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April 19, 2021 10:56AM
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:
(base) 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)

Does this mean afni has been installed properly or something is missing?
thanks,
Rosella



Edited 1 time(s). Last edit at 04/19/2021 11:46AM by rosella.
Subject Author Posted

AFNI installation

rosella April 19, 2021 10:56AM

Re: AFNI installation

ptaylor April 19, 2021 06:21PM



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