3dMVM error- bad syntax for -gltCode? Package missing?

AFNI version info (afni -ver): 17.1.04

Hello AFNI Minds-

I’m trying to do a group comparison between four different patient groups on contrast-elicited activation by a commonly used faces-places n-back task. The patient groups have different cell sizes, so I need to use 3dMVM. The task has block design wherein participants match positive, fearful, and expressionless (neu) faces as well as places (scenes) under each of 2-back and 0-back conditions… i.e. eight total trial types. I’m trying to infer from 3dMVM example 1 how to specify the dataTable and core command syntax, but I keep getting errors that I’m not modeling the first contrast set correctly.

-dataTable looks like

subj		group		condition	stimulus	InputFile
s1		control		2-back		pos		../subjects/VCU1001/NBTaskStats+tlrc’[1]’
s1		control		2-back		neu		../subjects/VCU1001/NBTaskStats+tlrc’[5]’
s1		control		2-back		fear		../subjects/VCU1001/NBTaskStats+tlrc’[9]’
s1		control		2-back		place		../subjects/VCU1001/NBTaskStats+tlrc’[13]’
s1		control		0-back		pos		../subjects/VCU1001/NBTaskStats+tlrc’[3]’
s1		control		0-back		neu		../subjects/VCU1001/NBTaskStats+tlrc’[7]’
s1		control		0-back		fear		../subjects/VCU1001/NBTaskStats+tlrc’[11]’
s1		control		0-back		place		../subjects/VCU1001/NBTaskStats+tlrc’[15]’
s2		heroin		2-back		pos		../subjects/VCU1007/NBTaskStats+tlrc’[1]’   etc

Draft c-shell script reads:

3dMVM -prefix group-diffs -jobs 4 \
-bsVars group \
-wsVars "mem-demand*stimulus" \
-mask NBack_3dCL_mask+tlrc \
-num_glt 4 \
-gltLabel 1 2bk_vs_0bk -gltCode 1 'mem-demand : 1*2-back stimulus: 1*pos 1*neu 1*fear 1*place -1*pos -1*neu -1*fear -1*place'\
-gltLabel 2 demand_heroinVcont -gltCode 2 'group : 1* heroin -1*control mem-demand : 1*2-back -1*0-back' \
-gltLabel 3 demand_heroinVcont -gltCode 3 'group : 1* amph -1*control mem-demand : 1*2-back -1*0-back' \
-gltLabel 4 demand_heroinVcont -gltCode 4 'group : 1* poly -1*control mem-demand : 1*2-back -1*0-back' \
-dataTable @3dMVM-DataTable-BETA.txt

(this wonky forum platform is erasing my back-spaces and is introducing italics)

Error reads :

[sdc@galileo scripts]$ ./5n2_groupmap-maker-Nback-multi-group 
Read 645 items
Loading required package: lme4
Loading required package: Matrix
Loading required package: lsmeans
Loading required package: estimability
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'KR', 'S', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to lsmeans() for follow-up tests
- Get and set global package options with: afex_options()
- Set orthogonal sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************

Attaching package: ‘afex’

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

    lmer

Loading required package: car
Error in `$<-.data.frame`(`*tmp*`, "Subj", value = integer(0)) : 
  replacement has 0 rows, data has 128
Calls: $<- -> $<-.data.frame
Execution halted
[sdc@galileo scripts]$ 

Could someone illuminate? Is my system missing some critical library or package, or did I have a syntax error in my 3dMVM command?

Thanks

Jim

Hi, Jim-

Thaaat is a pretty classic version of AFNI---is it really from 2017?? I would strongly recommend updating your version, to have many new features and probably helpful fixes/updates. I know that table reading has improved lately in 3dMVM, for example.

Re. the wonky features: well, please try the code formatting with putting multiline code between triple backslashes and "inline code" between single backslashes, as described here. I wrapped some of your code text in your post with that, but it will surely be useful for future posts.

I will let @Gang comment on the details of 3dMVM.

--pt

Jim,

Change the label of the first column from subj to Subj, and then try it again. If you update your AFNI, it may directly help in identifying and resolving this issue.

Gang Chen

Hi Everyone,

I am helping Dr. Bjork troubleshoot this issue. I installed the latest version of AFNI, however, I'm unable to install the afex and phia packages. When I attempt to install them, I receive the error "package is not available for R version 3.6.0". Which version of R should I use to install these packages?

Below is the output from the afni_check script.

