3dLMEr command not found

isa · September 28, 2023, 1:45pm

Hi Rick,

Thank you for your help. I am going to install xcode again. Unfortunately, I cannot remember when I updated the operating system.

I will let you know what the outcome of the xcode install is.

Thank you very much for your help,

isabelle

isa · September 28, 2023, 3:08pm

Hi Rick,

I installed xcode again, and the R-packages. This is the output of the R-package install:

The downloaded source packages are in
	‘/private/var/folders/3h/_kn_9jy55t34cyp9ty1hls4r0000gn/T/RtmpVYl0Yq/downloaded_packages’
++ Note:  @ 10:35:12
   	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: lmerTest
	This package has been installed on the computer: paran
	This package has been installed on the computer: psych
	This package has been installed on the computer: brms
	This package has been installed on the computer: corrplot
	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`Preformatted text`

I tried running the 3dLMER script again, and it started by then this happened:

3dLMEr \
-prefix LME_Picture \	
-jobs 12 \
-model 'Polarity*Negation+(1|Subj)+(1|Subj:Polarity)+(1|Subj:Negation)'	\
-SS_type 3                                                                      \
-gltCode More-Less 'Polarity : 1*More -1*Less'			\
-gltCode None-Yes 'Negation : 1*None -1*Yes'			\
-gltCode More_YesvsNone 'Polarity : 1*More Negation : 1*None -1*Yes'	\
-gltCode Less_YesvsNone 'Polarity : 1*Less Negation : 1*None -1*Yes'	\
-dataTable @Datatable.txt
	? -prefix LME_Picture \
? -jobs 12 \
? -model 'Polarity*Negation+(1|Subj)+(1|Subj:Polarity)+(1|Subj:Negation)'\
? -SS_type 3                                                                      \
? -gltCode More-Less 'Polarity : 1*More -1*Less'\
? -gltCode None-Yes 'Negation : 1*None -1*Yes'\
? -gltCode More_YesvsNone 'Polarity : 1*More Negation : 1*None -1*Yes'\
? -gltCode Less_YesvsNone 'Polarity : 1*Less Negation : 1*None -1*Yes'\
? -dataTable @Datatable.txt
updating R_LD_LIBRARY_PATH ...
Read 36 items

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
8 response values
2 levels for factor Negation : None Yes 

Contingency tables of subject distributions among the categorical variables:

***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files for effect estimates: Done!


Range of input data: [-54.795, 52.531]

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or something else
is likely inappropriate.

Loading required package: lmerTest
Loading required package: lme4
Loading required package: Matrix

Attaching package: ‘lmerTest’

The following object is masked from ‘package:lme4’:

    lmer

The following object is masked from ‘package:stats’:

    step

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’
boundary (singular) fit: see help('isSingular')
[1] "Great, test run passed at voxel (18, 21, 16)!"
[1] "Start to compute 50 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "09/28/23 11:05:31.113"
Loading required package: snow
Package snow loaded successfully!

Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
  12 nodes produced errors; first error: there is no package called ‘phia’
Calls: clusterEvalQ -> clusterCall -> checkForRemoteErrors
Execution halted

Thank you again for your help. Please let me know what is the best way to proceed.

Kindest regards,

isabelle

Gang · September 28, 2023, 5:03pm

Isabelle,

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

What is your R version?

R --version

You may need to first upgrade your R version and then reinstall those R packages. Additionally, you might need to rebuild R_io.so, @rickr?

Gang

rickr · September 28, 2023, 5:44pm

Hi Isabelle,

Yes, you are at a bad point here.

that AFNI version was built against R 3.6.3
you do not have the R libraries
the needed R libraries are no longer available for R 3.6.3

That means you might need to start over with AFNI, R and the R libraries (unless someone has a set of R libraries built for 3.6.3, which I do not).

What OS and version are you running? That part was not in the afni_system_check.py output.

rick

isa · September 28, 2023, 6:34pm

Hi Rick and Gang,

Thank you for the prompt reply. I have Ventura 13.3.1

The r-version that I have is:

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)

Ok, so if I have to reinstall AFNI and R, what is the best way to proceed?

