[Gate-users] Problems with installing Gate_v7.1

David Boersma david.boersma at physics.uu.se
Mon Dec 19 15:11:07 CET 2016


Hi Elnur,

Not using the latest version is often a good strategy to get a mature, 
bug-fixed version of a product. But that only works with releases that 
are maintained and which get bugfix-releases over time. That would be 
nice but it requires more manpower than we have available in the GATE 
collaboration. When we find a bug, then we only fix it in the 
development version on github, and only the next release will contain 
the bugfix.

Maybe we will some day change our policy, when we get more people 
helping out with development & maintenance, so that bugfixes can be 
backported. The release of 7.1 would be called 7.1.0 instead. And if 
during development of new features for for 7.2, 7.3 etc we find some bug 
that also affects 7.1, then we would fix it also in the 7.1 code and 
make a "bugfix release" of 7.1, call it 7.1.1, 7.1.2, etc. The higher 
the last number, the more stable.

But that is not how we work now. Bugfixes are only in the newest 
version, so if that was your motivation, then you'd better use the 
latest release.

You should never do "unset PATH". I am sorry that I was unclear about 
that. The PATH variable contains the list of directories where 
executable programs should be found corresponding to the commands that 
you type in the shell. If you "unset PATH" then it is empty, undefined, 
so the shell cannot find any commands (except the "builtin" shell 
commands, such as "export" and "source" and a few others).

You did eventually the right thing, namely remove the line from .bashrc 
that adds matlab to your PATH. Unfortunately you still get that weird 
linking error. (It is really a silly error, because as far as I know we 
are not using any libNet.so or SSL functionality at all in Gate.) It 
could be due to inconsistent cmake/ccmake installs, or (more likely) a 
faulty ROOT install, or something else entirely.

How did you install cmake and ccmake? Did you compile them from source 
or did you use a package manager? When I built cmake from source, the 
"make install" step also installed a corresponding ccmake version (this 
requires the "devel" package the "curses" or "ncurses" library to be on 
my system), so I did not install ccmake separately.

How did you install ROOT? A binary tarball, a source tarball (compile 
from source), or with a package manager? If from a binary tarball then 
maybe you just need to "sudo apt-get install libssl-dev" (this should 
install libssl.so on your system) and try again. (With the other two 
options you should have already gotten into trouble when 
building/installing ROOT, way before installing Gate.) If that does not 
help, could you check if this command mentions any ssl linking:

root-config --libs

HTH,
David B.


