Installation problem on a Mac

sing · July 24, 2020, 4:18am

Dear ALL,

I was trying to install AFNI on my Mac, but got stuck in the stage involving R.

When I ran “sudo rPkgsInstall -pkgs ALL”, I got the following:

updating R_LD_LIBRARY_PATH …

oo Warning:
Failed to load R_io.so with this error message:

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

When I ran “afni_system_check.py -check_all”, I got the following:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.5.0
version: Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/sing/abin/afni
afni version : Precompiled binary macos_10.12_local: Jul 23 2020
: AFNI_20.2.06 ‘Aulus Vitellius’
AFNI_version.txt : AFNI_20.2.06, macos_10.12_local, Jul 23 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/sing/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/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/sing/abin/R_io.so’:
dlopen(/Users/sing/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/sing/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 : /Library/Frameworks/R.framework/Resources

checking for $HOME files…
.afnirc : missing
.sumarc : missing
.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 : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Users/sing/abin

PYTHONPATH =
R_LIBS =
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 /Users/sing/abin

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

** no package manager found (okay for bootcamp)
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)

========================= 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
please run: cp /Users/sing/abin/AFNI.afnirc ~/.afnirc
please run: “suma -update_env” for .sumarc
insufficient data for AFNI bootcamp
OS X version might be old
consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace

Any pointers will be much appreciated!

Thank you,
Sing

ptaylor · July 24, 2020, 12:02pm

Hi, Sing-

The problem is your R version: you have R-4.0, which is noted in the AFNI system check output here:


R version : R version 4.0.2 (2020-06-22) -- "Taking Off Again"

At the moment, on a Mac you need R-3.6.*

The correct version of R is specified as part of the install instructions here-- the link at the top of this section gets you the correct version:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html#install-r
…and/or the Mac App installer should also get you the right R version (but since you are mostly setup already, I would probably just get the R-3.6.* directly, above).

Please note that there are some other steps noted in the system check output in the bottom section to do to complete your install-- mostly copy+pasting things into the terminal.

–pt

sing · July 24, 2020, 4:45pm

Thanks a lot, Paul!

I routinely use R and just updated to the most recent version. I have now set up my computer with both versions (3.6.3 and 4.0.2) of R with RSwitch so that I can switch between the two versions.

I will proceed with the other steps in the installation now.

Thanks,
Sing

ptaylor · July 24, 2020, 4:55pm

Hi, Sing-

OK, sounds good.

–pt