Windows & Keyboard short cut issues, Mac OS X 10.12.6

aclynn11 · August 15, 2017, 8:41pm

Hi All,

I’ve been having trouble with the AFNI GUI windows and keyboard shortcuts with 10.12. I have updated binaries but am still having issues.

For example, when clustering, I am not able to type a custom value into the text field. When using the sliding bar to adjust threshold I must use a mouse, and cannot fine tune with arrow keys. And, when attempting to play through a time series in the graph window, keyboard short cuts do not work.

Is anyone else experiencing this issue?

Andrew

ptaylor · August 15, 2017, 9:48pm

What are the outputs of:


echo $DYLD_LIBRARY_PATH

and


afni_system_check.py -check_all

?

–pt

aclynn11 · August 15, 2017, 11:39pm

echo $DYLD_LIBRARY_PATH is blank.
Looks like i need to reset this path according to the output txt below.

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/andrew_lynn/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 9 2017
: AFNI_17.2.07
AFNI_version.txt : AFNI_17.2.07, macosx_10.7_local, Aug 09 2017
which python : /Library/Frameworks/Python.framework/Versions/2.7/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.2.4 (2016-03-10) – “Very Secure Dishes”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/andrew_lynn/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.2/Resources/bin/R)
python : 3
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/Users/andrew_lynn/miniconda/bin/python2.7
/usr/bin/python
python2 : 2
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/Users/andrew_lynn/miniconda/bin/python2.7
python3 : 1 (/Library/Frameworks/Python.framework/Versions/3.4/bin/python3.4)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
/bin/sh: SurfMesh: command 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 = /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/fsl/bin:/Users/andrew_lynn/miniconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/andrew_lynn/abin:/Applications/Gedit.app/Contents/MacOS

PYTHONPATH =
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/andrew_lynn/abin

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.39.3
which brew : /usr/local/bin/brew
brew version : Homebrew 0.9.5 (git revision b0ea; last commit 2016-03-15)
which port : /opt/local/bin/port
port version : Error: Current platform “darwin 16” does not match expected platform “darwin 15”

++ found ‘brew’ at /usr/local/bin/brew
++ found PyQt4 under /usr/local/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
– recent OS X, cannot check DYLD_LIBRARY_PATH in shell ‘tcsh’, cheating …
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

login shell ‘bash’, trusting user to translate from ‘tcsh’
shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
AFNI programs show FAILURE
insufficient data for AFNI bootcamp
consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in bash
please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh

ptaylor · August 16, 2017, 3:17am

OK, so you can set it as described in Step 1b here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html
… and see how that goes.

-pt

aclynn11 · August 16, 2017, 5:25pm

Hmm, it’s weird. The export has been added to my ~/.bashrc profile, multiple time now, in fact (see below). However, each time I open a new terminal and open afni it seem i need to export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace on the command line.

Sorry for being a bit naive here. I thought once added to my bash profile that it would run that each time I open a new window and therefore set the path…

cat ~/.bashrc export PATH=/usr/local/bin:$PATH:$HOME/abin

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

alias ls=“ls --color”

alias ll=“ls --color -l”

export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace

export PATH=$PATH:~/abin

export DYLD_FALLBACK_LIBRARY_PATH=$DYLD_FALLBACK_LIBRARY_PATH:~/abin

ahdir=apsearch -afni_help_dir
if [ -f “$ahdir/all_progs.COMP.bash” ]
then
. $ahdir/all_progs.COMP.bash
fi

export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace
export DYLD_LIBRARY_PATH=/opt/X11/lib/flat_namespace

ptaylor · August 16, 2017, 5:46pm

From the “afni_system_check.py” run above, if you look in the “summary, please fix” section, it notes:
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
… which you should consider doing. I wonder if you have a ~/.bash_profile file that isn’t sourcing your ~/.bashrc file? If you do have a ~/.bash_profile file, then make sure it includes a line like:


~ $HOME/.bashrc

Also, you might want to go to:
System Preferences → Users & Groups, then “unlock” the lock thing, then right click on your user icon in the list on the lefthand part of the panel, and select “Advanced options…”. In the list of fields that appear then, go to “Login shell” and make sure it is “/bin/bash” (on Macs, I think default is “/bin/tcsh”).

Finally, as noted by afni_system_check.py above as well, you should make sure to
* please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh

–pt