Den 19/12/2016 kl. 13:40, skrev Elnur Sadihov:
> I don't understand what happened after the command 'unset PATH', but I
> just closed terminal and opened it again - basic commands work again.
> Below there are additional lines with 'export' and 'source', which are
> written in my .bashrc:
>
> export PATH=$PATH:/usr/local/MATLAB/R2014b/bin/glnxa64
>
> export LD_PRELOAD='/usr/$LIB/libstdc++.so.6'
> export DISPLAY=:0
>
> export PATH=$PATH:/home/elnur/Programs/2.2.0.4-install/bin
> export PATH=$PATH:/home/elnur/Programs/2.2.0.4-install/include
> export
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/elnur/Programs/2.2.0.4-install/lib
>
> source /home/elnur/Programs/root_v5.34/bin/thisroot.sh
> source /home/elnur/Programs/geant4.10.01.p03-install/bin/geant4.sh
>
> export
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/elnur/Programs/lmf_v3.0/lib/Linux-g++
>
> #export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu
>
> I run 'printenv | grep -i matlab':
>
> elnur at elnur-System-Product-Name:~$ printenv | grep -i matlab
> PATH=/home/elnur/Programs/geant4.10.01.p03-install/bin:/home/elnur/Programs/root_v5.34/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/elnur/Programs/2.2.0.4-install/bin:/home/elnur/Programs/2.2.0.4-install/include:/usr/local/MATLAB/R2014b/bin/glnxa64
>
> Now I commented the line 'export
> PATH=$PATH:/usr/local/MATLAB/R2014b/bin/glnxa64' in .bashrc.
> After reopening terminal the command 'printenv | grep -i matlab' doesn't
> give anything, as it has to be.
>
> I run 'ccmake ../gate_v7.1' and this time I turned off options 'Download
> benchmarks data' and 'Download examples data'. Then I run 'make -j4' and
> again got the same error. Below there is a log:
>
> ----------------------------------------------------------------------------------------------------------------------------------
> elnur at elnur-System-Product-Name:~/Programs/gate_v7.1-build$ make -j4
> Scanning dependencies of target itkzlib
> Scanning dependencies of target MetaIO
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> [ 90%] Building CXX object
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> Building CXX object CMakeFiles/Gate.dir/source/general/src/GateGPUIO.cc.o
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> [ 99%] Building CXX object
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> [ 99%] [ 99%] Building CXX object
> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/SymMatrix.cc.o
> Building CXX object
> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/Vector.cc.o
> [ 99%] Building CXX object
> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/DiagMatrix.cc.o
> [ 99%] Building CXX object
> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/SymMatrixInvert.cc.o
> [ 99%] Building CXX object
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> [ 99%] Building CXX object
> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/GenMatrix.cc.o
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> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/MatrixInvert.cc.o
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> [100%] Building CXX object
> CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/RandomObjects/RandMultiGauss.cc.o
> Linking CXX executable Gate
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_CTX_free at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_CTX_use_certificate_chain_file at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_get_error at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_CTX_use_PrivateKey_file at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `EVP_sha1 at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_read at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_set_quiet_shutdown at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSLv23_method at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_CTX_new at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_peek at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_new at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `HMAC at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_write at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_CTX_load_verify_locations at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_free at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_set_fd at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_connect at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_library_init at OPENSSL_1.0.0'
> /home/elnur/Programs/root_v5.34/lib/libNet.so: undefined reference to
> `SSL_shutdown at OPENSSL_1.0.0'
> collect2: error: ld returned 1 exit status
> make[2]: *** [Gate] Error 1
> make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
> make: *** [all] Error 2
>
> ------------------------------------------------------------------------------------------------------------------------------------------------
>
> Best regards,
> Elnur
>
> 2016-12-19 13:40 GMT+03:00 David Boersma <david.boersma at physics.uu.se
> <mailto:david.boersma at physics.uu.se>>:
>
>     Hi Elnur,
>
>     Just for my curiosity, why do you prefer the 7.1 release over the
>     latest 7.2 release?
>
>     Thanks for explicitly listing all relevant versions and a full build
>     log! I have some random hints and remarks that may hopefully be some
>     first steps in solving your problem.
>
>     * cmake/ccmake versions are different, that is weird. The ccmake
>     program is just an interactive UI wrapper around cmake and it should
>     report the same version. If not, then something may be wrong funny
>     with your shell environment, in particular the PATH variable. How
>     did you determine these versions? Is that the package version
>     number, or the output of "cmake --version" and "ccmake --version"?
>     The latter is the most important.
>
>     * The cmake warnings mention MATLAB directories. You do not need
>     MATLAB for building GATE, so I think you can silence these warnings
>     by removing /usr/local/MATLAB/R2014b/bin from your PATH and maybe
