AFNI installation

AFNI Message Board
1

Hi
I am trying to install AFNI on my machine following instructions provided step by step.
the output I receive when running afni_system_check.py -check_all is the following:
i biolab@rocco:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.16.0-10-amd64
version: #1 SMP Debian 3.16.81-1 (2020-01-17)
distribution: Debian GNU/Linux 8 (jessie)
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/biolab/abin/afni
afni version : Precompiled binary linux_openmp_64: Apr 16 2021
: AFNI_21.1.02 ‘Domitian’
AFNI_version.txt : AFNI_21.1.02, linux_openmp_64, Apr 16 2021
which python : /home/biolab/anaconda3/bin/python
python version : 3.8.5
which R : /usr/bin/R
R version : R version 3.1.1 (2014-07-10) – “Sock it to Me”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/biolab/abin/afni)
R : 1 (/usr/bin/R)
python : 2
/home/biolab/anaconda3/bin/python3.8
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 3
/home/biolab/anaconda3/bin/python3.8
/usr/local/bin/python3.6
/usr/bin/python3.4

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: lmerTest!
    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 -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /home/biolab/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/bin/python3.6)
/usr/local/bin/python3.6

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/home/biolab/anaconda3/bin:/home/biolab/anaconda3/condabin:/home/biolab/mrtrix3/bin:/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/mrtrix3_RC2/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/home/biolab/Downloads/workbench/bin_linux64:/home/biolab/abin:/opt/basis/lib/cmake/basis

PYTHONPATH =
R_LIBS = /home/biolab/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
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/biolab/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.0.9.8.5 for amd64 compiled on Jan 22 2019 12:32:31

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

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • missing R packages (see rPkgsInstall)[/i]
    Does this mean afni has been installed properly or something is missing?
    thanks,
    Rosella
2

Hi, Rosella-

Jumping to the bottom section, " summary, please fix:", there is one primary thing to address in the sense of “fix” (the shell note is just so you are aware):


* missing R packages (see rPkgsInstall)

Zooming up to the R package install section, indeed we see in more detail:


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!
These packages are not installed on the computer: metafor!

So, a problem with some R package dependencies.

Looking at this line in your system check:


R version : R version 3.1.1 (2014-07-10) -- "Sock it to Me"

… we get the R version number, which is too old to support these newer packages. You would have to update your R base version to be able to install the remaining dependencies. In practice, this means removing/uninstalling R completely (so no stale packages get left and cause confusion with the updated R), and then install all the AFNI-required R packages with “rPkgsInstall -pkgs ALL”, as well as any other R packages you might want.

Note that the R packages are for Gang’s group analysis programs, so you might not need those right now (perhaps down the road), so you could with some of this later, depending on what you want to analyze/look at now with AFNI.

–pt