afni.nimh.nih.gov

Dear AFNI users,

I am trying to run ANOVA using 3dMVM. When I run the script I get, the following error:
updating R_LD_LIBRARY_PATH ...
Loading required package: lme4
Loading required package: Matrix
Error: package or namespace load failed for ‘afex’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘data.table’
Execution halted

I am using R 3.6 in MacOS Catalina (vesrion 10.15.6). When I re-install R packages (rPkgsInstall -pkgs ALL) I get the following error :

Warning messages:
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘data.table’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘Rmpi’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘gsl’ had non-zero exit status

Then I tried to install just data. table using rPkgsInstall -pkgs data.table.

I again get the same warning message:

Warning message:
In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘data.table’ had non-zero exit status


Following is the AFNI check message afni_system_check.py -check_all:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Sun Jul 5 00:43:10 PDT 2020; root:xnu-6153.141.1~9/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 4
apparent login shell: sh
shell RC file: .profile (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/matava/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 1 2020
: AFNI_20.2.16 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.16, macos_10.12_local, Sep 01 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/matava/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/usr/bin/python3


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

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

R RHOME : /Library/Frameworks/R.framework/Resources

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

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/matava/abin:/Users/matava/abin:/Users/matava/abin

PYTHONPATH = /sw/lib/qt4-x11/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/matava/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.9

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)

========================= summary, please fix: =========================
* just be aware: login shell 'sh', but our code examples use 'tcsh'
* shell sh : found login shell setup file .profile
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace