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Compilation Error: Ubuntu 16.04 LTS

Posted: Fri May 04, 2018 11:18 am
by pron.a
Dear Brainvisa team,

I am trying to compile Brainvisa on a Ubuntu 16.04LTS Virtual Machine from sources using the current standard bug_fix version. I followed all the instructions to compile on this ubuntu version and I managed to do it once perfectly. However since two weeks the compilation crashes every time when it comes to a subcomponent of aimsfree (minc-header)
I put a file enclosed with the error obtained.

have a nice day


Edit: I dont manage to attach the file so I just copy past the log here I may be totally indigest sorry about that

[ 58%] Building CXX object build_files/aims-free/aimsdata/src/aimsminc/CMakeFiles/aimsminc.dir/io/
/home/meca/softs/brainvisa/source/aims/aims-free/bug_fix/aimsdata/src/aimsminc/io/ In member function ‘void aims::MincHeader::read()’:
/home/meca/softs/brainvisa/source/aims/aims-free/bug_fix/aimsdata/src/aimsminc/io/ error: ‘milog_init’ was not declared in this scope
/home/meca/softs/brainvisa/source/aims/aims-free/bug_fix/aimsdata/src/aimsminc/io/ error: ‘milog_set_verbosity’ was not declared in this scope
build_files/aims-free/aimsdata/src/aimsminc/CMakeFiles/aimsminc.dir/build.make:86: recipe for target 'build_files/aims-free/aimsdata/src/aimsminc/CMakeFiles/aimsminc.dir/io/' failed
make[2]: *** [build_files/aims-free/aimsdata/src/aimsminc/CMakeFiles/aimsminc.dir/io/] Error 1
CMakeFiles/Makefile2:32379: recipe for target 'build_files/aims-free/aimsdata/src/aimsminc/CMakeFiles/aimsminc.dir/all' failed
make[1]: *** [build_files/aims-free/aimsdata/src/aimsminc/CMakeFiles/aimsminc.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
Traceback (most recent call last):
File "/home/meca/softs/brainvisa/tmp/brainvisa-cmake/bin/bv_maker", line 1182, in process
File "/home/meca/softs/brainvisa/tmp/brainvisa-cmake/bin/bv_maker", line 3422, in build
File "/home/meca/softs/brainvisa/tmp/brainvisa-cmake/bin/bv_maker", line 229, in system
raise OSError(txt)
OSError: Command failed: 'make' '-j1'
From directory: /home/meca/softs/brainvisa/build/bug_fix

bv_maker summary:
OK step sources: /home/meca/softs/brainvisa/source, started: 2018/05/04 10:58, stopped: 2018/05/04 10:59
OK step configure: /home/meca/softs/brainvisa/build/bug_fix, started: 2018/05/04 10:59, stopped: 2018/05/04 11:02
FAILED step build: /home/meca/softs/brainvisa/build/bug_fix, started: 2018/05/04 11:02, stopped: 2018/05/04 11:57

Re: Compilation Error: Ubuntu 16.04 LTS

Posted: Mon May 07, 2018 11:53 am
by riviere
Hi Alex,
There seems to be a problem with the Minc lib configurartion: it is detected (since it tries to compile the minc module) but the headers location is not correct.
Can you try moving away the CMakeCache.txt file in the root build directory, and try again doing bv_maker configure build ?
If the problem is still here, then we will have to look deeper...

Re: Compilation Error: Ubuntu 16.04 LTS

Posted: Tue May 08, 2018 2:37 pm
by pron.a
Hello Denis,

thanks for your answer :) . I removed the CmakeCache.txt file and relaunched configure and build steps but I still had the error.
Actually, I then looked into the CmakeCache file (the one generated after the relaunch) and I found that bv_maker was using a static version of the libminc library coming with the FreeSurfer version installed on the VM. After setting back first the dynamic version of the library coming with the system the build step ended up correctly.