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              3.10.0-1160.108.1.el7.x86_64
version:              #1 SMP Wed Jan 24 08:37:16 CST 2024
distribution:         Scientific Linux 7.9 (Nitrogen)
number of CPUs:       8
apparent login shell: tcsh
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/sdc/abin/afni
afni version         : Precompiled binary linux_centos_7_64: Mar 18 2024 
                     : AFNI_24.0.14 'Caracalla'
AFNI_version.txt     : AFNI_24.0.14, linux_centos_7_64, Mar 18 2024, official
which python         : /home/sdc/miniconda3/envs/py3_afni_tiny/bin/python
python version       : 3.12.2
which R              : /usr/bin/R
R version            : R version 3.6.0 (x86_64-redhat-linux-gnu)

instances of various programs found in PATH:
    afni    : 1   (/home/sdc/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 2 
      /home/sdc/miniconda3/envs/py3_afni_tiny/bin/python3.12
      /usr/bin/python2.7
    python2 : 1   (/usr/bin/python2.7)
    python3 : 2 
      /home/sdc/miniconda3/envs/py3_afni_tiny/bin/python3.12
      /usr/bin/python3.6


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           : /usr/bin/tcsh
which Xvfb           : /usr/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: brms!
        These packages are not installed on the computer: metafor!
        

R RHOME : /usr/lib64/R

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /home/sdc/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.8.0

++ module loaded: flask
   module file : /home/sdc/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/flask/__init__.py
   flask version : 2.2.5

++ module loaded: flask_cors
   module file : /home/sdc/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/flask_cors/__init__.py
   flask_cors version : 3.0.10

-------------------------------- env vars --------------------------------
PATH                       = /home/sdc/miniconda3/envs/py3_afni_tiny/bin:/home/sdc/miniconda3/condabin:/usr/local/misc/mricrogl_lx:/home/sdc/bin:/usr/local/FSL/fsl_6_0_2/bin:/usr/lib64/qt-3.3/bin:/home/sdc/perl5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/sdc/abin

PYTHONPATH                 = 
R_LIBS                     = /home/sdc/R
LD_LIBRARY_PATH            = 
DYLD_LIBRARY_PATH          = 
DYLD_FALLBACK_LIBRARY_PATH = 
CONDA_SHLVL                = 1
CONDA_DEFAULT_ENV          = py3_afni_tiny

----------------------------- 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, 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 /home/sdc/abin

------------------------------ OS specific -------------------------------
which yum            : /usr/bin/yum
yum version          : 3.4.3


=========================  summary, please fix:  =========================
*  missing R packages (see rPkgsInstall)
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)

Thanks,
Eddie

This can become very difficult, because once the R community moves forward, their libraries often can no longer be installed with old versions of R.

Our CentOS build machine does not have a set of R libraries that I could pass along, unfortunately. That would probably work if we had made them way back when. And trying to install the libraries now fails, at least for some of them.

  • rick

Hi Rick,

So it sounds like you are saying that 3dMVM is no longer compatible with Red Hat 7 clones? Is it known to work with Red Hat 8 clones?

I receive a FAILURE error (see below) for 3dMVM when installing AFNI on Rocky Linux 8.9. I followed the Rocky Linux 8 instructions from the discussion board and used the Rocky Linux 8 binaries.

https://github.com/afni/afni/blob/master/src/other_builds/OS_notes.linux_rocky_8.txt
https://afni.nimh.nih.gov/pub/dist/tgz/linux_rocky_8.tgz

Below are the afni_check and rPkgsInstall outputs.

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              4.18.0-513.11.1.el8_9.0.1.x86_64
version:              #1 SMP Sun Feb 11 10:42:18 UTC 2024
distribution:         Rocky Linux 8.9 (Green Obsidian)
number of CPUs:       6
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /home/sdc/abin/afni
afni version         : Precompiled binary linux_rocky_8: Mar 18 2024 
                     : AFNI_24.0.14 'Caracalla'
AFNI_version.txt     : AFNI_24.0.14, linux_rocky_8, Mar 18 2024, official
which python         : /home/sdc/miniconda3/envs/py3_afni_tiny/bin/python
python version       : 3.12.1
which R              : /usr/bin/R
R version            : R version 4.3.3 (x86_64-redhat-linux-gnu)

instances of various programs found in PATH:
    afni    : 1   (/home/sdc/abin/afni)
    R       : 1   (/usr/bin/R)
    python  : 2 
      /home/sdc/miniconda3/envs/py3_afni_tiny/bin/python3.12
      /usr/libexec/platform-python3.6
    python2 : 0 
    python3 : 2 
      /home/sdc/miniconda3/envs/py3_afni_tiny/bin/python3.12
      /usr/libexec/platform-python3.6

** 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                : FAILURE
        Error in library(data.table) : there is no package called ‘data.table’
        Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
        Execution halted

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh           : /usr/bin/tcsh
which Xvfb           : /usr/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: lme4!
        These packages are not installed on the computer: lmerTest!
        These packages are not installed on the computer: gamm4!
        These packages are not installed on the computer: data.table!
        These packages are not installed on the computer: brms!
        

