Hello,
I am installing the AFNI program. I am able to launch the program. But when I entered the following command:
afni_system_check.py -check_all
Programs such as 3dSkullStrip and 3dRSFC show failure. I don't understand why because I have entered the folllowing command:
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0
Both libgsl.so and libgsl.so.0 are present in their respective directory.
The output from the command is shown below. Any help would be much appreciated.
Thank you!
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-42-generic
version: #62-Ubuntu SMP Fri Oct 7 23:11:45 UTC 2016
distribution: Ubuntu 16.04 xenial
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/michael/abin/afni
afni version : Precompiled binary linux_openmp_64: Oct 13 2016
AFNI_version.txt : AFNI_16.3.03, linux_openmp_64, Oct 13 2016
which python : /usr/bin/python
python version : 2.7.12
which R : /usr/bin/R
R version : R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/michael/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
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: Error 40
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: Error 40
SurfMesh : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /home/michael/bin:/home/michael/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/michael/abin:/home/michael/abin:/home/michael/abin:/home/michael/abin
PYTHONPATH =
R_LIBS = /home/michael/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH = /home/michael/abin
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/michael/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.2.12 (amd64)
have Ubuntu system: Ubuntu 16.04 xenial
============================ summary comments ============================
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