>     other variables. If you are on a system where you manage your shell
>     environment with the "module" command, then something like "module
>     remove matlab" should help. Otherwise run something like "printenv |
>     grep -i matlab" to check which shell variables need adjustment
>     ("export VARNAME=NEWVALUE" or "unset VARNAME").
>
>     * As far as I can see, "make -j4" step results in two fatal errors
>     (out of a possible four!), one regarding a download failure and one
>     about SSL linking problems with a ROOT shared library. The first one
>     may be solved by running make one more time, or by downloading the
>     problematic test file by hand. The second one seems to indicate that
>     something might be wrong with your ROOT installation. It is also
>     possible that the MATLAB things in your environment are interfering
>     destructively with the ROOT linking, so try that first.
>
>     Hope that helps a bit,
>     David Boersma
>
>
>     Den 19/12/2016 kl. 09:00, skrev Elnur Sadihov:
>
>         Hello everyone,
>
>         I'm trying to install Gate_v7.1 on Ubuntu 14.04 LTS.
>         Installed packages:
>         cmake 3.6.1
>         ccmake 2.8.12.2
>         CLHEP 2.2.0.4
>         root 5.34
>         geant4.10.01.p03
>
>
>         I follow compilation instructions
>         http://wiki.opengatecollaboration.org/index.php/Compilation_Instructions_V7.1
>         <http://wiki.opengatecollaboration.org/index.php/Compilation_Instructions_V7.1>
>
>         After configuring Gate_v.7.1 I press 'g' to generate the compilation
>         environment. But Warning appears:
>
>          CMake Warning at CMakeLists.txt:195 (ADD_EXECUTABLE):
>            Cannot generate a safe runtime search path for target Gate
>         because
>         files in
>            some directories may conflict with libraries in implicit
>         directories:
>
>              runtime library [libQtOpenGL.so.4] in
>         /usr/lib/x86_64-linux-gnu may be
>          hidden by files in:
>                /usr/local/MATLAB/R2014b/bin/glnxa64
>              runtime library [libQtGui.so.4] in
>         /usr/lib/x86_64-linux-gnu may be
>          hidden by files in:
>                /usr/local/MATLAB/R2014b/bin/glnxa64
>              runtime library [libQtCore.so.4] in
>         /usr/lib/x86_64-linux-gnu may be
>          hidden by files in:
>                /usr/local/MATLAB/R2014b/bin/glnxa64
>
>            Some of these libraries may not be found correctly.
>
>         Then I run command 'make -j4' and it finally gives the error. Below
>         there is a log:
>
>         Scanning dependencies of target itkzlib
>         Scanning dependencies of target GateBenchmarkData
>         Scanning dependencies of target GateExampleData
>         Scanning dependencies of target MetaIO
>         [  0%] Generating
>         /home/elnur/Programs/gate_v7.1/benchmarks/benchPET/benchPET.pdf
>         [  0%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/TAC_Example.png
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=0a63785ee8d79c3031523f20c0b7c4cc&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=0a63785ee8d79c3031523f20c0b7c4cc&algorithm=MD5>"
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=35a91d8d91d208cf300cfe02c41f0899&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=35a91d8d91d208cf300cfe02c41f0899&algorithm=MD5>"
>         [  0%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/adler32.o
>         [  1%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaUtils.o
>         [  1%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/compress.o
>         [  1%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/crc32.o
>         -- [download 100% complete]
>         -- [download 100% complete]
>         [  2%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/deflate.o
>         [  2%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/gzio.o
>         -- [download 0% complete]
>         -- [download 52% complete]
>         -- [download 0% complete]
>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/35a91d8d91d208cf300cfe02c41f0899"
>         [  2%] Generating
>         /home/elnur/Programs/gate_v7.1/benchmarks/benchPET/benchmarkPET-GATE-Reference.gif
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d84562b93ae060451f5b5554f7dda606&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d84562b93ae060451f5b5554f7dda606&algorithm=MD5>"
>         [  2%] -- [download 100% complete]
>         Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/inffast.o
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/0a63785ee8d79c3031523f20c0b7c4cc"
>         [  2%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_1.bin
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=730355e81d3c478e92b09f3764f126c4&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=730355e81d3c478e92b09f3764f126c4&algorithm=MD5>"
>         [  2%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/inflate.o
>         [  2%] -- [download 100% complete]
>         Building CXX object itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaArrow.o
>         -- [download 100% complete]
>         [  2%] [  2%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaBlob.o
>         Building C object itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/inftrees.o
>         [  2%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/trees.o
>         -- [download 0% complete]
>         [  2%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaCommand.o
>         -- [download 0% complete]
>         [  2%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/uncompr.o
>         [  3%] Building C object
>         itk-mhd/itkzlib/CMakeFiles/itkzlib.dir/zutil.o
>         -- [download 60% complete]
>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/d84562b93ae060451f5b5554f7dda606"
>         Linking C static library libitkzlib.a
>         [  3%] Generating
>         /home/elnur/Programs/gate_v7.1/benchmarks/benchPET/benchmarkPET-fGATE.gif
