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  

|
May 20, 2017 01:18PM
Dear experts
I am facing some problems when installing AFNI, and below is my check report.
ps. i believed that i have installed fink already
Thanks a lot!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Tue May 9 11:48:28 PDT 2017; root:xnu-3789.70.9~16/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/dogdogman/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: May 12 2017
: AFNI_17.1.05
AFNI_version.txt : AFNI_17.1.05, macosx_10.7_Intel_64, May 12 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/dogdogman/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 : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/dogdogman/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : success

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

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7

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

PYTHONPATH = /Users/dogdogman/Python

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ 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 /Users/dogdogman/abin

------------------------------ OS specific -------------------------------

++ found PyQt4 under /sw/lib/qt4-mac/lib/python2.7/site-packages
++ 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, cannot check DYLD_LIBRARY_PATH in cur shell, cheating ...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* consider installing fink
* consider adding /sw/lib/qt4-mac/lib/python2.7/site-packages to PYTHONPATH
* please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh
Subject Author Posted

AFNI installation problem

jimmy601521 May 20, 2017 01:18PM

Re: AFNI installation problem

ptaylor May 21, 2017 03:32PM

Re: AFNI installation problem

jimmy601521 May 28, 2017 02:19PM