Hello
I'm running ubuntu 20.04.
I followed the instruction on your
web site.
But when I get to the step:
rPkgsInstall -pkgs ALL
There were many error messages.
The output to
afni_system_check.py -check_all
is:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.4.0-48-generic
version: #52-Ubuntu SMP Thu Sep 10 10:58:49 UTC 2020
distribution: Ubuntu 20.04 focal
number of CPUs: 18
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/cslaw/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 2 2020
: AFNI_20.3.00 'Vespasian'
AFNI_version.txt : AFNI_20.3.00, linux_ubuntu_16_64, Oct 02 2020
which python : /usr/bin/python
python version : 2.7.18rc1
which R : /usr/bin/R
R version : R version 4.0.2 (2020-06-22) -- "Taking Off Again"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/cslaw/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)
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 : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: brms!
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
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/cslaw/sct_4.3/bin:/home/cslaw/sct_4.3/bin:/home/cslaw/sct_4.3/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cslaw/abin:/home/cslaw/abin:/home/cslaw/abin
PYTHONPATH =
R_LIBS = /home/cslaw/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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/cslaw/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.2ubuntu0.1 (amd64)
have Ubuntu system: Ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 2 2020
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
Could you please help?
Christine
