3dLMEr is a newish program and your version of AFNI is pretty old. I'd update AFNI and try again. Depending on how AFNI was installed on your system in the first place, this works for me:
@update.afni.binaries -defaults
then if 3dLMEr still isn't working after that then I'd post the output of this command to this thread:
As Sam notes, updating would be a good idea, as that is pretty old. But there are 2 other things to note here, ignoring the real contents of the command.
One is that the shell is showing "3dLMEr-prefix" as the command without a wildcard match. Make sure you have a space after 3dLMEr, before the -prefix option (there does seem to be a space in the displayed command).
The other is that the -dataTable contents might be better off moved to a text file, since there are no quotes around the sub-brick selectors (e.g. [1] should be "[1]"). But if you move this to a file (e.g. my_datatable.txt), then no quotes are necessary (in the text file), and the command can finish with -dataTable my_datatable.txt, say. The No match error is from the shell, saying that wildcard matching is failing. It has nothing to do with 3dLMEr specifically, but is because the shell sees the [1] for example, and looks for a file with that actually in the name. Use the quotes to block the shell from evaluating that as a wildcard character.
Again, I am ignoring the contents of the command, which I will leave to Gang to ponder...
Thank you! I tried updating using the command you provided, but I keep getting this error: @update.afni.binaries -defaults
-- running @update.afni.binaries version 3.16, September 16, 2020
-- have AFNI binaries under /Users/Isa/abin
-- install dir: using existing /Users/Isa/abin
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f
-- attempting to install package macos_10.12_local under
install dir: /Users/Isa/abin...
-- have install dir
++ working in new temp dir, .tmp.install
++ getting install prog: curl -O -f bin/misc/@update.afni.binaries ...
curl -O -f https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 241 0 0 0 0 0 0 --:--:-- 0:00:03 --:--:-- 0
curl: (22) The requested URL returned error: 403
** failed, trying macos_10.12_local/@update.afni.binaries ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 254 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (22) The requested URL returned error: 403
** failed again, skipping check for new installer
++ downloading test file: curl -O -f macos_10.12_local/afni ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 237 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (22) The requested URL returned error: 403
** failed to download test file
(maybe package macos_10.12_local is not available)
[MacBook-Pro-5:~] Isa%
I also try to download AFNI from the website, but I get the error 403 Forbidden--you do not have permission to access.
Let me investigate this a little and get back to you. I think the afni server was rebooted and might still be in the process of being set up. More later...
Thank you. I tried again today but this time, I get the following error:
deleting old temporary directory...
rm: .tmp.install: Operation not permitted
++ working in new temp dir, .tmp.install
mkdir: .tmp.install: File exists
** failed to create new or remove old temp dir, .tmp.install
For ls -ls ~/abin it is: drwxr-xr-x 931 Isa staff 29792 13 Sep 09:53 /Users/Isa/abin
For ls -ld ~/abin/afni it is: -rwxr-xr-x 1 Isa staff 12201072 16 Apr 2021 /Users/Isa/abin/afni
For ls -ld ~/abin/.tmp* it is: drwxr-xr-x 2 Isa staff 64 13 Sep 09:53 /Users/Isa/abin/.tmp.install
whoami Isa
Hmmm, this is all owned by you. But presumably there is something that is not, possibly all of the .tmp.install contents. For example, this command will probably show one or even hundreds of files:
find ~/abin \! -user Isa
Assuming so, you should just remove that directory tree, maybe via sudo.
sudo rm -fr /Users/Isa/abin/.tmp.install
We could work around that, but there is no reason to leave you in a bad state.
Does that seem reasonable?
I also typed 3dLMEr in the terminal, and I got this:
================== Welcome to 3dLMEr ==================
Program for Voxelwise Linear Mixed-Effects (LME) Analysis
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Version 1.0.4, Aug 22, 2023
SSCC/NIMH, National Institutes of Health, Bethesda MD 20892, USA
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
When I do the system check, this is the output. It is missing R packages. Are they needed for 3dLMEr?
