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  

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June 21, 2019 10:58AM
Hi, I am doing a new install on MacOS. Here is the result of the check:

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Wed Apr 24 20:50:53 PDT 2019; root:xnu-3789.73.49~1/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/greenlab/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 19 2019
: AFNI_19.1.22 'Caligula'
AFNI_version.txt : AFNI_19.1.22, macos_10.12_local, Jun 19 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) -- "Single Candle"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/greenlab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 0


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

oo Warning:
These packages are not installed on the computer: brms!


checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/greenlab/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: 29 Apr 2019 [rickr]: AFNI_pamenc command newline
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 /Users/greenlab/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.6

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'bash'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* missing R packages (see rPkgsInstall)

However, when I run: rPkgsInstall -pkgs ALL

++ Note: @ 10:56:01
This package has been installed on the computer: brms

Warning message:
package ‘brms’ is not available (for R version 3.4.1)


Do I need the brms package? Or should I install a different version of R?

Thank you in advance for your help!
Subject Author Posted

New install question

dwall June 21, 2019 10:58AM

Re: New install question

ptaylor June 21, 2019 01:34PM

Re: New install question

dwall June 21, 2019 04:54PM