Thank you,

isabelle

rickr · September 28, 2023, 7:29pm

Hi Isabelle,

Is homebrew used for anything besides AFNI? Your version is pretty old, and it would surely need to be updated as well. It looks like you will need to :

update homebrew
install homebrew packages to build with
build a new AFNI package
build new R libraries

I know this is painful. This is even more work than starting with a fresh system, since you have to account for all of the old software. And I hope you don't hit a snag for python2, it is possible.

Anyway, what do you need homebrew for besides AFNI?
How about python, since we are at it?

rick

isa · September 28, 2023, 7:44pm

Hi Rick,

Yikes, I did not realize that I was in that much trouble. I do not use homebrew for anything else or Python for that matter.

Does that simply things?

Isabelle

rickr · September 28, 2023, 8:05pm

Yes, it is simpler if we do not need to preserve the old homebrew and python. I see that your python comes via conda, so if need be, that could be dropped. We can see.

You should probably do a setup following the newer instructions (for Intel).
Looking at these notes: macos_12_intel_a_admin.zsh ...

Your homebrew version is pretty old, so you might want to start by updating it:

brew update
brew upgrade

After that, run the 2 brew install commands that are not for xquartz.

brew install python netpbm cmake gfortran
brew install libpng jpeg expat freetype fontconfig openmotif  \
             libomp gsl glib pkg-config gcc libiconv autoconf \
             libxt mesa mesa-glu libxpm

How about trying that much and seeing how it goes?
Then we can move on to AFNI and the R packages, which will probably go pretty smoothly.

rick

isa · September 28, 2023, 8:41pm

I tried the brew update command and this is what I got:

brew update
/usr/local/Library/Homebrew/version.rb:186:in `initialize': Version value must be a string (TypeError)
	from /usr/local/Library/Homebrew/os/mac/version.rb:24:in `initialize'
	from /usr/local/Library/Homebrew/os/mac.rb:15:in `new'
	from /usr/local/Library/Homebrew/os/mac.rb:15:in `version'
	from /usr/local/Library/brew.rb:31:in `<main>'

I am not off to a good start... I wish I knew more about how to fix these issues.

Thank you for your help,

isabelle

isa · September 28, 2023, 8:47pm

I also dried this and it failed.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
==> This script will install:
/opt/homebrew/bin/brew
/opt/homebrew/share/doc/homebrew
/opt/homebrew/share/man/man1/brew.1
/opt/homebrew/share/zsh/site-functions/_brew
/opt/homebrew/etc/bash_completion.d/brew
/opt/homebrew

Press RETURN/ENTER to continue or any other key to abort:
==> /usr/bin/sudo /usr/sbin/chown -R Isa:admin /opt/homebrew
==> /usr/bin/sudo /bin/chmod g+rwx /Users/Isa/Library/Caches/Homebrew
==> /usr/bin/sudo /usr/sbin/chown -R Isa /Users/Isa/Library/Caches/Homebrew

chown: /Users/Isa/Library/Caches/Homebrew: Operation not permitted
Failed during: /usr/bin/sudo /usr/sbin/chown -R Isa /Users/Isa/Library/Caches/Homebrew

thank you again

isabelle

rickr · September 28, 2023, 8:47pm

The problem seems to be that not even homebrew wants to upgrade from an old version.

Try to just uninstall homebrew, and then start over with the install on our page (but still skip xcode).

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh)"

If this has problems, I will send you a message about a more direct conversation.

rick

isa · September 28, 2023, 8:59pm

Unfortunately, it has problems. If I create a new user on this computer and install AFNI there, would that be a solution to my problem? I could then follow the instructions for a M1 chip (this is what I have).

