Hi all,
Noticed a couple of similar posts but they were older. Stumbled on a problem when trying to run 3dLME, seems that R libraries are not compatible. I’ve uninstalled and re-installed R to no avail. Hope I’ve included the relevant info below to help diagnose the problem! Please let me know what other info might be helpful. Many thanks for your help!
- SCRIPT USED and output with error:
[dk12r4003mac4:~/abin] user% /Volumes/LBM_HallKD/Data/Scripts/@3dLME_AllFoodXdiet.sh
set nonomatch
set mask = /Volumes/LBM_HallKD/Data/CFR_data/02-anatomical_masks/reward_circuit_mask_resampled+tlrc
set out_dir=/Volumes/LBM_HallKD/Data/CFR_data/
set prefix = 3dLME
cd /Volumes/LBM_HallKD/Data/CFR_data/
3dLME
-prefix 3dLME -jobs 4
-mask /Volumes/LBM_HallKD/Data/CFR_data/02-anatomical_masks/reward_circuit_mask_resampled+tlrc
-model 1
-ranEff ~1
-corStr order : AR1
-SS_type 3
-num_glt 3
-gltLabel 1 LFvLC -gltCode 1 diet : 1lowfat - 1lowcarb
-gltLabel 2 LFvB -gltCode 2 diet : 1lowfat - 1baseline
-gltLabel 3 LCvB -gltCode 3 diet : 1lowcarb - 1baseline
-num_glf 1
-glfLabel 1 dietcond -glfCode 1 diet : 1lowcarb & 1lowfat & 1*baseline
-dataTable Subj diet InputFile s307 baseline /Volumes/LBM_HallKD/Data/CFR_data/stats_files/psc_stats_files/func.o_s307_pscr_d1.psc.Composite.AM2_with_GAM.blur6mm.scale+tlrc.HEAD[ples_composite#0_Coef]
[… file list truncated for brevity…]
updating R_LD_LIBRARY_PATH …
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object ‘/Users/darceyvl/abin/R_io.so’:
dlopen(/Users/darceyvl/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/darceyvl/abin/R_io.so
Reason: image not found
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted
-
MacOS: Mojave 10.14.6
-
AFNI version: Precompiled binary macos_10.12_local: Jul 5 2020 (Version AFNI_20.2.00 ‘Aulus Vitellius’)
-
R software
R was installed using the https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html#install-r
The first three lines from the output of the command line at the terminal: R --version
R version 3.6.3 (2020-02-29) – “Holding the Windsock”
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Attempt to update R Packages (via terminal):
sudo rPkgsInstall -pkgs ALL
updating R_LD_LIBRARY_PATH …
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object ‘/Users/darceyvl/abin/R_io.so’:
dlopen(/Users/darceyvl/abin/R_io.so, 6): Library not loaded: /sw/lib/libjpeg.9.dylib
Referenced from: /Users/darceyvl/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 13.0.0 or later, but libjpeg.9.dylib provides version 12.0.0
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted
[dk12r4003mac4:~/abin] darceyvl% touch hello
[dk12r4003mac4:~/abin] darceyvl% ls hello
hello
–>Error in R (via R conosole):
first.in.path ← function(file) {
- ff ← paste(strsplit(Sys.getenv(‘PATH’),‘:’)[[1]],‘/’, file, sep=‘’)
- ff<-ff[lapply(ff,file.exists)==TRUE];
- #cat(‘Using ‘, ff[1],’\n’);
- return(gsub(‘//’,‘/’,ff[1], fixed=TRUE))
- }
source(first.in.path(‘AFNIio.R’))
Error in if (file == “”) { : missing value where TRUE/FALSE neededfirst.in.path ← function(file) {
- ff ← paste(strsplit(Sys.getenv(‘PATH’),‘:’)[[1]],‘/’, file, sep=‘’)
- ff<-ff[lapply(ff,file.exists)==TRUE];
- #cat(‘Using ‘, ff[1],’\n’);
- return(gsub(‘//’,‘/’,ff[1], fixed=TRUE))
- }
source(first.in.path(‘AFNIio.R’))
Error in if (file == “”) { : missing value where TRUE/FALSE needed(ll ← find.in.path(‘R_io.so’))
Error in find.in.path(“R_io.so”) : could not find function “find.in.path”
dyn.load(ll)
Error in dyn.load(ll) : object ‘ll’ not found