-check_all problems

Hi I have installed afni in ubuntu 18 and the -check_all script is giving me some errors:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.15.0-34-generic
version: #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018
distribution: debian buster/sid
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/vicente/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 12 2018
: AFNI_18.2.16
AFNI_version.txt : AFNI_18.2.16, linux_ubuntu_16_64, Sep 12 2018
which python : /home/vicente/anaconda3/bin/python
python version : 2.7.15
which R : /usr/bin/R
R version : R version 3.4.4 (2018-03-15) – “Someone to Lean On”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/vicente/abin/afni)
R : 1 (/usr/bin/R)
python : 2
python2 : 2
python3 : 1 (/usr/bin/python3.6)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: cannot open shared object file: No such file or directory : success
3dAllineate : success
3dRSFC: error while loading shared libraries: cannot open shared object file: No such file or directory
SurfMesh : success
3dClustSim : 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 /home/vicente/anaconda3/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/antsbin/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/home/vicente/anaconda3/bin:/usr/local/fsl/bin:/home/vicente/bin:/home/vicente/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/MATLAB/R2018a/bin/:/home/vicente/bin:/home/vicente/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/vicente/abin

R_LIBS = /home/vicente/R


------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/vicente/abin

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.3ubuntu0.1 (amd64)

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • AFNI programs show FAILURE
  • insufficient data for AFNI bootcamp
    Do you know how could i solve the AFNI programs falilure?


The problem is that GSL libraries are not being found.

It looks also like you have an odd version/flavor of Linux? It looks like Ubuntu, but is “buster” (debian “testing” level), and so not a stable release. What is the output of:

lsb_release -a

And/or can you please describe more about the OS you have installed to use?

And to check for GSL lib files that might just have a different number, what is the output of:

find /usr/lib -name "libgsl*"