What is the best way to proceed?

isabelle

bash-3.2$ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh)"
/bin/bash: line 250: /opt/homebrew/bin/brew: No such file or directory
REJECT: bin
Warning: This script will remove:
/Users/Isa/Library/Caches/Homebrew/
/usr/local/.git/
/usr/local/.gitignore
/usr/local/.yardopts
/usr/local/CODEOFCONDUCT.md
/usr/local/CONTRIBUTING.md
/usr/local/Cellar/
/usr/local/LICENSE.txt
/usr/local/Library//
/usr/local/README.md
/usr/local/SUPPORTERS.md
/usr/local/bin/brew
/usr/local/share/doc/homebrew/
/usr/local/share/man/man1/brew.1
Are you sure you want to uninstall Homebrew? This will remove your installed packages! [y/N] y
==> Removing Homebrew installation...
unlink: /usr/local/bin/lzmainfo: Permission denied
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d
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unlink: /usr/local/lib/libgirepository-1.0.dylib: Permission denied
unlink: /usr/local/lib/libpixman-1.0.dylib: Permission denied
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unlink: /usr/local/lib/libtiff.dylib: Permission denied
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unlink: /usr/local/lib/libpangomm-1.4.1.dylib: Permission denied
unlink: /usr/local/lib/libQtUiTools_debug.prl: Permission denied
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unlink: /usr/local/lib/libQtCLucene.4.8.6.dylib: Permission denied
unlink: /usr/local/lib/libgtk-x11-2.0.0.dylib: Permission denied
unlink: /usr/local/share/man/man5/fonts-conf.5: Permission denied
unlink: /usr/local/share/man/man5/png.5: Permission denied
unlink: /usr/local/share/man/man3/FcDefaultSubstitute.3: Permission denied
unlink: /usr/local/share/man/man3/FcIsLower.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrCmpIgnoreCase.3: Permission denied
unlink: /usr/local/share/man/man3/FcLangGetCharSet.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetSubtractCount.3: Permission denied
unlink: /usr/local/share/man/man3/FcDirScan.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrStrIgnoreCase.3: Permission denied
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unlink: /usr/local/share/man/man3/FcLangSetCreate.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetSubtract.3: Permission denied
unlink: /usr/local/share/man/man3/FcCacheCopySet.3: Permission denied
unlink: /usr/local/share/man/man3/FcFreeTypeCharSetAndSpacing.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigReference.3: Permission denied
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unlink: /usr/local/share/man/man3/FcDirCacheLoadFile.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetDestroy.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFcodec.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcNameParse.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFReadRawTile.3tiff: Permission denied
unlink: /usr/local/share/man/man3/TIFFReadRawStrip.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetIntersectCount.3: Permission denied
unlink: /usr/local/share/man/man3/FcCacheCreateTagFile.3: Permission denied
unlink: /usr/local/share/man/man3/FcMatrixMultiply.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigGetConfigDirs.3: Permission denied
unlink: /usr/local/share/man/man3/FcNameUnregisterObjectTypes.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigGetFontDirs.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetEqual.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigSubstitute.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFSetDirectory.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetAddChar.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFReadDirectory.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcConfigDestroy.3: Permission denied
unlink: /usr/local/share/man/man3/FcFontSetSortDestroy.3: Permission denied
unlink: /usr/local/share/man/man3/FcFini.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternRemove.3: Permission denied
unlink: /usr/local/share/man/man3/FcDirCacheValid.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigEnableHome.3: Permission denied
unlink: /usr/local/share/man/man3/FcFileIsDir.3: Permission denied
unlink: /usr/local/share/man/man3/FcGetLangs.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternDuplicate.3: Permission denied
unlink: /usr/local/share/man/man3/FcCacheNumFont.3: Permission denied
unlink: /usr/local/share/man/man3/FcNameRegisterConstants.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFWriteRawStrip.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcInitLoadConfigAndFonts.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternEqualSubset.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFReadRGBAImage.3tiff: Permission denied
