Hi!

I updated AFNI om my ubuntu 18 machine:

Precompiled binary linux_openmp_64: Feb 14 2020 (Version AFNI_20.0.09 'Galba')

I ran

afni_system_check -check_all

And ran into some expected problems (like an R-package missing due to, I presume, new functionality). But the real problem here are these errors:

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : FAILURE
        3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : FAILURE
        3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

I.e. the problem is libgsl.so.0. It also complained about libxp6 but I could fix that (sudo -E apt-get install libxp6).

I found a post on the message board here which suggested to install the GNU Science Toolbox via

sudo -E apt-get install libgsl0ldbl

But that command tells me that

However the following packages replace it:
  libgsl23 libgslcblas0:i386 libgsl23:i386 libgslcblas0

E: Package 'libgsl0ldbl' has no installation candidate

And libgsl23 is already installed. I don't seem to have the libgsl.so.0 file. This is the content:

ls /usr/lib/x86_64-linux-gnu/libgsl*
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0  /usr/lib/x86_64-linux-gnu/libgslcblas.so.0.0.0  /usr/lib/x86_64-linux-gnu/libgsl.so.19  /usr/lib/x86_64-linux-gnu/libgsl.so.23  /usr/lib/x86_64-linux-gnu/libgsl.so.23.0.0

I exported this variable so that AFNI sees

LD_LIBRARY_PATH = /usr/lib/x86_64-linux-gnu/

And I ran according the installation guide:

sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19

But nothing seems to help. Google confuses me since all posts assume that you have the libgsl.so.0 file.

Any ideas?! Thanks!



Edited 1 time(s). Last edit at 02/18/2020 04:47AM by Robin.