When I run afni_system_check.py with my newer version of AFNI (from November) I get this:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-358.11.1.el6.x86_64
version: #1 SMP Wed Jun 12 03:34:52 UTC 2013
distribution: CentOS 6.4 Final
number of CPUs: 64
apparent login shell: bash
--------------------- AFNI and related program tests ---------------------
which afni : /ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200/afni
afni version : Precompiled binary linux_gcc32: Nov 21 2014
which python : /ncf/tools/current/apps/arch/linux_x86_64/python/2.7.3/bin/python
python version : 2.7.3
which R : which: no R in (/ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200:/ncf/tools/current/code/bin:/ncf/tools/current/code/bin/linux_x86_64:/ncf/tools/current/code/lib/perl/Common:/ncf/tools/current/code/lib/shell:/ncf/tools/current/apps/arch/linux_x86_64/fsl/4.0.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/mongodb/2.2.0/bin:/ncf/tools/current/apps/arch/linux_x86_64/php/5.4.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/fsfast/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/mni/bin:/ncf/tools/current/apps/arch/linux_x86_64/dcmtk/3.6/bin:/ncf/tools/current/apps/arch/linux_x86_64/xjview/8.4:/ncf/tools/current/apps/arch/linux_x86_64/caret/5.0:/ncf/tools/current/apps/arch/linux_x86_64/mricron/2009_12:/ncf/tools/current/apps/arch/linux_x86_64/python/2.7.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/java/1.6.0_24/bin:/ncf/tools/current/code/lib/c/linux_x86_64:/ncf/tools/current/code/bin/.package_loaders:/usr/local/bin:/usr/lib64/qt-3.3/bin:/lsf/7.0/linux2.6-glibc2.3-x86_64/etc:/lsf/7.0/linux2.6-glibc2.3-x86_64/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin)
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/ncf/tools/apps/arch/linux_x86_64/afni/2014_12_13_1200/afni)
R : 0
python : 2
/ncf/tools/apps/arch/linux_x86_64/python/2.7.3/bin/python2.7
/usr/bin/python
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
checking for $HOME files...
.afnirc : missing
.sumarc : found
.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 = /ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200:/ncf/tools/current/code/bin:/ncf/tools/current/code/bin/linux_x86_64:/ncf/tools/current/code/lib/perl/Common:/ncf/tools/current/code/lib/shell:/ncf/tools/current/apps/arch/linux_x86_64/fsl/4.0.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/mongodb/2.2.0/bin:/ncf/tools/current/apps/arch/linux_x86_64/php/5.4.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/fsfast/bin:/ncf/tools/current/apps/arch/linux_x86_64/freesurfer/4.0.2/mni/bin:/ncf/tools/current/apps/arch/linux_x86_64/dcmtk/3.6/bin:/ncf/tools/current/apps/arch/linux_x86_64/xjview/8.4:/ncf/tools/current/apps/arch/linux_x86_64/caret/5.0:/ncf/tools/current/apps/arch/linux_x86_64/mricron/2009_12:/ncf/tools/current/apps/arch/linux_x86_64/python/2.7.3/bin:/ncf/tools/current/apps/arch/linux_x86_64/java/1.6.0_24/bin:/ncf/tools/current/code/lib/c/linux_x86_64:/ncf/tools/current/code/bin/.package_loaders:/usr/local/bin:/usr/lib64/qt-3.3/bin:/lsf/7.0/linux2.6-glibc2.3-x86_64/etc:/lsf/7.0/linux2.6-glibc2.3-x86_64/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin
PYTHONPATH = /ncf/nrg/sw/lib/pylib/2.0:/ncf/tools/current/code/lib/python/Neuroinfo_Toolkit/1.5.2
LD_LIBRARY_PATH = /lsf/7.0/linux2.6-glibc2.3-x86_64/lib
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
atlas : found TT_N27+tlrc under /ncf/tools/current/apps/arch/linux_x86_64/afni/2014_12_13_1200
------------------------------ OS specific -------------------------------
---------------------------- general comments ----------------------------
* consider copying AFNI.afnirc to ~/.afnirc
* consider running "apsearch -update_all_afni_help"