unlink: /usr/local/share/man/man3/TIFFswab.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcObjectSetBuild.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetHasChar.3: Permission denied
unlink: /usr/local/share/man/man3/FcFontSetList.3: Permission denied
unlink: /usr/local/share/man/man3/FcInitLoadConfig.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigSetRescanInterval.3: Permission denied
unlink: /usr/local/share/man/man3/FcCacheSubdir.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFFlush.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcFreeTypeCharSet.3: Permission denied
unlink: /usr/local/share/man/man3/FcLangSetUnion.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFFieldWriteCount.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcPatternGet-Type.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetCount.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFWriteEncodedTile.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcToLower.3: Permission denied
unlink: /usr/local/share/man/man3/FcMatrixEqual.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigAppFontAddFile.3: Permission denied
unlink: /usr/local/share/man/man3/FcFontMatch.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFFieldDataType.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcPatternGet.3: Permission denied
unlink: /usr/local/share/man/man3/FcMatrixRotate.3: Permission denied
unlink: /usr/local/share/man/man3/FcValueEqual.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFmemory.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcStrSetDel.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrListNext.3: Permission denied
unlink: /usr/local/share/man/man3/FcAtomicDeleteNew.3: Permission denied
unlink: /usr/local/share/man/man3/FcLangSetDel.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrSetMember.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternBuild.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetIntersect.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternEqual.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrStr.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFquery.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcStrSetCreate.3: Permission denied
unlink: /usr/local/share/man/man3/FcDirCacheLoad.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFReadRGBATile.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcStrFree.3: Permission denied
unlink: /usr/local/share/man/man3/FcMatrixScale.3: Permission denied
unlink: /usr/local/share/man/man3/FcFontRenderPrepare.3: Permission denied
unlink: /usr/local/share/man/man3/FcAtomicReplaceOrig.3: Permission denied
unlink: /usr/local/share/man/man3/FcFontSetSort.3: Permission denied
unlink: /usr/local/share/man/man3/FcMatrixShear.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFError.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcInitReinitialize.3: Permission denied
unlink: /usr/local/share/man/man3/FcCacheNumSubdir.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigGetCacheDirs.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternReference.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrListFirst.3: Permission denied
unlink: /usr/local/share/man/man3/FcObjectSetCreate.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigAppFontAddDir.3: Permission denied
unlink: /usr/local/share/man/man3/FcAtomicOrigFile.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetMerge.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigSubstituteWithPat.3: Permission denied
unlink: /usr/local/share/man/man3/FcCacheDir.3: Permission denied
unlink: /usr/local/share/man/man3/FcAtomicLock.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrDowncase.3: Permission denied
unlink: /usr/local/share/man/man3/FcValueDestroy.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternDel.3: Permission denied
unlink: /usr/local/share/man/man3/FcNameRegisterObjectTypes.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigHome.3: Permission denied
unlink: /usr/local/share/man/man3/FcDirCacheUnload.3: Permission denied
unlink: /usr/local/share/man/man3/FcIsUpper.3: Permission denied
unlink: /usr/local/share/man/man3/FcObjectSetDestroy.3: Permission denied
unlink: /usr/local/share/man/man3/FcCharSetDelChar.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFFieldName.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcGetVersion.3: Permission denied
unlink: /usr/local/share/man/man3/FcLangSetHash.3: Permission denied
