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

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janelleliu
September 23, 2020 01:57PM
Oh yes, I should have specified - I have a few versions of R downloaded!

Output of that command is:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distribution: 10.15.6
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/liuj10/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 17 2020
: AFNI_20.2.18 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.18, macos_10.12_local, Sep 17 2020
which python : /Users/liuj10/opt/anaconda2/bin/python
python version : 2.7.16
which R : /Users/liuj10/opt/anaconda2/bin/R
R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/liuj10/abin/afni)
R : 2
/Users/liuj10/opt/anaconda2/bin/R
/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R
python : 2
/Users/liuj10/opt/anaconda2/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python2 : 2
/Users/liuj10/opt/anaconda2/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python3 : 1 (/usr/bin/python3)


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 : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/liuj10/abin/R_io.so':
dlopen(/Users/liuj10/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/liuj10/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

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

R RHOME : /Users/liuj10/opt/anaconda2/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 : /Users/liuj10/opt/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /usr/local/ANTs/bin/:/Users/liuj10/opt/anaconda2/bin:/Users/liuj10/opt/anaconda2/condabin:/usr/local/fsl/bin:/usr/local/DTIPrepTools-0.1.1-Linux/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2019a.app/bin:/opt/X11/bin:/Users/liuj10/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 : 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/liuj10/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.5.1

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.64.3/lib/libglib-2.0.dylib
++ 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: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* consider installing gcc under homebrew

Thanks!
-Janelle



Edited 1 time(s). Last edit at 09/23/2020 02:02PM by janelleliu.
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Subject Author Posted

R command not found

janelleliu September 22, 2020 01:59PM

Re: R command not found

ptaylor September 22, 2020 03:26PM

Re: R command not found

janelleliu September 22, 2020 07:42PM

Re: R command not found

ptaylor September 23, 2020 07:13AM

Re: R command not found

janelleliu September 23, 2020 01:57PM

Re: R command not found

janelleliu September 24, 2020 02:01PM

Re: R command not found

ptaylor September 29, 2020 04:49PM

Re: R command not found

janelleliu September 30, 2020 03:15PM

Re: R command not found

ptaylor September 30, 2020 08:14PM

Re: R command not found

janelleliu October 01, 2020 02:02PM

Re: R command not found

discoraj October 07, 2020 02:25PM

Re: R command not found

gang October 07, 2020 03:05PM