[Gate-users] Building GATE v9.1 on Ubuntu 20.04

[Schneider Tim]

Dear Khalid, dear David,

Thank you for your answers! I couldn’t find GATE in the Ubuntu Software Centre but that is likely a problem with the proxies of our institute which we weren’t really able to fix yet.

Concerning the versions of GATE and Geant4, sorry for the confusion. Indeed, we tried first GATE 9.1 together with Geant4 10.7.3 and then GATE 9.0 together with Geant4 10.6.3. We get the same error in both cases.

One thing to note is that we forced the C++ standard to version 17 when building Geant4, like this: -DGEANT4_BUILD_CXXSTD=17. I didn’t have to do this for a previous GATE 9.0 installation, also on an Ubuntu 20.04 machine. But this time, without specifying the C++ standard, we get another error trying to build GATE which refers to some root files actually…

I will try again installing GATE with some slightly different root versions. But any other tips and hints are very welcome!

Thanks,
Tim


Am 16/02/2022 um 10:49 schrieb David Boersma <david.boersma at gmail.com<mailto:david.boersma at gmail.com>>:

Hi Tim,

Just an observation from the sidelines (these days I can spend much less time on GATE than I did in the past): the subject of your mail is about version 9.1, but in the build output messages I see source paths with version 9.0 in them. Can you clarify which version you are really trying to build? That can be important for whoever is going to try to reproduce this error.

In principle the newest release is preferred. In case the above errors were really obtained with 9.0 source code, could you then try to upgrade to 9.1? Moreover, the next release is also just around the corner, this might also solve your problem (but maybe introduce a host of new ones :o) ).

Good luck!
David



On Tue, Feb 15, 2022 at 5:36 PM Schneider Tim <Tim.Schneider at curie.fr<mailto:Tim.Schneider at curie.fr>> wrote:
Dear Gaters,

We are trying to install GATE v9.1 on an Ubuntu 20.04 machine and we’re having some quite strange errors during the make step:

/home/angela/geant4.10.06.p03-install/include/Geant4/CLHEP/Geometry/BasicVector3D.h:468:3: note: candidate: ‘std::ostream& std::operator<<(std::ostream&, int)’
  468 |   operator<<(std::ostream &, const BasicVector3D<double> &);
      |   ^~~~~~~~
/home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:307<http://gatearftablemgr.cc:307>:56: error: invalid use of incomplete type ‘class GateARFTable’
  307 |     GateARFTable* arfTable = new GateARFTable(tableName);
      |                                                        ^
In file included from /home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:14<http://gatearftablemgr.cc:14>:
/home/angela/Gate-9.0/source/arf/include/GateARFTableMgr.hh:14:7: note: forward declaration of ‘class GateARFTable’
   14 | class GateARFTable;
      |       ^~~~~~~~~~~~
/home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:308<http://gatearftablemgr.cc:308>:13: error: invalid use of incomplete type ‘class GateARFTable’
  308 |     arfTable->Initialize(tableBuffer[4], tableBuffer[5]);
      |             ^~
In file included from /home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:14<http://gatearftablemgr.cc:14>:
/home/angela/Gate-9.0/source/arf/include/GateARFTableMgr.hh:14:7: note: forward declaration of ‘class GateARFTable’
   14 | class GateARFTable;
      |       ^~~~~~~~~~~~
/home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:309<http://gatearftablemgr.cc:309>:13: error: invalid use of incomplete type ‘class GateARFTable’
  309 |     arfTable->SetEnergyReso(tableBuffer[2]);
      |             ^~
In file included from /home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:14<http://gatearftablemgr.cc:14>:
/home/angela/Gate-9.0/source/arf/include/GateARFTableMgr.hh:14:7: note: forward declaration of ‘class GateARFTable’
   14 | class GateARFTable;
      |       ^~~~~~~~~~~~
/home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:310<http://gatearftablemgr.cc:310>:13: error: invalid use of incomplete type ‘class GateARFTable’
  310 |     arfTable->SetERef(tableBuffer[3]);
      |             ^~
In file included from /home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:14<http://gatearftablemgr.cc:14>:
/home/angela/Gate-9.0/source/arf/include/GateARFTableMgr.hh:14:7: note: forward declaration of ‘class GateARFTable’
   14 | class GateARFTable;
      |       ^~~~~~~~~~~~
/home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:322<http://gatearftablemgr.cc:322>:13: error: invalid use of incomplete type ‘class GateARFTable’
  322 |     arfTable->FillTableFromBuffer(tableBuffer);
      |             ^~
In file included from /home/angela/Gate-9.0/source/arf/src/GateARFTableMgr.cc:14<http://gatearftablemgr.cc:14>:
/home/angela/Gate-9.0/source/arf/include/GateARFTableMgr.hh:14:7: note: forward declaration of ‘class GateARFTable’
   14 | class GateARFTable;
      |       ^~~~~~~~~~~~
make[2]: *** [CMakeFiles/GateLib.dir/build.make:128: CMakeFiles/GateLib.dir/source/arf/src/GateARFTableMgr.cc.o] Error 1
make[2]: *** [CMakeFiles/GateLib.dir/build.make:154: CMakeFiles/GateLib.dir/source/digits_hits/src/GateActions.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:290: CMakeFiles/GateLib.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

This is actually only the lost couple of lines, there are many more such errors and warnings like these before the build completely fails.

The ccmake options look like this:

 BUILD_TESTING                    OFF
 CMAKE_BACKWARDS_COMPATIBILITY    2.4
 CMAKE_BUILD_TYPE                 Release
 CMAKE_INSTALL_PREFIX             /home/angela/gate-install
 EXECUTABLE_OUTPUT_PATH
 GATE_COMPILE_GATEDIGIT           OFF
 GATE_COMPILE_WITH_NATIVE         OFF
 GATE_USE_DAVIS                   OFF
 GATE_USE_ECAT7                   OFF
 GATE_USE_GEANT4_UIVIS            ON
 GATE_USE_ITK                     OFF
 GATE_USE_LMF                     OFF
 GATE_USE_OPTICAL                 OFF
 GATE_USE_RTK                     OFF
 GATE_USE_SYSTEM_CLHEP            OFF
 GATE_USE_TORCH                   OFF
 GATE_USE_XRAYLIB                 OFF
 Geant4_DIR                       /home/angela/geant4.10.06.p03-install/lib/Geant4-10.6.3
 LIBRARY_OUTPUT_PATH
 PTL_DIR                          /home/angela/geant4.10.06.p03-install/lib/Geant4-10.6.3/PTL
 ROOTCINT_EXECUTABLE              /home/angela/root/bin/rootcint


There was initially another problem that seemed to originate from root and Geant4 having been compiled with different C++ standards. We rebuilt Geant4 enforcing the C++ 17 standard and root is actually the downloaded binary which seems to work fine.

Does anyone have an idea what the error during the GATE build could be and how to fix it?

Thanks a lot in advance!

Best,
Tim
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220216/8c1d23c0/attachment-0001.html>