unlink: /usr/local/share/man/man3/FcAtomicDestroy.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFstrip.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcConfigFilename.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFFieldTag.3tiff: Permission denied
unlink: /usr/local/share/man/man3/TIFFReadRGBAStrip.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcConfigUptoDate.3: Permission denied
unlink: /usr/local/share/man/man3/FcDirCacheRescan.3: Permission denied
unlink: /usr/local/share/man/man3/FcUtf16ToUcs4.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternHash.3: Permission denied
unlink: /usr/local/share/man/man3/FcLangSetGetLangs.3: Permission denied
unlink: /usr/local/share/man/man3/libtiff.3tiff: Permission denied
unlink: /usr/local/share/man/man3/TIFFSetField.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcLangSetCopy.3: Permission denied
unlink: /usr/local/share/man/man3/FcConfigGetCurrent.3: Permission denied
unlink: /usr/local/share/man/man3/FcLangNormalize.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrBasename.3: Permission denied
unlink: /usr/local/share/man/man3/FcAtomicUnlock.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternCreate.3: Permission denied
unlink: /usr/local/share/man/man3/FcPatternFilter.3: Permission denied
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unlink: /usr/local/share/man/man3/FcStrCopy.3: Permission denied
unlink: /usr/local/share/man/man3/FcStrCopyFilename.3: Permission denied
unlink: /usr/local/share/man/man3/TIFFsize.3tiff: Permission denied
unlink: /usr/local/share/man/man3/FcConfigGetCache.3: Permission denied
unlink: /usr/local/share/man/man3/FcFontSort.3: Permission denied
unlink: /usr/local/share/man/man1/tiff2ps.1: Permission denied
unlink: /usr/local/share/man/man1/fc-validate.1: Permission denied
unlink: /usr/local/share/man/man1/fc-scan.1: Permission denied
unlink: /usr/local/share/man/man1/lzma.1: Permission denied
unlink: /usr/local/share/man/man1/gsl-config.1: Permission denied
unlink: /usr/local/share/man/man1/tiffdither.1: Permission denied
unlink: /usr/local/share/man/man1/fax2tiff.1: Permission denied
unlink: /usr/local/share/man/man1/lzmore.1: Permission denied
unlink: /usr/local/share/man/man1/tiff2rgba.1: Permission denied
unlink: /usr/local/share/man/man1/cjpeg.1: Permission denied
Warning: Failed to delete /usr/local/.gitignore
rm: /usr/local/.gitignore: Permission denied
Warning: Failed to delete /usr/local/.yardopts
rm: /usr/local/.yardopts: Permission denied
Warning: Failed to delete /usr/local/CODEOFCONDUCT.md
rm: /usr/local/CODEOFCONDUCT.md: Permission denied
Warning: Failed to delete /usr/local/CONTRIBUTING.md
rm: /usr/local/CONTRIBUTING.md: Permission denied
Warning: Failed to delete /usr/local/Cellar
rm: /usr/local/Cellar: Permission denied
Warning: Failed to delete /usr/local/LICENSE.txt
rm: /usr/local/LICENSE.txt: Permission denied
Warning: Failed to delete /usr/local/Library/
rm: /usr/local/Library/: Permission denied
Warning: Failed to delete /usr/local/README.md
rm: /usr/local/README.md: Permission denied
Warning: Failed to delete /usr/local/SUPPORTERS.md
rm: /usr/local/SUPPORTERS.md: Permission denied
Warning: Failed to delete /usr/local/bin/brew
rm: /usr/local/bin/brew: Permission denied
Warning: Failed to delete /usr/local/share/man/man1/brew.1
rm: /usr/local/share/man/man1/brew.1: Permission denied
==> Removing empty directories...
Password:
Sorry, try again.
Password:
==> /usr/bin/sudo /usr/bin/find /usr/local/bin /usr/local/etc /usr/local/include /usr/local/lib /usr/local/opt /usr/local/sbin /usr/local/share /usr/local/var /usr/local/Cellar /usr/local/Frameworks -name .DS_Store -delete
==> /usr/bin/sudo /usr/bin/find /usr/local/bin /usr/local/etc /usr/local/include /usr/local/lib /usr/local/opt /usr/local/sbin /usr/local/share /usr/local/var /usr/local/Cellar /usr/local/Frameworks -depth -type d -empty -exec rmdir {} ;
==> /usr/bin/sudo rmdir /usr/local
rmdir: /usr/local: Operation not permitted
Warning: Failed during: /usr/bin/sudo rmdir /usr/local
Warning: Homebrew partially uninstalled (but there were steps that failed)!
To finish uninstalling rerun this script with `sudo`.
The following possible Homebrew files were not deleted:
/usr/local/.com.apple.installer.keep
/usr/local/.git/
/usr/local/.gitignore
/usr/local/.yardopts
/usr/local/CODEOFCONDUCT.md
/usr/local/CONTRIBUTING.md
/usr/local/LICENSE.txt
/usr/local/Library/
/usr/local/README.md
/usr/local/SUPPORTERS.md
/usr/local/bin/
/usr/local/etc/
/usr/local/fsl/
/usr/local/gfortran/
/usr/local/include/
/usr/local/lib/
/usr/local/man/
/usr/local/remotedesktop/
/usr/local/share/
/usr/local/var/
You may wish to remove them yourself.

