[Gate-users] gate7.1 installation on mac OSX 10.10
Pete Z. Wu
pzw at ns.ph.liv.ac.uk
Mon Sep 21 05:08:14 CEST 2015
Hi Again,
Please find below the entire output as viewed form the command line on
macbook pro OSX10. The cmake command and its flags are also shown
below. Please can someone help me to resolve my problem regarding the
installation of gate v7.1?
root at machintosh$ cd gate_v7.1-build/
root at machintosh$ pwd
/usr/local/gate_v7.1-build
root at machintosh$ cmake
-DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
-DGATE_DOWNLOAD_BENCHMARKS_DATA=ON -DGATE_DOWNLOAD_EXAMPLES_DATA=ON
-DGATE_USE_ECAT7=OFF -DGATE_USE_LMF=OFF -DGATE_USE_OPTICAL=ON
-DGATE_USE_GPU=OFF -DGATE_USE_GEANT4_UIVIS=ON
-DGEANT4_USE_SYSTEM_CLHEP=OFF /usr/local/gate_v7.1
-- The C compiler identification is AppleClang 6.0.0.6000051
-- The CXX compiler identification is AppleClang 6.0.0.6000051
-- Check for working C compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc --
works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ --
works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ROOT 5.34/32 in /opt/local/libexec/root5
-- Found PkgConfig: /opt/local/bin/pkg-config (found version "0.28")
-- Found LibXml2: /Library/Frameworks/libxml2.framework
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
GEANT4_USE_SYSTEM_CLHEP
-- Build files have been written to: /usr/local/gate_v7.1-build
root at machintosh$ make -j2
Scanning dependencies of target itkzlib
Scanning dependencies of target MetaIO
[ 0%] Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/adler32.o
[ 0%] Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/compress.o
[ 0%] Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/crc32.o
[ 0%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaUtils.o
[ 0%] Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/deflate.o
[ 1%] Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/gzio.o
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[ 1%] Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/zutil.o
[ 2%] Linking C static library libitkzlib.a
[ 2%] Built target itkzlib
[ 3%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaArrow.o
Scanning dependencies of target GateBenchmarkData
[ 3%] Generating /usr/local/gate_v7.1/benchmarks/benchPET/benchPET.pdf
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=35a91d8d91d208cf300cfe02c41f0899&algorithm=MD5"
[ 3%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaBlob.o
[ 3%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaCommand.o
[ 3%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaContour.o
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-- Downloaded object:
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/usr/local/gate_v7.1/benchmarks/benchPET/benchmarkPET-GATE-Reference.gif
-- Fetching
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[ 4%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaEllipse.o
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[ 4%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaGaussian.o
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaImage.o
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-- Downloaded object:
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[ 5%] Generating
/usr/local/gate_v7.1/benchmarks/benchPET/benchmarkPET-fGATE.gif
-- Fetching
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[ 5%] Building CXX object
itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaImageUtils.o
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaLandmark.o
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaLine.o
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-- Downloaded object:
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[ 5%] Generating /usr/local/gate_v7.1/benchmarks/benchPET/benchmarkPET.gif
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=942c49a51c32068549574a985d242f42&algorithm=MD5"
[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaMesh.o
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaObject.o
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-- Downloaded object:
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[ 5%] Generating
/usr/local/gate_v7.1/benchmarks/benchSPECT/SPECT-reference-results.gif
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=996b4c4b5b5e12e3e4073aab2804e4c6&algorithm=MD5"
[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaOutput.o
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-- Fetching
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[ 6%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaTube.o
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-- Fetching
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[ 6%] Building CXX object
itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaTubeGraph.o
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-- Fetching
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[ 5%] Building CXX object
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaLandmark.o
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[ 5%] Generating /usr/local/gate_v7.1/benchmarks/benchPET/benchmarkPET.gif
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=942c49a51c32068549574a985d242f42&algorithm=MD5"
[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaMesh.o
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaObject.o
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-- Fetching
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[ 5%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaOutput.o
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[ 6%] Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaScene.o
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-- Fetching
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-- Fetching
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[ 6%] Building CXX object
itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaTubeGraph.o
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CMakeFiles/Gate.dir/source/geometry/src/GateDMapoperators.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedVolumeSolid.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageRegularParametrisedVolume.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageRegularParametrisedVolumeMessenger.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateLinearRepeater.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateLinearRepeaterMessenger.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateMaterialDatabase.cc.o
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In file included from
/usr/local/gate_v7.1/source/geometry/src/GateMaterialDatabase.cc:19:
/usr/local/gate_v7.1/source/general/include/GateXMLDocument.hh:16:10:
fatal error:
'libxml/xmlmemory.h' file not found
#include <libxml/xmlmemory.h>
^
1 error generated.
make[2]: ***
[CMakeFiles/Gate.dir/source/geometry/src/GateMaterialDatabase.cc.o]
Error 1
make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 22%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_6.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d5a777f0731cae74ec51e94eff676385&algorithm=MD5"
-- [download 76% complete]
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CMakeFiles/Gate.dir/source/geometry/src/GateHoleParameterisation.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateHype.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateHypeMessenger.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageBox.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageNestedParametrisation.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageNestedParametrisedVolume.cc.o
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/6e1dd112c3ff48913d55e5754ccb0510"
[ 20%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_5.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d746dd3bf5942a29c470aefff9280236&algorithm=MD5"
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[ 20%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageNestedParametrisedVolumeMessenger.cc.o
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[ 20%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedSubVolume.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedSubVolumeMessenger.cc.o
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[ 20%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedSubVolumeSolid.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedVolume.cc.o
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[ 21%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedVolumeMessenger.cc.o
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[ 21%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedVolumeSolid.cc.o
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[ 21%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageRegularParametrisedVolume.cc.o
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[ 21%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateImageRegularParametrisedVolumeMessenger.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateLinearRepeater.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateLinearRepeaterMessenger.cc.o
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[ 22%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateMaterialDatabase.cc.o
-- [download 75% complete]
In file included from
/usr/local/gate_v7.1/source/geometry/src/GateMaterialDatabase.cc:19:
/usr/local/gate_v7.1/source/general/include/GateXMLDocument.hh:16:10:
fatal error:
'libxml/xmlmemory.h' file not found
#include <libxml/xmlmemory.h>
^
1 error generated.
make[2]: ***
[CMakeFiles/Gate.dir/source/geometry/src/GateMaterialDatabase.cc.o]
Error 1
make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 22%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_6.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d5a777f0731cae74ec51e94eff676385&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/d746dd3bf5942a29c470aefff9280236"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_7.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=af5b5dbef7a9aa37d1b554d2fab7bdd0&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/d746dd3bf5942a29c470aefff9280236"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_7.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=af5b5dbef7a9aa37d1b554d2fab7bdd0&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/d5a777f0731cae74ec51e94eff676385"
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-- Downloaded object:
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-- [download 68% complete]
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[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_8.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=a9cd0e61d8f9f0a033b5ebb9054aebe1&algorithm=MD5"
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-- Downloaded object:
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/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_9.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=5ca0fd75b6c76fb7cc18e782dfc14576&algorithm=MD5"
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[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_8.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=a9cd0e61d8f9f0a033b5ebb9054aebe1&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/af5b5dbef7a9aa37d1b554d2fab7bdd0"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_9.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=5ca0fd75b6c76fb7cc18e782dfc14576&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/a9cd0e61d8f9f0a033b5ebb9054aebe1"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_1.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=ee84d77dc3ebd445548c5b0950c6558e&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/5ca0fd75b6c76fb7cc18e782dfc14576"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_10.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=6277cb5a4c6e724161c8cf3595f885c1&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/a9cd0e61d8f9f0a033b5ebb9054aebe1"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_1.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=ee84d77dc3ebd445548c5b0950c6558e&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/5ca0fd75b6c76fb7cc18e782dfc14576"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_10.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=6277cb5a4c6e724161c8cf3595f885c1&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/ee84d77dc3ebd445548c5b0950c6558e"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_2.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=0ecbce48f40182180e886377904c8a5b&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/6277cb5a4c6e724161c8cf3595f885c1"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_3.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=044a158a2617c05ed8fb657a27ed23ff&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/ee84d77dc3ebd445548c5b0950c6558e"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_2.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=0ecbce48f40182180e886377904c8a5b&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/6277cb5a4c6e724161c8cf3595f885c1"
[ 23%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_3.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=044a158a2617c05ed8fb657a27ed23ff&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/044a158a2617c05ed8fb657a27ed23ff"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_4.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=63d5e31f2052aace22eb2b448488f462&algorithm=MD5"
