Hi I am using an iMac and get the following error when I try to source reco.R.
How do I fix this ?
Many thanks
Ri
-----------------------------------------------------------
source('<path>/R/reco.R')
++ Note NSB.path.set(...): NSB.path.set(getsrc)
-->eval(ei, envir)
-->eval(ei, envir)
-->withVisible(eval)
-->source("<path>/R/reco.R")
Loading profile from <path>/profile.csv
Sourcing from <path>/R
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object '/Users/rdatta4/abin/R_io.so':
dlopen(/Users/rdatta4/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/rdatta4/abin/R_io.so
Reason: image not found
** Error NSB.afni.io.src(...): NSB.afni.io.src()
-->eval(ei, envir)
-->eval(ei, envir)
-->withVisible(eval(ei, envir))
-->source("<path>/R/reco.R")
Failed to source /Users/rdatta4/abin/AFNIio.R AFNI R/W functions will not work
rPkgsInstall -pkgs ALL -check
updating R_LD_LIBRARY_PATH ...
++ Note: @ 14:57:49
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: lmerTest
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
This package has been verified on the computer: corrplot
This package has been verified on the computer: metafor
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 20.6.0
version: Darwin Kernel Version 20.6.0: Mon Apr 24 23:00:57 PDT 2023; root:xnu-7195.141.49.701.3~1/RELEASE_X86_64
distribution: 10.16
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/rdatta4/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 19 2022
: AFNI_22.2.07 'Marcus Aurelius'
AFNI_version.txt : AFNI_22.2.07, macos_10.12_local, Aug 19 2022
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/rdatta4/abin/afni)
R : 2
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/bin/R
/Users/rdatta4/anaconda3/envs/rnsbiom4/bin/R
python : 2
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/Users/rdatta4/anaconda3/envs/rnsbiom4/bin/python3.11
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 3
/usr/bin/python3
/usr/local/Cellar/python@3.11/3.11.3/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/Users/rdatta4/anaconda3/envs/rnsbiom4/bin/python3.11
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
matplotlib version : 1.3.1
** need maptplotlib version 2.2+ for APQC
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.11/3.11.3/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python@3.7/3.7.16/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.9 (sym link to /usr/local/Cellar/python@3.9/3.9.16/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Applications/ANTs/install/bin:/usr/local/opt/python@3.7/bin:/Applications/ITK-SNAP.app/Contents/bin:/Applications/MATLAB_R2021a.app/bin:/bin:/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/Applications/freesurfer/7.3.2/bin:/Applications/freesurfer/7.3.2/fsfast/bin:/usr/local/fsl/bin:/Applications/freesurfer/7.3.2/mni/bin:/Users/rdatta4/anaconda3/envs/rnsbiom4/bin:/Users/rdatta4/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/aria2/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/rdatta4/gproj/nsbiom/scr:/Users/rdatta4/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 : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/rdatta4/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /usr/local/bin/brew
brew version : Homebrew 4.0.16
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
** consider linking /usr/local/Cellar/gcc/13.1.0/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.76.2/lib/libglib-2.0.dylib
++ 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 'bash'...
++ 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 'bash', but our code examples use 'tcsh'
* check for partial install of PyQt4
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)