Fixing Afni libraries

AFNI Message Board
1

Hello everyone -

A few weeks ago, I installed a few modules for Freesurfer, and now all of a sudden all of my afni libraries are messed up. I’m running Mac OS Sierra.

After running afni_system_check, the output is below. Does anyone know how to update these libraries without completely uninstalling and re-installing afni? Some of afni is still intact, but clearly without these functions below, I cannot preprocess.

Thank you in advance!
Steffie

afni version : Precompiled binary macosx_10.7_Intel_64: Jan 3 2017
AFNI_version.txt : AFNI_17.0.00, macosx_10.7_Intel_64, Jan 03 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.3.2 (2016-10-31) – “Sincere Pumpkin Patch”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/steffie/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 1 (/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

testing ability to start various programs…
afni : success
suma : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/steffie/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/steffie/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/steffie/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/steffie/abin/SurfMesh
Reason: image not found

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

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

PYTHONPATH = /usr/local/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/steffie/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.1.7

++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files, e.g. /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 comments ============================

  • have python3 but not python2
  • AFNI programs show FAILURE
  • insufficient data for AFNI bootcamp
  • consider running: brew install pyqt
  • consider linking /usr/local/Cellar/gcc/6.3.0_1/lib/gcc/6/libgomp.1.dylib under /usr/local/lib
  • consider linking /usr/local/Cellar/glib/2.50.2/lib/libglib-2.0.dylib under /usr/local/lib
  • cannot tell if DYLD_LIBRARY_PATH includes /opt/X11/lib/flat_namespace
2

Hi,
Can you post your .bash_profile and/or .bashrc files from your home directory?
And it looks like you use fink and homebrew? Is that correct?
thanks, Justin

3

Also, to avoid dealing with many of those libraries,
install the macosx_10.7_local package, instead of
the _Intel_64 version:

@update.afni.binaries -package macosx_10.7_local
  • rick
4

Rick:
Thanks for the fix.

I had been having a similar but more specific problem, where only 3dAllineate would fail when I ran afni_system_check.py -check_all. I would get the following error:

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /usr/local/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib

I ran @update.afni.binaries -package macosx_10.7_local, as you suggested and it fixed the problem.

My teeth are whiter, I lost 10 pounds…ok maybe not.

Thanks.
Alex

5

Yes thanks Rick! The @update_binaries code worked like a champ, and now I have “success” everywhere. Let’s hope that translates to science!
cheers,
Steffie

6

I am using AFNI macosx_10.10_icc under macOS 10.12 with Homebrew.
I can get around with the dylib issues by installing glib via brew as following:
brew install glib

7

Hi Cecil -

Thanks for your response. I tried your recent suggestion as well re: instally pyqt4 using brew, but I end up with a “Permission Denied” error for each brew install, in which I guess brew can’t write to my usr/local/lib directory. I tried to ‘sudo’ it, but that is no longer supported via homebrew for security reasons. Did you get this error?

Thanks,
Steffie

8

@blueberriesforsal
I didn’t encounter those permission issues. You may want to run “brew doctor” and contact the author of pyqt4 formula.

9

Hi-

It might be worth noting that PyQt4 is (presently) just needed for opening the uber_*py GUIs. Odds are, those might not be the most important features in your processing lifestream. Therefore, it might not be a huge deal to ignore PyQt4 stuff at the moment; for setting up FMRI processing, instead of uber_subject.py, it might be easier, more flexible, and faster to take an example from the afni_proc.py help (say, from Examples #9-11), and work from there.

That being said, to get PyQt4, we have suggested the fink route rather than that of Homebrew; see Step #4 here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html

That being said, if you want your Homebrew to brew more readily, in this case, there are two ways to go: change the permissions in your /usr/local/… path, or make ‘brew’ sudoable. As noted here, the latter is not recommended/supported by Homebrew:
https://github.com/Homebrew/legacy-homebrew/issues/9953#issuecomment-6741795
(part of the larger discussion here: https://github.com/Homebrew/legacy-homebrew/issues/9953)
More about changing permissions of /usr/local are discussed here, in regards to this issue:
http://stackoverflow.com/questions/19039404/error-cowardly-refusing-to-sudo-brew-install-for-installing-glue-0-3-for-mac

–pt