R RHOME : /usr/lib64/R

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /home/sdc/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.8.0

++ module loaded: flask
   module file : /home/sdc/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/flask/__init__.py
   flask version : 2.2.5

++ module loaded: flask_cors
   module file : /home/sdc/miniconda3/envs/py3_afni_tiny/lib/python3.12/site-packages/flask_cors/__init__.py
   flask_cors version : 3.0.10

-------------------------------- env vars --------------------------------
PATH                       = /usr/local/cuda-12.2/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/cuda-12.2/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/software/fsl/share/fsl/bin:/home/sdc/miniconda3/envs/py3_afni_tiny/bin:/home/sdc/miniconda3/condabin:/home/sdc/.local/bin:/home/sdc/bin:/usr/local/cuda-12.2/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/software/fsl/share/fsl/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/sdc/abin/afni:/opt/puppetlabs/bin:/home/sdc/abin/afni:/home/sdc/abin

PYTHONPATH                 = 
R_LIBS                     = /home/sdc/R
LD_LIBRARY_PATH            = 
DYLD_LIBRARY_PATH          = 
DYLD_FALLBACK_LIBRARY_PATH = 
CONDA_SHLVL                = 2
CONDA_DEFAULT_ENV          = py3_afni_tiny

----------------------------- 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, 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 3 modifications across 3 files:
   
      file             path  flatdir  apsearch        follower
      ---------------  ----  -------  --------        --------
      .cshrc           0     0        1               0     
      .tcshrc          0     0        0               1     
      .bashrc          1     0        1               0     
   
------------------------------ 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 /home/sdc/abin

------------------------------ OS specific -------------------------------
which dnf            : /usr/bin/dnf
dnf version          : 4.7.0
which yum            : /usr/bin/yum
yum version          : 4.7.0


=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  AFNI programs show FAILURE
*  missing R packages (see rPkgsInstall)
*  dot file test : want 3 modifications across 3 files:
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)
Installing packages into ‘/home/sdc/R’
(as ‘lib’ is unspecified)
also installing the dependencies ‘fs’, ‘purrr’, ‘tidyr’, ‘stringi’, ‘callr’, ‘pkgload’, ‘processx’, ‘ps’, ‘broom’, ‘stringr’, ‘testthat’, ‘StanHeaders’, ‘RcppParallel’, ‘pkgbuild’, ‘pbkrtest’, ‘car’, ‘reshape2’, ‘nloptr’, ‘rstan’, ‘rstantools’, ‘bayesplot’, ‘bridgesampling’

trying URL 'http://cloud.r-project.org/src/contrib/fs_1.6.3.tar.gz'
Content type 'application/x-gzip' length 1185603 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://cloud.r-project.org/src/contrib/purrr_1.0.2.tar.gz'
Content type 'application/x-gzip' length 220868 bytes (215 KB)
==================================================
downloaded 215 KB

trying URL 'http://cloud.r-project.org/src/contrib/tidyr_1.3.1.tar.gz'
Content type 'application/x-gzip' length 809058 bytes (790 KB)
==================================================
downloaded 790 KB

trying URL 'http://cloud.r-project.org/src/contrib/stringi_1.8.3.tar.gz'
Content type 'application/x-gzip' length 11917752 bytes (11.4 MB)
==================================================
downloaded 11.4 MB

trying URL 'http://cloud.r-project.org/src/contrib/callr_3.7.5.tar.gz'
Content type 'application/x-gzip' length 102852 bytes (100 KB)
==================================================
downloaded 100 KB

trying URL 'http://cloud.r-project.org/src/contrib/pkgload_1.3.4.tar.gz'
Content type 'application/x-gzip' length 78189 bytes (76 KB)
==================================================
downloaded 76 KB

trying URL 'http://cloud.r-project.org/src/contrib/processx_3.8.4.tar.gz'
Content type 'application/x-gzip' length 163983 bytes (160 KB)
==================================================
downloaded 160 KB

