R set-up AFNI error

juliaml2019 · August 22, 2023, 5:27pm

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

pmolfese · August 22, 2023, 9:14pm

Hi Julia,

You're running into an error because the version of R you have installed is now outdated. Since you're on an ARM Mac system, the recommendation is to install a new version of R (https://cran.r-project.org) and then use the build_afni.py tool.

You'll need to do a little bit of prep following the instructions in two parts:

The first one sets up all the dependencies that AFNI needs to compile, the second one gives instructions to do the actual compilation. In your case you'd be doing:
build_afni.py -build_root $HOME/afni/build -package macos_13_ARM_clang

Let us know if you get stuck on any part of the process.

-Peter

juliaml2019 · August 23, 2023, 9:32pm

Thanks for your quick reply, Peter.

I'm getting an error here:

curl -O https://cran.r-project.org/bin/macosx/base/R-4.2.3.pkg
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0Warning: Failed to open the file R-4.2.3.pkg: Read-only file system
  0 88.6M    0 16384    0     0  10958      0  2:21:22  0:00:01  2:21:21 11010
curl: (23) Failure writing output to destination

Thank you again for your help!
Julia

pmolfese · August 24, 2023, 1:15pm

Looks like you may not have permission to write to whatever directory you're currently in. Can you try in another directory?

I would also try either directly from the webpage or to use this link for the current version as of Aug 24, 2023.

curl -O https://cran.r-project.org/bin/macosx/big-sur-arm64/base/R-4.3.1-arm64.pkg

juliaml2019 · August 29, 2023, 6:30pm

Thanks, Peter. That worked and now I've moved onto the User Privileges documentation.

I'm getting the following error after the -bindir $HOME/abin command:

:abin jlaing2$  -bindir $HOME/abin
-bash: -bindir: command not found

Thanks for your continued help!

rickr · August 29, 2023, 6:38pm

Hello,

That -bindir option is part of the previous command, but it might be the default anyway.
What is the output of:

cat ~/abin/AFNI_version.txt

If that looks okay, note that the subsequent init_user_dotfiles.py also has a line continuation character that connects the next line with it (so -do_updates ... is part of the command).

rick

juliaml2019 · August 29, 2023, 6:56pm

Thanks, Rick. Here's the output of

cat ~/abin/AFNI_version.txt

AFNI_23.2.08
anyos_text
Aug 22 2023
local

When I do the next command, ~/abin/init_user_dotfiles.py -shell_list bash zsh tcsh \ -do_updates path apsearch -dir_bin ~/abin

I get the following error:

env: python: No such file or directory

Thanks again for your help,
Julia

rickr · August 29, 2023, 9:01pm

Hi Julia,

In the earlier system_check post, it shows a valid python. Did you reboot after finishing the admin steps? Either way, it might be enough to just start a new zsh, maybe by opening a new terminal. Open a new terminal window and try:

which python

If that works (shows a path to python), try the command again from the new terminal.

rick

juliaml2019 · September 1, 2023, 1:04pm

Thanks, Rick. That command did show a path to python so I went ahead with that next command in a new terminal window, which appeared to work:

~ % ~/abin/init_user_dotfiles.py -shell_list bash zsh tcsh \              
        -do_updates path apsearch -dir_bin ~/abin

output:

-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, 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 4 dot files

When I try the next command,

build_afni.py -build_root $HOME/afni/build -package macos_13_ARM_clang

I get this output/error:


-- current AFNI: AFNI_23.2.08, anyos_text, Aug 22 2023
-- cleaning old build root dir, /Users/jlaing2/afni/build
-- backing up dir build_src
-- preparing build_root dir, /Users/jlaing2/afni/build
-- have default git tag LAST_TAG, will checkout AFNI_23.2.08
-- checking out git tag AFNI_23.2.08
-- using repo branch (detached), tag AFNI_23.2.08
-- will reuse existing atlas directory, afni_atlases_dist

-- will run 'make' build of package macos_13_ARM_clang
-- copying other_builds/Makefile.macos_13_ARM_clang to Makefile
-- building make target 'itall'
++ building ...
   consider monitoring the build in a separate window with:
       cd /Users/jlaing2
       tail -f /Users/jlaing2/afni/build/build_src/log_make.txt
       # use ctrl-c to terminate 'tail' command (not the build)
** error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
** error: 
-- status: building FAILURE
   see 'make' log file /Users/jlaing2/afni/build/build_src/log_make.txt

       ------------------------------
       to possibly rsync atlases:
          rsync -av /Users/jlaing2/afni/build/afni_atlases_dist/ /Users/jlaing2/abin/
       
       ------------------------------
       shell/system command history is in:
          /Users/jlaing2/afni/build/hist_commands.txt
       ------------------------------
       screen text history is in:
          /Users/jlaing2/afni/build/hist_messages.txt

I did try to open up a new terminal window to run this latest command to see if that made a difference, but same error.

Thank you for your continued help! It's very much appreciated.

Julia

rickr · September 1, 2023, 4:00pm

Hi Julia,

Would you please send me a private message, attaching that afni/build/build_src/log_make.txt file, along with the text output from:

~/abin/afni_system_check.py -check_all

I will ponder some ways to evaluate the current setup.
Thanks,

rick