rickr · September 28, 2023, 9:04pm

Some of these issues are with permissions, so it is not clear who installed what.
What is the output from:

ls -l /usr/local/bin/ccmake

The permissions will need be cleared up no matter what you do.

rick

isa · September 28, 2023, 9:12pm

This is the output:

lrwxr-xr-x 1 Isa admin 32 23 Aug 2019 /usr/local/bin/ccmake -> ../Cellar/cmake/3.2.2/bin/ccmake

Years ago, someone did some things to my computer in order to run a program for DTI data that used Python and other software, perhaps, this is where it all began...

Thank you for your help, it is greatly appreciated.

isabelle

rickr · September 28, 2023, 10:14pm

Right, I should have assumed it was a link. How about one of these:

ls -lL /usr/local/bin/ccmake
ls -l /usr/local/Cellar/cmake/3.2.2/bin/ccmake

Mostly, we are trying to set some sort of record for thread length... :)

rick

isa · September 29, 2023, 1:15pm

Hi Rick,

The output for: ls -lL /usr/local/bin/ccmake

: ccmake: No such file or directory

For this command:
ls -l /usr/local/Cellar/cmake/3.2.2/bin/ccmake

No such file or directory

Thank you for your help.

isabelle

isa · October 2, 2023, 4:36pm

Hi Rick,

Would it be possible to talk about whether these issues can be fixed or if I should erase my computer to reinstall AFNI and R?

Thank you kindly for your help,

isabelle

rickr · October 2, 2023, 4:43pm

Looking back through this, I think the cleanup script should be run with sudo:

sudo /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh)"

Given that one more try. I will send you a private message about this.

Thanks,

rick

isa · October 2, 2023, 4:58pm

Perfect, I just ran it and this is the output:

sudo /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/uninstall.sh)"
Password:
/bin/bash: line 250: /opt/homebrew/bin/brew: No such file or directory
REJECT: bin
Warning: This script will remove:
/usr/local/.git/
/usr/local/.gitignore
/usr/local/.yardopts
/usr/local/CODEOFCONDUCT.md
/usr/local/CONTRIBUTING.md
/usr/local/LICENSE.txt
/usr/local/Library//
/usr/local/README.md
/usr/local/SUPPORTERS.md
/usr/local/bin/brew
/usr/local/share/man/man1/brew.1
Are you sure you want to uninstall Homebrew? This will remove your installed packages! [y/N] y
==> Removing Homebrew installation...
==> Removing empty directories...
==> /usr/bin/sudo /usr/bin/find /usr/local/bin /usr/local/etc /usr/local/include /usr/local/lib /usr/local/share /usr/local/var -name .DS_Store -delete
==> /usr/bin/sudo /usr/bin/find /usr/local/bin /usr/local/etc /usr/local/include /usr/local/lib /usr/local/share /usr/local/var -depth -type d -empty -exec rmdir {} ;
==> /usr/bin/sudo rmdir /usr/local
rmdir: /usr/local: Operation not permitted
Warning: Failed during: /usr/bin/sudo rmdir /usr/local
Warning: Homebrew partially uninstalled (but there were steps that failed)!
To finish uninstalling rerun this script with `sudo`.
The following possible Homebrew files were not deleted:
/usr/local/.com.apple.installer.keep
/usr/local/bin/
/usr/local/etc/
/usr/local/fsl/
/usr/local/gfortran/
/usr/local/include/
/usr/local/lib/
/usr/local/man/
/usr/local/remotedesktop/
/usr/local/share/
/usr/local/var/
You may wish to remove them yourself.

rickr · October 2, 2023, 5:33pm

That looks great! Maybe it is time to actually being the setup process.

I hope you have been enjoying this character building exercise so far...

rick