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4844097d2a516347c6a4f39ece654125&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4844097d2a516347c6a4f39ece654125&algorithm=MD5>"
>         [  3%] Built target itkzlib
>         [  3%] Generating
>         /home/elnur/Programs/gate_v7.1/benchmarks/benchPET/benchmarkPET.gif
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=942c49a51c32068549574a985d242f42&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=942c49a51c32068549574a985d242f42&algorithm=MD5>"
>         -- [download 1% complete]
>         -- [download 100% complete]
>         -- [download 100% complete]
>         -- [download 2% complete]
>         -- [download 3% complete]
>         -- [download 0% complete]
>         -- [download 0% complete]
>         -- [download 74% complete]
>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/4844097d2a516347c6a4f39ece654125"
>         [  3%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=996b4c4b5b5e12e3e4073aab2804e4c6&algorithm=MD5>"
>         -- [download 77% complete]
>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/942c49a51c32068549574a985d242f42"
>         [  3%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaContour.o
>         -- [download 4% complete]
>         -- [download 100% complete]
>         [  3%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaDTITube.o
>         [  3%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaEllipse.o
>         -- [download 5% complete]
>         [  3%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_10.bin
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=494a61c7968269d98f8ccf35bfb0dfdd&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=494a61c7968269d98f8ccf35bfb0dfdd&algorithm=MD5>"
>         [  4%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaGroup.o
>         -- [download 0% complete]
>         -- [download 6% complete]
>         -- [download 50% complete]
>         -- [download 100% complete]
>         [  4%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaGaussian.o
>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/996b4c4b5b5e12e3e4073aab2804e4c6"
>         [  4%] Generating
>         /home/elnur/Programs/gate_v7.1/benchmarks/benchSPECT/resultsSPECTfgate.gif
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=031974ea6bbf21a4cbfd7737d4f67d1c&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=031974ea6bbf21a4cbfd7737d4f67d1c&algorithm=MD5>"
>         -- [download 7% complete]
>         [  4%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaImage.o
>         -- [download 100% complete]
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>         -- [download 8% complete]
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>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/031974ea6bbf21a4cbfd7737d4f67d1c"
>         [  5%] Generating
>         /home/elnur/Programs/gate_v7.1/benchmarks/benchSPECT/benchSPECTresult.pdf
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=8d2397bec547c7e89ac3d1bf3483f428&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=8d2397bec547c7e89ac3d1bf3483f428&algorithm=MD5>"
>         -- [download 3% complete]
>         -- [download 100% complete]
>         -- [download 10% complete]
>         -- [download 4% complete]
>         [  5%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaImageUtils.o
>         -- [download 11% complete]
>         [  5%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaLandmark.o
>         -- [download 5% complete]
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>         -- [download 44% complete]
>         [  5%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaLine.o
>         -- [download 12% complete]
>         -- [download 89% complete]
>         -- [download 100% complete]
>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/8d2397bec547c7e89ac3d1bf3483f428"
>         [  5%] Built target GateBenchmarkData
>         [  5%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_2.bin
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4373ca3fd7b365b6a327b4f443abac50&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4373ca3fd7b365b6a327b4f443abac50&algorithm=MD5>"
>         -- [download 6% complete]
>         [  5%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaMesh.o
>         -- [download 13% complete]
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>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaObject.o
>         -- [download 1% complete]
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>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaOutput.o
>         -- [download 5% complete]
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>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaScene.o
>         -- [download 14% complete]
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>         -- [download 16% complete]
>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaSurface.o
>         -- [download 17% complete]
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>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaTube.o
>         -- [download 21% complete]
>         -- [download 20% complete]
>         -- [download 22% complete]
>         -- [download 14% complete]
>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaVesselTube.o
>         -- [download 23% complete]
>         -- [download 24% complete]
>         -- [download 25% complete]
>         -- [download 21% complete]
>         [  6%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaTransform.o
>         -- [download 26% complete]
>         -- [download 15% complete]
>         [  7%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaTubeGraph.o
>         -- [download 27% complete]
>         -- [download 22% complete]
>         -- [download 28% complete]
>         [  7%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaForm.o
>         -- [download 16% complete]
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>         -- [download 29% complete]
>         -- [download 30% complete]
>         [  7%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaArray.o
