AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
October 25, 2019 10:06AM
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
Subject Author Posted

trouble installing R packages for Ubuntu 18.04 AFNI install

alfarmer8 October 25, 2019 10:06AM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor October 25, 2019 11:57AM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

alfarmer8 October 25, 2019 12:32PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor October 25, 2019 05:30PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

pereanez December 31, 2019 02:03PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor December 31, 2019 03:33PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 25, 2020 09:20AM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor August 25, 2020 10:10AM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 25, 2020 02:22PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor August 25, 2020 03:00PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 25, 2020 04:01PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 27, 2020 12:36PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor August 27, 2020 01:37PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 27, 2020 02:28PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor August 27, 2020 02:50PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 27, 2020 03:02PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor August 27, 2020 03:21PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 27, 2020 05:10PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

ptaylor August 27, 2020 05:22PM

Re: trouble installing R packages for Ubuntu 18.04 AFNI install

chammo20 August 28, 2020 12:17PM