbstractSlider::setMinimum(int)'
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx: In member function 'void vvInte
nsityValueSlider::Update()':
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx:191: warning: passing 'double' f
or argument 1 to 'void QAbstractSlider::setMaximum(int)'
/home/md1bat/Source/vv/vv/vvIntensityValueSlider.cxx:192: warning: passing 'double' f
or argument 1 to 'void QAbstractSlider::setMinimum(int)'
[ 57%] Building CXX object vv/CMakeFiles/vvLib.dir/moc_vvIntensityValueSlider.o
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[ 60%] Building CXX object vv/CMakeFiles/vvLib.dir/vvAnimatedGIFWriter.o
Linking CXX static library ../lib/libvvLib.a
[ 60%] Built target vvLib
Scanning dependencies of target vv
[ 60%] Building CXX object vv/CMakeFiles/vv.dir/vv.o
/home/md1bat/Source/vv/vv/vv.cxx: In function 'int main(int, char**)':
/home/md1bat/Source/vv/vv/vv.cxx:131: warning: converting to 'int' from 'double'
/home/md1bat/Source/vv/vv/vv.cxx:132: warning: converting to 'int' from 'double'
/home/md1bat/Source/vv/vv/vv.cxx:134: warning: converting to 'int' from 'double'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory: In destr
uctor 'std::auto_ptr<_Tp>::~auto_ptr() [with _Tp = QXmlStreamReader]':
/home/md1bat/Source/vv/vv/vvToolCreatorBase.h:38: instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory:259: warn
ing: possible problem detected in invocation of delete operator:
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory:259: warn
ing: invalid use of undefined type 'struct QXmlStreamReader'
/home/md1bat/Source/vv/vv/vvReadState.h:8: warning: forward declaration of 'struct QX
mlStreamReader'
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory:259: note
: neither the destructor nor the class-specific operator delete will be called, even
if they are declared when the class is defined.
Linking CXX executable ../bin/vv
c++: unrecognized option '-static-libstdc++'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle.o): In function `QGtkStyle::drawPrimit
ive(QStyle::PrimitiveElement, QStyleOption const*, QPainter*, QWidget const*) const':
qgtkstyle.cpp:(.text+0x3426): undefined reference to `g_type_check_instance_cast'
qgtkstyle.cpp:(.text+0x343a): undefined reference to `g_object_set_data'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle.o): In function `QGtkStyle::styleHint(
QStyle::StyleHint, QStyleOption const*, QWidget const*, QStyleHintReturn*) const':
qgtkstyle.cpp:(.text+0x523d): undefined reference to `g_object_get'
qgtkstyle.cpp:(.text+0x52d1): undefined reference to `g_object_get'
qgtkstyle.cpp:(.text+0x53bd): undefined reference to `g_object_get'
qgtkstyle.cpp:(.text+0x54c3): undefined reference to `g_object_get'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle.o): In function `QGtkStyle::pixelMetri
c(QStyle::PixelMetric, QStyleOption const*, QWidget const*) const':
qgtkstyle.cpp:(.text+0x5a3e): undefined reference to `g_object_get'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o):qgtkstyle_p.cpp:(.text+0x23a): mo
re undefined references to `g_object_get' follow
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::a
ddWidgetToMap(_GtkWidget*)':
qgtkstyle_p.cpp:(.text+0x7b4): undefined reference to `g_type_check_instance_is_a'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::a
ddAllSubWidgets(_GtkWidget*, void*)':
qgtkstyle_p.cpp:(.text+0x999): undefined reference to `g_type_check_instance_is_a'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::s
etupGtkWidget(_GtkWidget*)':
qgtkstyle_p.cpp:(.text+0xa0a): undefined reference to `g_type_check_instance_is_a'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::g
etGConfString(QString const&, QString const&)':
qgtkstyle_p.cpp:(.text+0x18a1): undefined reference to `g_type_init'
qgtkstyle_p.cpp:(.text+0x1917): undefined reference to `g_object_unref'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::s
etupGtkFileChooser(_GtkWidget*, QWidget*, QString const&, QString const&, QString*, Q
Flags<QFileDialog::Option>, bool, QMap<_GtkFileFilter*, QString>*)':
qgtkstyle_p.cpp:(.text+0x274c): undefined reference to `g_object_set'
qgtkstyle_p.cpp:(.text+0x2766): undefined reference to `g_object_set'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::o
penFilenames(QWidget*, QString const&, QString const&, QString const&, QString*, QFla
gs<QFileDialog::Option>)':
qgtkstyle_p.cpp:(.text+0x3991): undefined reference to `g_object_set'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::i
nitGtkWidgets() const':
qgtkstyle_p.cpp:(.text+0x551b): undefined reference to `g_signal_connect_data'
qgtkstyle_p.cpp:(.text+0x56b9): undefined reference to `g_signal_connect_data'
/home/md1bat/Build/QT/lib/libQtGui.a(qgtkstyle_p.o): In function `QGtkStylePrivate::g
etGConfBool(QString const&, bool)':
qgtkstyle_p.cpp:(.text+0x5a72): undefined reference to `g_type_init'
qgtkstyle_p.cpp:(.text+0x5ae0): undefined reference to `g_object_unref'
collect2: ld returned 1 exit status
make[5]: *** [bin/vv] Error 1
make[4]: *** [vv/CMakeFiles/vv.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [Stamp/VV/VV-build] Error 2
make[1]: *** [CMakeFiles/VV.dir/all] Error 2
make: *** [all] Error 2
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