Dear Peter.
Thanks for looking into this. The output of the call you sent (afni_system_check.py -check_all) is:

(in the other following post I am going to paste the output of the call that was mentioned here in the output (uber_subject.py -help_install)

============ afni_system_check.py version 0.6, March 14, 2014 ============

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 13.1.0
version: Darwin Kernel Version 13.1.0: Thu Jan 16 19:40:37 PST 2014; root:xnu-2422.90.20~2/RELEASE_X86_64
distribution: 10.9.2 x86_64
number of CPUs: 4
apparent login shell: bash

--------------------- AFNI and related program tests ---------------------
which afni :
which python : /usr/bin/python
python version : 2.7.5
which R :
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 0
R : 0
python : 1 (/usr/bin/python)

testing ability to start various programs...
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
uber_subject.py : FAILURE
/bin/sh: uber_subject.py: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found

checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
---------------------------------------------------------
** python module not found: PyQt4

-> please see the output of "uber_subject.py -help_install"


------------------------------- path vars --------------------------------
PATH = /Applications/y/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

PYTHONPATH =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
Traceback (most recent call last):
File "/Users/NEURO-222/afni/afni_system_check.py", line 285, in <module>
sys.exit(main())
File "/Users/NEURO-222/afni/afni_system_check.py", line 279, in main
rv = me.execute()
File "/Users/NEURO-222/afni/afni_system_check.py", line 265, in execute
if self.sys_check: self.show_system_info()
File "/Users/NEURO-222/afni/afni_system_check.py", line 260, in show_system_info
self.sinfo.show_data_info()
File "/Users/NEURO-222/afni/lib_system_check.py", line 116, in show_data_info
print 'atlas : did not find %s %s' % (atlas, estr)
NameError: global name 'estr' is not defined