afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.15.0-47-generic
version: #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022
distribution: Ubuntu 22.04.1 LTS
number of CPUs: 32
apparent login shell: sh (current shell is bash)
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/wyue/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 18 2022
: AFNI_22.2.12 ‘Marcus Aurelius’
AFNI_version.txt : AFNI_22.2.12, linux_ubuntu_16_64, Sep 18 2022
which python : /home/wyue/miniconda3/envs/py39_afni_tiny/bin/python
python version : 3.9.13
which R : /usr/bin/R
R version : R version 4.2.1 (2022-06-23) – “Funny-Looking Kid”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/wyue/abin/afni)
R : 1 (/usr/bin/R)
python : 3
/home/wyue/miniconda3/envs/py39_afni_tiny/bin/python3.9
/home/wyue/miniconda3/bin/python3.9
/usr/bin/python3.10
python2 : 0
python3 : 3
/home/wyue/miniconda3/envs/py39_afni_tiny/bin/python3.9
/home/wyue/miniconda3/bin/python3.9
/usr/bin/python3.10
** have python3 but not python2
testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.19: 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.19: cannot open shared object file: No such file or directory
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages…
rPkgsInstall -pkgs ALL -check : success
R RHOME : /usr/lib/R
checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /home/wyue/miniconda3/envs/py39_afni_tiny/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.5.2
-------------------------------- env vars --------------------------------
PATH = /home/wyue/miniconda3/envs/py39_afni_tiny/bin:/home/wyue/miniconda3/bin:/home/wyue/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/home/wyue/abin:/home/wyue/abin:/home/wyue/abin:/home/wyue/abin:/home/wyue/abin
PYTHONPATH =
R_LIBS = /home/wyue/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (937292M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/wyue/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.7 (amd64)
have Ubuntu system: Ubuntu 22.04.1 LTS
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Sep 18 2022
========================= summary, please fix: =========================
- just be aware: login shell ‘sh’, but our code examples use ‘tcsh’
- AFNI programs show FAILURE
I met this problem