>         -- [download 24% complete]
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>         [  7%] Building CXX object
>         itk-mhd/MetaIO/CMakeFiles/MetaIO.dir/metaFEMObject.o
>         -- [download 18% complete]
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>         -- [download 38% complete]
>         Linking CXX static library libMetaIO.a
>         -- [download 21% complete]
>         [  7%] Built target MetaIO
>         [  7%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_3.bin
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=ef43ddc95ae120b5d05eb09cb9371e2a&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=ef43ddc95ae120b5d05eb09cb9371e2a&algorithm=MD5>"
>         -- [download 39% complete]
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/4373ca3fd7b365b6a327b4f443abac50"
>         [  7%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_4.bin
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=6e1dd112c3ff48913d55e5754ccb0510&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=6e1dd112c3ff48913d55e5754ccb0510&algorithm=MD5>"
>         -- [download 66% complete]
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/ef43ddc95ae120b5d05eb09cb9371e2a"
>         [  7%] Generating
>         /home/elnur/Programs/gate_v7.1/examples/example_TimeActivityCurve/data/NCAT_act_5.bin
>         -- [download 75% complete]
>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d746dd3bf5942a29c470aefff9280236&algorithm=MD5
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d746dd3bf5942a29c470aefff9280236&algorithm=MD5>"
>         -- [download 76% complete]
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/6e1dd112c3ff48913d55e5754ccb0510"
>         [  8%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=d5a777f0731cae74ec51e94eff676385&algorithm=MD5>"
>         -- [download 52% complete]
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>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/730355e81d3c478e92b09f3764f126c4"
>         [  8%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=af5b5dbef7a9aa37d1b554d2fab7bdd0&algorithm=MD5>"
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>         -- Fetching
>         "http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=5ca0fd75b6c76fb7cc18e782dfc14576&algorithm=MD5
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelInterfileReaderMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSPECTHeadSystem.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelArrayStore.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxelOutput.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTwistedTrdMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateRegularParameterizedMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateBoxReplica.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateParameterisedCollimator.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateFictitiousVoxelMapParameterizedMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateRotationMoveMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSystemListMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVoxelBoxParameterized.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVGeometryVoxelReaderMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGenericMoveMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTorus.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateEcatAccelSystem.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTwistedTrap.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateEllipso.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSurfaceListMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateDMapoperators.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateObjectMoveMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateOrbitingMoveMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSystemListManager.cc.o
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/af5b5dbef7a9aa37d1b554d2fab7bdd0"
>         [ 20%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=ee84d77dc3ebd445548c5b0950c6558e&algorithm=MD5>"
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>         CMakeFiles/Gate.dir/source/geometry/src/GateOscTranslationMove.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVolumePlacementMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateAngularRepeater.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVolumePlacement.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVolumeMessenger.cc.o
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/ee84d77dc3ebd445548c5b0950c6558e"
>         [ 25%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=6277cb5a4c6e724161c8cf3595f885c1&algorithm=MD5>"
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVGeometryVoxelTranslator.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTrpd.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateMaterialDatabase.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateDMapVol.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVImageVolumeMessenger.cc.o
>         -- [download 84% complete]
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>         [ 26%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GatePolyhedra.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedSubVolumeMessenger.cc.o
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>         [ 26%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateSurfaceList.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTwistedTubs.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateMDBFile.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVGeometryVoxelStoreMessenger.cc.o
>         -- [download 12% complete]
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>         [ 27%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateTwistedBox.cc.o
>         -- [download 14% complete]
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxel.cc.o
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/a9cd0e61d8f9f0a033b5ebb9054aebe1"