Thanks,
isabelle
--------------------- AFNI and related program tests ---------------------
which afni : /Users/Isa/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 18 2023
: AFNI_23.2.10 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.10, macos_10.12_local, Sep 18 2023, official
which python : /Applications/anaconda/bin/python
python version : 2.7.11
which R : /Library/Frameworks/R.framework/Resources/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
instances of various programs found in PATH:
afni : 1 (/Users/Isa/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/Applications/anaconda/bin/python2.7)
python2 : 1 (/Applications/anaconda/bin/python2.7)
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.5/bin/python3.5
/usr/bin/python3
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: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /Library/Frameworks/R.framework/Resources
++ module loaded: matplotlib.pyplot
module file : /Applications/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.pyc
matplotlib version : 1.5.0
** need maptplotlib version 2.2+ for APQC
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.5/bin/python3.5)
/usr/local/bin/python3.5 (sym link to /Library/Frameworks/Python.framework/Versions/3.5/bin/python3.5)
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/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/Isa/abin:/Users/Isa/abin:/Applications/anaconda/bin:/Applications/scilpy/scripts:/Users/Isa/mrtrix2/bin:/Users/Isa/antsbin/bin:/Users/Isa/tract_querier/scripts:/Applications/anaconda/lib/python2.7/site-packages/:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/opt/homebrew/opt/python/libexec/bin
----------------------------- eval dot files -----------------------------
()
----------- AFNI $HOME files -----------
()
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- no .tcshrc, will create one as a follower of .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)
no modifications needed across 2 dot files
------------------------------ 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 .
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.2
which brew : /usr/local/bin/brew
brew version : 0.9.5
-- consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.44.1/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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
This shows that possibly none of the packages are installed, which is a little confusing. Did 3dLMEr previously work? Forgetting the "No match" shell error, did any of the R programs previously work, even for just -help output? It would seem perhaps not, but that seems strange...
Yes, they have worked before, and the -help output works. I just tried it again. This is why I am puzzled because I had the R packages installed before. Should I go ahead and reinstall, although they appear to be there?
Given that R_LIBS is not set, it might be good to verify that there isn't a ~/R or ~/sw/Rsomething directory containing the libraries. It seems very odd for that aspect to change. Your R version is the same as that of our build system, so at least there is no difference there.
Do you see any R directory there? Is there anything shown by:
I moved the table into a text file, and I don't get an error but the program still crashes because of this (see text below). If I run the afni check command, I get the same output as before.
I installed the r packages again using this command: rPkgsInstall -pkgs "lmerTest,phia,snow" I have a lot of warnings, but phia and lmer are installed (see text below).
Thank you for your help.
isabelle
(OUTPUT OF AFNI CHECK)
Loading required package: lmerTest
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘lmerTest’
Loading required package: phia
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘phia’
Possible reasons:
0) Make sure that R package lmerTest has been installed. See the 3dLME
help documentation for more details.
1) Inappropriate model specification with options -model, or -qVars.
2) In correct specifications for random effect with -ranEff.
3) Mistakes in data table. Check the data structure shown above, and verify
whether there are any inconsistencies.
4) Inconsistent variable names which are case sensitive. For example, factor
named Scanner in model specification and then listed as scanner in the table hader
would cause grief for 3dLMEr.
** Error:
Quitting due to model test failure...
(OUTPUT OF INSTALLING R PACKAGE)
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘fs’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/fs’
* installing *source* package ‘diffobj’ ...
** package ‘diffobj’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘diffobj’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/diffobj’
* installing *source* package ‘brio’ ...
** package ‘brio’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘brio’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/brio’
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘digest’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/digest’
* installing *source* package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘jsonlite’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/jsonlite’
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘ps’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ps’
* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘colorspace’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/colorspace’
* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘utf8’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/utf8’
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘Matrix’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Matrix’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Matrix’
* installing *source* package ‘farver’ ...
** package ‘farver’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘farver’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/farver’
* installing *source* package ‘fansi’ ...
** package ‘fansi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘fansi’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/fansi’
* installing *source* package ‘magrittr’ ...
** package ‘magrittr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘magrittr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/magrittr’
* installing *source* package ‘SparseM’ ...