trying URL 'http://cloud.r-project.org/src/contrib/ps_1.7.6.tar.gz'
Content type 'application/x-gzip' length 129489 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'http://cloud.r-project.org/src/contrib/broom_1.0.5.tar.gz'
Content type 'application/x-gzip' length 641849 bytes (626 KB)
==================================================
downloaded 626 KB

trying URL 'http://cloud.r-project.org/src/contrib/stringr_1.5.1.tar.gz'
Content type 'application/x-gzip' length 176599 bytes (172 KB)
==================================================
downloaded 172 KB

trying URL 'http://cloud.r-project.org/src/contrib/testthat_3.2.1.tar.gz'
Content type 'application/x-gzip' length 739745 bytes (722 KB)
==================================================
downloaded 722 KB

trying URL 'http://cloud.r-project.org/src/contrib/StanHeaders_2.32.6.tar.gz'
Content type 'application/x-gzip' length 2395238 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'http://cloud.r-project.org/src/contrib/RcppParallel_5.1.7.tar.gz'
Content type 'application/x-gzip' length 1629119 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'http://cloud.r-project.org/src/contrib/pkgbuild_1.4.4.tar.gz'
Content type 'application/x-gzip' length 48794 bytes (47 KB)
==================================================
downloaded 47 KB

trying URL 'http://cloud.r-project.org/src/contrib/pbkrtest_0.5.2.tar.gz'
Content type 'application/x-gzip' length 75295 bytes (73 KB)
==================================================
downloaded 73 KB

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/reshape2_1.4.4.tar.gz'
Content type 'application/x-gzip' length 37307 bytes (36 KB)
==================================================
downloaded 36 KB

trying URL 'http://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'http://cloud.r-project.org/src/contrib/rstan_2.32.6.tar.gz'
Content type 'application/x-gzip' length 1555968 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'http://cloud.r-project.org/src/contrib/rstantools_2.4.0.tar.gz'
Content type 'application/x-gzip' length 99340 bytes (97 KB)
==================================================
downloaded 97 KB

trying URL 'http://cloud.r-project.org/src/contrib/bayesplot_1.11.1.tar.gz'
Content type 'application/x-gzip' length 4971186 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

trying URL 'http://cloud.r-project.org/src/contrib/bridgesampling_1.1-2.tar.gz'
Content type 'application/x-gzip' length 1679600 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'http://cloud.r-project.org/src/contrib/afex_1.3-1.tar.gz'
Content type 'application/x-gzip' length 3785869 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'http://cloud.r-project.org/src/contrib/phia_0.3-1.tar.gz'
Content type 'application/x-gzip' length 545361 bytes (532 KB)
==================================================
downloaded 532 KB

trying URL 'http://cloud.r-project.org/src/contrib/lme4_1.1-35.1.tar.gz'
Content type 'application/x-gzip' length 2942848 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'http://cloud.r-project.org/src/contrib/lmerTest_3.1-3.tar.gz'
Content type 'application/x-gzip' length 195633 bytes (191 KB)
==================================================
downloaded 191 KB

trying URL 'http://cloud.r-project.org/src/contrib/gamm4_0.2-6.tar.gz'
Content type 'application/x-gzip' length 14969 bytes (14 KB)
==================================================
downloaded 14 KB

trying URL 'http://cloud.r-project.org/src/contrib/data.table_1.15.2.tar.gz'
Content type 'application/x-gzip' length 5386087 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

