Hi, I'm having trouble installing AFNI for Ubuntu 18.04. I've followed the instructions for AFNI installation on the NIH page, but I can't get past the R packages install. It looks like the dependencies for the required R packages aren't installing, but when I try to install the dependencies manually in R it says they aren't available. Any help would be much appreciated!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.0.0-31-generic
version: #33~18.04.1-Ubuntu SMP Tue Oct 1 10:20:39 UTC 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/anna/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 21 2019
: AFNI_19.3.08 'Nero'
AFNI_version.txt : AFNI_19.3.08, linux_ubuntu_16_64, Oct 21 2019
which python : /usr/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/anna/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
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: brms!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python binaries under /usr/local/bin:
/usr/local/bin/python2.7
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/anna/abin
PYTHONPATH =
R_LIBS = /home/anna/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/anna/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.12 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 21 2019
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