** package ‘SparseM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘SparseM’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/SparseM’
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp’
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘cli’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cli’
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘glue’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/glue’
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘isoband’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/isoband’
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘rlang’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rlang’
ERROR: dependency ‘cli’ is not available for package ‘desc’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/desc’
ERROR: dependency ‘rlang’ is not available for package ‘ellipsis’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ellipsis’
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/processx’
ERROR: dependency ‘colorspace’ is not available for package ‘munsell’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/munsell’
* installing *source* package ‘MatrixModels’ ...
** package ‘MatrixModels’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
namespace ‘Matrix’ 1.2-18 is being loaded, but >= 1.6.0 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘MatrixModels’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MatrixModels’
ERROR: dependency ‘Rcpp’ is not available for package ‘minqa’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/minqa’
ERROR: dependency ‘Rcpp’ is not available for package ‘RcppEigen’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen’
ERROR: dependencies ‘cli’, ‘glue’, ‘rlang’ are not available for package ‘lifecycle’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/lifecycle’
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/callr’
ERROR: dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘rlang’ are not available for package ‘gtable’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gtable’
ERROR: dependencies ‘farver’, ‘lifecycle’, ‘munsell’, ‘rlang’ are not available for package ‘scales’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/scales’
ERROR: dependencies ‘cli’, ‘glue’, ‘lifecycle’, ‘rlang’ are not available for package ‘vctrs’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/vctrs’
ERROR: dependencies ‘SparseM’, ‘MatrixModels’ are not available for package ‘quantreg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/quantreg’
ERROR: dependencies ‘callr’, ‘cli’, ‘desc’, ‘processx’ are not available for package ‘pkgbuild’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/pkgbuild’
ERROR: dependencies ‘cli’, ‘fansi’, ‘glue’, ‘lifecycle’, ‘rlang’, ‘utf8’, ‘vctrs’ are not available for package ‘pillar’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/pillar’
ERROR: dependencies ‘cli’, ‘desc’, ‘fs’, ‘glue’, ‘pkgbuild’, ‘rlang’ are not available for package ‘pkgload’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/pkgload’
ERROR: dependencies ‘fansi’, ‘lifecycle’, ‘magrittr’, ‘pillar’, ‘rlang’, ‘vctrs’ are not available for package ‘tibble’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tibble’
ERROR: dependency ‘tibble’ is not available for package ‘rematch2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rematch2’
ERROR: dependencies ‘cli’, ‘glue’, ‘gtable’, ‘isoband’, ‘lifecycle’, ‘rlang’, ‘scales’, ‘tibble’, ‘vctrs’ are not available for package ‘ggplot2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ggplot2’
ERROR: dependencies ‘cli’, ‘diffobj’, ‘fansi’, ‘glue’, ‘rematch2’, ‘rlang’, ‘tibble’ are not available for package ‘waldo’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/waldo’
ERROR: dependencies ‘brio’, ‘callr’, ‘cli’, ‘desc’, ‘digest’, ‘ellipsis’, ‘jsonlite’, ‘lifecycle’, ‘magrittr’, ‘pkgload’, ‘processx’, ‘ps’, ‘rlang’, ‘waldo’ are not available for package ‘testthat’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/testthat’
ERROR: dependency ‘testthat’ is not available for package ‘nloptr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/nloptr’
ERROR: dependencies ‘minqa’, ‘nloptr’, ‘Rcpp’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/lme4’
ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘lme4’, ‘scales’ are not available for package ‘car’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/car’
ERROR: dependencies ‘lme4’, ‘ggplot2’ are not available for package ‘lmerTest’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/lmerTest’
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/3h/_kn_9jy55t34cyp9ty1hls4r0000gn/T/RtmpTZWmMV/downloaded_packages’
++ Note: @ 09:16:47
This package has been installed on the computer: lmerTest
This package has been installed on the computer: phia
Thanks for the info, and sorry for dropping this (please feel free to ping me if I seem to forget a thread).
But that error is odd, and suggests that the Xcode commandlinetools are not installed. Did you recently upgrade the OS version perhaps? If so, you might have to go through this again:
xcode-select --install
If we cannot resolve this quickly, it might be good to have some more direct communication. I am sorry this is lingering.
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.