Hi all,
I'm trying to run a 3dMVM script, but am getting the following error:
updating R_LD_LIBRARY_PATH ...
Error in library("afex") : there is no package called ‘afex’
Execution halted
The output to afni_system_check-py -check_all is below:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.4.0
version: Darwin Kernel Version 22.4.0: Mon Mar 6 21:01:02 PST 2023; root:xnu-8796.101.5~3/RELEASE_ARM64_T8112
distribution: 13.3
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/jlaing2/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 9 2023
: AFNI_23.2.04 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.04, macos_10.12_local, Aug 09 2023, official
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.11.4
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
instances of various programs found in PATH:
afni : 1 (/Users/jlaing2/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.11/3.11.4_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
python2 : 0
python3 : 1 (/usr/bin/python3)
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: metafor!
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/homebrew/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.2
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/jlaing2/abin:/usr/local/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/Users/jlaing2/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.zshrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (471482M Avail)
top history: ...3 [rickr]: renamed GroupAna_cases scripts and output
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_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/jlaing2/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
** no package manager found (okay for bootcamp)
++ 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 'zsh'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* dot file test : want 1 modifications across 3 files:
rPkgsInstall -pkgs ALL provides the following output:
updating R_LD_LIBRARY_PATH ...
Warning: dependency ‘pbkrtest’ is not available
also installing the dependency ‘car’
Warning: unable to access index for repository http://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6:
cannot open URL 'http://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
installing the source packages ‘car’, ‘afex’, ‘phia’
trying URL 'http://cloud.r-project.org/src/contrib/car_3.1-2.tar.gz'
Content type 'application/x-gzip' length 579829 bytes (566 KB)
==================================================
downloaded 566 KB
trying URL 'http://cloud.r-project.org/src/contrib/afex_1.3-0.tar.gz'
Content type 'application/x-gzip' length 3567552 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
trying URL 'http://cloud.r-project.org/src/contrib/phia_0.2-1.tar.gz'
Content type 'application/x-gzip' length 547339 bytes (534 KB)
==================================================
downloaded 534 KB
ERROR: dependency ‘pbkrtest’ is not available for package ‘car’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/car’
ERROR: dependencies ‘pbkrtest’, ‘car’ are not available for package ‘afex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/afex’
ERROR: dependency ‘car’ is not available for package ‘phia’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/phia’
The downloaded source packages are in
‘/private/var/folders/xc/1zz7s0bx3x96kn9knhnzcz4dnh7zwz/T/RtmpmQJ08x/downloaded_packages’
++ Note: @ 12:26:21
This package has been installed on the computer: afex
This package has been installed on the computer: phia
This package has been installed on the computer: metafor
Warning messages:
1: package ‘metafor’ is not available (for R version 3.6.3)
2: In install.packages(pkgs_miss, dep = NA, repos = site) :
installation of package ‘car’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = NA, repos = site) :
installation of package ‘afex’ had non-zero exit status
4: In install.packages(pkgs_miss, dep = NA, repos = site) :
installation of package ‘phia’ had non-zero exit status
Any help would be very appreciated!
Thank you,
Julia