-- [download 98% complete]
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/0ecbce48f40182180e886377904c8a5b"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_5.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4d2109f58e05d361e7a0e5ff6169fc58&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/044a158a2617c05ed8fb657a27ed23ff"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_4.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=63d5e31f2052aace22eb2b448488f462&algorithm=MD5"
-- [download 98% complete]
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/0ecbce48f40182180e886377904c8a5b"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_5.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4d2109f58e05d361e7a0e5ff6169fc58&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/4d2109f58e05d361e7a0e5ff6169fc58"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_6.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=466062ad3402869b3fed72652ecaea76&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/63d5e31f2052aace22eb2b448488f462"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_7.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=dd78d8a34738054369705f879e9c4b4b&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/4d2109f58e05d361e7a0e5ff6169fc58"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_6.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=466062ad3402869b3fed72652ecaea76&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/63d5e31f2052aace22eb2b448488f462"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_7.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=dd78d8a34738054369705f879e9c4b4b&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/466062ad3402869b3fed72652ecaea76"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_8.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=1567a80b4d198d884be028994c0b35b2&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/dd78d8a34738054369705f879e9c4b4b"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_9.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4ec2181490f547e767f4c599791c42e3&algori
complete]
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/466062ad3402869b3fed72652ecaea76"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_8.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=1567a80b4d198d884be028994c0b35b2&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/dd78d8a34738054369705f879e9c4b4b"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_atn_9.bin
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4ec2181490f547e767f4c599791c42e3&algorithm=MD5"
-- [download 25% complete]
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-thm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/1567a80b4d198d884be028994c0b35b2"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_PET.root
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=9c0989256d3b6e9b213359cd4a3b6daa&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/4ec2181490f547e767f4c599791c42e3"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_Voxel_Phantom.root
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=a44e7bc7c3f2690a9e94e4ef4c5d3f1a&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/1567a80b4d198d884be028994c0b35b2"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_PET.root
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=9c0989256d3b6e9b213359cd4a3b6daa&algorithm=MD5"
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-- Downloaded object:
"/usr/local/gate_v7.1-build/ExternalData/Objects/MD5/4ec2181490f547e767f4c599791c42e3"
[ 24%] Generating
/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_Voxel_Phantom.root
-- Fetching
"http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=a44e7bc7c3f2690a9e94e4ef4c5d3f1a&algorithm=MD5"
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CMake Error at
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:717 (message):
Object MD5=9c0989256d3b6e9b213359cd4a3b6daa not found at:
http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=9c0989256d3b6e9b213359cd4a3b6daa&algorithm=MD5 ("Timeout was
reached")
Call Stack (most recent call first):
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:739
(_ExternalData_download_object)
make[2]: ***
[/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_PET.root.md5-stamp]
Error 1
make[2]: *** Waiting for unfinished jobs....
-- [download 37% complete]
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-- [download 40% complete]
CMake Error at
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:717 (message):
Object MD5=a44e7bc7c3f2690a9e94e4ef4c5d3f1a not found at:
http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=a44e7bc7c3f2690a9e94e4ef4c5d3f1a&algorithm=MD5 ("Timeout was
reached")
Call Stack (most recent call first):
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:739
(_ExternalData_download_object)
make[2]: ***
[/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_Voxel_Phantom.root.md5-stamp] Error
1
make[1]: *** [CMakeFiles/GateExampleData.dir/all] Error 2
make: *** [all] Error 2
root at machintosh$
Your help would be appreciated.
Many thanks in advance,
Pete
Quoting Mojca Miklavec <mojca.miklavec.lists at gmail.com>:
> On Sun, Sep 20, 2015 at 7:15 PM, pzw <pzw at ns.ph.liv.ac.uk> wrote:
>> Dear GATE Experts,
>>
>> I’m trying to install gate v7.1 on my macbook pro running macOSX10.10. I
>> managed to successfully install this software before, however, I recently
>> needed to make changes to activate some optional settings. Therefore, I
>> recompiled gate with fag changes from OFF to ON for a few settings. However,
>> the compilation failed. I then tried to restore to the original basic Gate
>> installation using the commands shown below:
>>
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
>> -DGATE_DOWNLOAD_BENCHMARKS_DATA=ON /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
>> -DGATE_DOWNLOAD_EXAMPLES_DATA=ON /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
>> -DGATE_USE_ECAT7=OFF /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_LMF=OFF
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_OPTICAL=ON
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_GPU=OFF
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_GEANT4_UIVIS=ON
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1
>> -DGEANT4_USE_SYSTEM_CLHEP=OFF /usr/local/gate_v7.1
>>
>>> make -j4
>>> make install
>>
>>
>> However, the installation keeps failing at CMAKE stage. Can someone please
>> let me know what it is that I’m not doing correctly? I desperately need to
>> get this problem sorted out.
