Hi Gang,

Thanks for your quick response! I'm running the analysis on our computer cluster at Harvard. All of the necessary software has to be loaded through a modules system every time we log on (included in my .bashrc-see below). When I run the afni_system_check.py -check_all, the necessary R packages seem to be recognized. Am I missing something? Should I try on my local machine to see if I can get it to run there?

Thanks,
Laura

relevant .bashrc code:
module load afni/18.3.05-fasrc01
module load gcc/7.1.0-fasrc01
module load R/3.5.1-fasrc02
export R_LIBS_USER=~/apps/R_3.5.1-fasrc02:$R_LIBS_USER

output of afni_system_check.py
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-693.21.1.el7.x86_64
version: #1 SMP Wed Mar 7 19:03:37 UTC 2018
distribution: CentOS Linux 7.4.1708 Core
number of CPUs: 40
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /n/helmod/apps/centos7/Core/afni/18.3.05-fasrc01/afni
afni version : Precompiled binary linux_openmp_64: Nov 19 2018
: AFNI_18.3.05
AFNI_version.txt : AFNI_18.3.05, linux_openmp_64, Nov 19 2018
which python : /bin/python
python version : 2.7.5
which R : /n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/bin/R
R version : R version 3.5.1 (2018-07-02) -- "Feather Spray"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/n/sw/helmod/apps/centos7/Core/afni/18.3.05-fasrc01/afni)
R : 2
/n/sw/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/bin/R
/n/sw/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/lib64/R/bin/R
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 0


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages...
rPkgsInstall -pkgs ALL -check : success

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /n/helmod/apps/centos7/Core/fsl/6.0.0-fasrc01/bin:/n/helmod/apps/centos7/Core/OpenBLAS/0.2.20-fasrc03/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/libxml2/2.7.8-fasrc03/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/gsl/2.4-fasrc01/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/netcdf/4.5.0-fasrc02/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/hdf5/1.10.1-fasrc02/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/lib64/R/bin:/n/helmod/apps/centos7/Core/libtiff/4.0.9-fasrc01/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/pcre/8.41-fasrc01/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/xz/5.2.2-fasrc02/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/bzip2/1.0.6-fasrc02/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/curl/7.45.0-fasrc02/bin:/n/helmod/apps/centos7/Core/jdk/1.8.0_45-fasrc01/jre/bin:/n/helmod/apps/centos7/Core/jdk/1.8.0_45-fasrc01/db/bin:/n/helmod/apps/centos7/Core/jdk/1.8.0_45-fasrc01/bin:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/readline/6.3-fasrc03/bin:/n/helmod/apps/centos7/Core/gcc/7.1.0-fasrc01/bin:/n/helmod/apps/centos7/Core/afni/18.3.05-fasrc01:/n/helmod/apps/centos7/Core/freesurfer/6.0.0-fasrc01/mni/bin:/n/helmod/apps/centos7/Core/freesurfer/6.0.0-fasrc01/fsfast/bin:/n/helmod/apps/centos7/Core/freesurfer/6.0.0-fasrc01/tktools:/n/helmod/apps/centos7/Core/freesurfer/6.0.0-fasrc01/bin:/ncf/nrg/sw/apps/mricrogl/2017_07_14:/usr/local/bin:/opt/TurboVNC/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin

PYTHONPATH = /n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/libxml2/2.7.8-fasrc03/lib64/python2.7/site-packages:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/nlopt/2.4.2-fasrc03/lib/python2.7/site-packages:/opt/websockify/lib/python2.7/site-packages::

R_LIBS =
LD_LIBRARY_PATH = /n/helmod/apps/centos7/Core/OpenBLAS/0.2.20-fasrc03/lib:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/libxml2/2.7.8-fasrc03/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/nlopt/2.4.2-fasrc03/lib:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/gsl/2.4-fasrc01/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/netcdf/4.5.0-fasrc02/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/hdf5/1.10.1-fasrc02/lib:/n/helmod/apps/centos7/Core/szip/2.1-fasrc02/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/R_core/3.5.1-fasrc02/lib64/R/lib:/n/helmod/apps/centos7/Core/libtiff/4.0.9-fasrc01/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/pcre/8.41-fasrc01/lib:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/xz/5.2.2-fasrc02/lib64:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/bzip2/1.0.6-fasrc02/lib:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/zlib/1.2.8-fasrc08/lib:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/curl/7.45.0-fasrc02/lib:/n/helmod/apps/centos7/Core/jdk/1.8.0_45-fasrc01/jre/lib:/n/helmod/apps/centos7/Core/jdk/1.8.0_45-fasrc01/db/lib:/n/helmod/apps/centos7/Core/jdk/1.8.0_45-fasrc01/lib:/n/helmod/apps/centos7/Comp/gcc/7.1.0-fasrc01/readline/6.3-fasrc03/lib64:/n/helmod/apps/centos7/Core/gcc/7.1.0-fasrc01/lib64:/n/helmod/apps/centos7/Core/gcc/7.1.0-fasrc01/lib:/n/helmod/apps/centos7/Core/mpc/1.0.3-fasrc06/lib64:/n/helmod/apps/centos7/Core/mpfr/3.1.5-fasrc01/lib64:/n/helmod/apps/centos7/Core/gmp/6.1.2-fasrc01/lib64

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 /n/helmod/apps/centos7/Core/afni/18.3.05-fasrc01

------------------------------ OS specific -------------------------------
which yum : /bin/yum
yum version : There was a problem importing one of the Python modules


========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* 'afni' executable is owned by root
* consider running: cp /n/helmod/apps/centos7/Core/afni/18.3.05-fasrc01/AFNI.afnirc ~/.afnirc
* consider running "suma -update_env" for .sumarc
* consider running: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
* consider running: yum install PyQt4