Dear ptaylor,
After installed the "local" afni, the libraries problem fixed! Then I tried the "sudo rPkgsInstall -pkgs ALL" . The report also shows that the R packages missing. Below is the detail information!
Thank you in advance!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 17.7.0
version: Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64
distribution: 10.13.6 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/yao150/abin/afni
afni version : Precompiled binary macosx_10.7_local: Aug 20 2018
: AFNI_18.2.13
AFNI_version.txt : AFNI_18.2.13, macosx_10.7_local, Aug 20 2018
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) -- "Single Candle"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/yao150/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
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 : FAILURE
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms
Warning message:
In as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'zone/tz/2018e.1.0/zoneinfo/America/Indiana/Indianapolis'
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/yao150/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ... Jun 2018 [gangc]: added 0.BGA and updated 2.3groups
data dir : found AFNI_demos under $HOME
top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/yao150/abin
------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.7.2
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
++ 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, cheating to check DYLD_LIBRARY_PATH in cur shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