>>
>> Your help will be very much complete]
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CMake Error at
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:717 (message):
Object MD5=9c0989256d3b6e9b213359cd4a3b6daa not found at:
http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=9c0989256d3b6e9b213359cd4a3b6daa&algorithm=MD5 ("Timeout was
reached")
Call Stack (most recent call first):
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:739
(_ExternalData_download_object)
make[2]: ***
[/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_PET.root.md5-stamp]
Error 1
make[2]: *** Waiting for unfinished jobs....
-- [download 37% complete]
-- [download 38% complete]
-- [download 39% complete]
-- [download 40% complete]
CMake Error at
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:717 (message):
Object MD5=a44e7bc7c3f2690a9e94e4ef4c5d3f1a not found at:
http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=a44e7bc7c3f2690a9e94e4ef4c5d3f1a&algorithm=MD5 ("Timeout was
reached")
Call Stack (most recent call first):
/usr/local/gate_v7.1/cmake-modules/ExternalData.cmake:739
(_ExternalData_download_object)
make[2]: ***
[/usr/local/gate_v7.1/examples/example_ROOT_Analyse/data_Voxel_Phantom.root.md5-stamp] Error
1
make[1]: *** [CMakeFiles/GateExampleData.dir/all] Error 2
make: *** [all] Error 2
root at machintosh$
Your help would be appreciated.
Many thanks in advance,
Pete
Quoting Mojca Miklavec <mojca.miklavec.lists at gmail.com>:
> On Sun, Sep 20, 2015 at 7:15 PM, pzw <pzw at ns.ph.liv.ac.uk> wrote:
>> Dear GATE Experts,
>>
>> I’m trying to install gate v7.1 on my macbook pro running macOSX10.10. I
>> managed to successfully install this software before, however, I recently
>> needed to make changes to activate some optional settings. Therefore, I
>> recompiled gate with fag changes from OFF to ON for a few settings. However,
>> the compilation failed. I then tried to restore to the original basic Gate
>> installation using the commands shown below:
>>
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
>> -DGATE_DOWNLOAD_BENCHMARKS_DATA=ON /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
>> -DGATE_DOWNLOAD_EXAMPLES_DATA=ON /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install
>> -DGATE_USE_ECAT7=OFF /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_LMF=OFF
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_OPTICAL=ON
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_GPU=OFF
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1 -DGATE_USE_GEANT4_UIVIS=ON
>> /usr/local/gate_v7.1
>> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1
>> -DGEANT4_USE_SYSTEM_CLHEP=OFF /usr/local/gate_v7.1
>>
>>> make -j4
>>> make install
>>
>>
>> However, the installation keeps failing at CMAKE stage. Can someone please
>> let me know what it is that I’m not doing correctly? I desperately need to
>> get this problem sorted out.
>>
>> Your help will be very much appreciated.
>
> We won't be able to help you unless you provide the output / error
> reports, but I don't quite understand how exactly you call cmake. I
> would suggest you to try running
> ccmake ../path/to/sources
> and then set everything there. You 20appreciated.
>
> We won't be able to help you unless you provide the output / error
> reports, but I don't quite understand how exactly you call cmake. I
> would suggest you to try running
> ccmake ../path/to/sources
> and then set everything there. You can call cmake directly, but then
> you only need to call it once, not zillion times with different
> options each time. The above sequence of commands seems a bit weird.
> For example you could try to call it like this:
>
> cd /usr/local/gate_v7.1-build
> cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gate_v7.1-install \
> -DGATE_DOWNLOAD_BENCHMARKS_DATA=ON \
> -DGATE_DOWNLOAD_EXAMPLES_DATA=ON \
> -DGATE_USE_ECAT7=OFF \
> -DGATE_USE_LMF=OFF \
> -DGATE_USE_OPTICAL=ON \
> -DGATE_USE_GPU=OFF \
> -DGATE_USE_GEANT4_UIVIS=ON \
> -DGEANT4_USE_SYSTEM_CLHEP=OFF \
> /usr/local/gate_v7.1
> make -j4
> make install
>
> But you need to make sure to compile Geant4 with the same setting of
> GEANT4_USE_SYSTEM_CLHEP=OFF and you need to make sure that Gate can
> find both ROOT and Geant4.
>
> My suggestion would be to call "ccmake" instead of cmake with the same
> settings and then visually inspect whether everything is as expected.
>
> Mojca
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