>         [ 27%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=0ecbce48f40182180e886377904c8a5b&algorithm=MD5>"
>         -- [download 15% complete]
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxelParameterizedMessenger.cc.o
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>         [ 27%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateMultiSensitiveDetector.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxelOutputMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVoxelBoxParameterizedMessenger.cc.o
>         -- [download 5% complete]
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>         [ 27%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateCPETSystem.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSurface.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCTScannerSystem.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GatePara.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateFictitiousVoxelMapParameterized.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateVoxelBoxParameterization.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateFictitiousVoxelMapParam.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedVolume.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSphereRepeater.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelTabulatedTranslatorMessenger.cc.o
>         -- [download 60% complete]
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>         CMakeFiles/Gate.dir/source/geometry/src/GateSystemComponentMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateWedge.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateBoxReplicaPlacement.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCylinderMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateObjectRepeaterMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateBoxMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateCone.cc.o
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>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/5ca0fd75b6c76fb7cc18e782dfc14576"
>         [ 31%] -- [download 87% complete]
>         Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=044a158a2617c05ed8fb657a27ed23ff&algorithm=MD5>"
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>         CMakeFiles/Gate.dir/source/geometry/src/GateOutputVolumeID.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateObjectRepeaterListMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateFakeDetectorConstruction.cc.o
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>         [ 31%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateTrapMessenger.cc.o
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/0ecbce48f40182180e886377904c8a5b"
>         [ 31%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=63d5e31f2052aace22eb2b448488f462&algorithm=MD5>"
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGeneralTrpdMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateImageRegionalizedVolumeMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateBox.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateRotationMove.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelRangeTranslatorMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTorusMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateGenericTrapMessenger.cc.o
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>         CMakeFiles/Gate.dir/source/geometry/src/GateImageNestedParametrisedVolume.cc.o
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>         -- Downloaded object:
>         "/home/elnur/Programs/gate_v7.1-build/ExternalData/Objects/MD5/044a158a2617c05ed8fb657a27ed23ff"
>         [ 34%] Generating
>         /home/elnur/Programs/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
>         <http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=4d2109f58e05d361e7a0e5ff6169fc58&algorithm=MD5>"
>         -- [download 100% complete]
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>         [ 34%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateFictitiousVoxelMap.cc.o
>         -- [download 20% complete]
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>         CMakeFiles/Gate.dir/source/geometry/src/GateRegularParameterization.cc.o
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>         [ 34%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateVVolume.cc.o
>         -- [download 22% complete]
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>         [ 34%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateRegularParameterized.cc.o
>         -- [download 16% complete]
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>         [ 35%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateArrayRepeaterMessenger.cc.o
>         -- [download 25% complete]
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>         [ 35%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateTetraMessenger.cc.o
>         -- [download 69% complete]
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>         CMakeFiles/Gate.dir/source/geometry/src/GateTrap.cc.o
>         -- [download 33% complete]
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>         [ 35%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateTranslationMoveMessenger.cc.o
>         -- [download 42% complete]
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>         [ 35%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateLinearRepeater.cc.o
>         -- [download 46% complete]
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>         [ 35%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateHexagone.cc.o
>         -- [download 50% complete]
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>         [ 35%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateBoxComponent.cc.o
>         -- [download 32% complete]
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>         [ 36%] Building CXX object
>         CMakeFiles/Gate.dir/source/geometry/src/GateVSystem.cc.o
>         -- [download 62% complete]
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