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  

|
February 22, 2021 04:25PM
Hello,

I've been trying to install AFNI unsuccessfully for a while in a 10.11.6 Mac OS X El Captain. The error seems to be the following:
Error in dyn.load(ll) :
unable to load shared object '/Users/fernanda/abin/R_io.so':
dlopen(/Users/fernanda/abin/R_io.so, 6): Symbol not found: _getentropy

When running the afni_system_check.py, I got:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.6.0
version: Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64
distribution: 10.11.6
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/fernanda/abin/afni
afni version : Precompiled binary macos_10.12_local: Feb 10 2021
: AFNI_21.0.08 'Titus'
AFNI_version.txt : AFNI_21.0.08, macos_10.12_local, Feb 10 2021
which python : /Users/fernanda/anaconda3/bin/python
python version : 3.7.3
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/fernanda/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
/Users/fernanda/anaconda3/bin/python3.7
/usr/bin/python
python2 : 0
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/Users/fernanda/anaconda3/bin/python3.7

** have python3 but not python2

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/fernanda/abin/R_io.so':
dlopen(/Users/fernanda/abin/R_io.so, 6): Symbol not found: _getentropy
Referenced from: /Users/fernanda/abin/libpython2.7.dylib (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/fernanda/abin/libpython2.7.dylib
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

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

R RHOME : /Library/Frameworks/R.framework/Resources

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/fernanda/anaconda3/lib/python3.7/site-packages/matplotlib/pyplot.py

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/fernanda/anaconda3/bin:/Users/fernanda/anaconda3/condabin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/fernanda/abin:/Users/fernanda/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/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 : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/fernanda/abin

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

which brew : /usr/local/bin/brew
brew version : Homebrew 3.0.1-10-g0d36d54

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ 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:/opt/X11/lib/flat_namespace:/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:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
* consider installing gcc under homebrew
* consider installing glib under homebrew


Any help on how to resolve this issue would be very appreciated!

Thanks in advance,
Fernanda
Subject Author Posted

Installation issue

fpalhano February 22, 2021 04:25PM

Re: Installation issue

gang February 23, 2021 04:50PM

Re: Installation issue

fpalhano February 24, 2021 03:26PM