trying URL 'http://cloud.r-project.org/src/contrib/brms_2.21.0.tar.gz'
Content type 'application/x-gzip' length 4922418 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-20)’
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c init.cc -o init.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c id.cc -o id.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c utils.cc -o utils.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c file.cc -o file.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c path.cc -o path.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c getmode.cc -o getmode.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c link.cc -o link.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c fs.cc -o fs.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c dir.cc -o dir.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c error.cc -o error.o
g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c unix/getmode.cc -o unix/getmode.o
gcc -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bsd/setmode.c -o bsd/setmode.o
gcc -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bsd/strmode.c -o bsd/strmode.o
gcc -I"/usr/include/R" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -c bsd/reallocarray.c -o bsd/reallocarray.o
(cd libuv-1.44.2 \
&& CC="gcc" CPPFLAGS="-I/usr/local/include" CFLAGS="-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection  -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-z,relro  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld" ./configure --quiet)
/bin/sh: line 1: ./configure: Permission denied
make: *** [Makevars:31: libuv-1.44.2/Makefile] Error 126
ERROR: compilation failed for package ‘fs’
* removing ‘/home/sdc/R/fs’
* installing *source* package ‘purrr’ ...
** package ‘purrr’ successfully unpacked and MD5 sums checked
** using staged installation
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing ‘/home/sdc/R/purrr’
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
** using staged installation
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing ‘/home/sdc/R/stringi’
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing ‘/home/sdc/R/ps’
* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing ‘/home/sdc/R/RcppParallel’
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
* removing ‘/home/sdc/R/data.table’
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/home/sdc/R/processx’
ERROR: dependency ‘stringi’ is not available for package ‘stringr’
* removing ‘/home/sdc/R/stringr’
ERROR: dependency ‘RcppParallel’ is not available for package ‘StanHeaders’
* removing ‘/home/sdc/R/StanHeaders’
ERROR: dependency ‘RcppParallel’ is not available for package ‘rstantools’
* removing ‘/home/sdc/R/rstantools’
ERROR: dependencies ‘purrr’, ‘stringr’ are not available for package ‘tidyr’
* removing ‘/home/sdc/R/tidyr’
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/home/sdc/R/callr’
ERROR: dependency ‘stringr’ is not available for package ‘reshape2’
* removing ‘/home/sdc/R/reshape2’
ERROR: dependency ‘stringr’ is not available for package ‘bridgesampling’
* removing ‘/home/sdc/R/bridgesampling’
ERROR: dependencies ‘purrr’, ‘stringr’, ‘tidyr’ are not available for package ‘broom’
* removing ‘/home/sdc/R/broom’
ERROR: dependencies ‘callr’, ‘processx’ are not available for package ‘pkgbuild’
* removing ‘/home/sdc/R/pkgbuild’
ERROR: dependency ‘reshape2’ is not available for package ‘bayesplot’
* removing ‘/home/sdc/R/bayesplot’
ERROR: dependencies ‘fs’, ‘pkgbuild’ are not available for package ‘pkgload’
* removing ‘/home/sdc/R/pkgload’
ERROR: dependencies ‘StanHeaders’, ‘RcppParallel’, ‘pkgbuild’ are not available for package ‘rstan’
* removing ‘/home/sdc/R/rstan’
ERROR: dependencies ‘callr’, ‘pkgload’, ‘processx’, ‘ps’ are not available for package ‘testthat’
* removing ‘/home/sdc/R/testthat’
ERROR: dependencies ‘rstan’, ‘rstantools’, ‘bayesplot’, ‘bridgesampling’ are not available for package ‘brms’
* removing ‘/home/sdc/R/brms’
ERROR: dependency ‘testthat’ is not available for package ‘nloptr’
* removing ‘/home/sdc/R/nloptr’
ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
* removing ‘/home/sdc/R/lme4’
ERROR: dependencies ‘lme4’, ‘broom’ are not available for package ‘pbkrtest’
* removing ‘/home/sdc/R/pbkrtest’
ERROR: dependency ‘lme4’ is not available for package ‘lmerTest’
* removing ‘/home/sdc/R/lmerTest’
ERROR: dependency ‘lme4’ is not available for package ‘gamm4’
* removing ‘/home/sdc/R/gamm4’
ERROR: dependencies ‘pbkrtest’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/sdc/R/car’
ERROR: dependencies ‘lme4’, ‘pbkrtest’, ‘lmerTest’, ‘car’, ‘reshape2’ are not available for package ‘afex’
* removing ‘/home/sdc/R/afex’
ERROR: dependency ‘car’ is not available for package ‘phia’
* removing ‘/home/sdc/R/phia’

The downloaded source packages are in
	‘/tmp/RtmpWbpxP9/downloaded_packages’

++ Note:  @ 13:38:41
   	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: lme4
	This package has been installed on the computer: lmerTest
	This package has been installed on the computer: gamm4
	This package has been installed on the computer: data.table
	This package has been installed on the computer: brms

There were 29 warnings (use warnings() to see them)

Thanks,
Eddie

Hi Everyone,

Also, is there a container version of AFNI that already includes all the packages to run 3dMVM? I was able to run the docker://afni/afni_make_build container, but it still shows that the necessary packages for 3dMVM are missing (see below).

Thanks,
Eddie

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              4.18.0-513.11.1.el8_9.0.1.x86_64
version:              #1 SMP Sun Feb 11 10:42:18 UTC 2024
distribution:         Ubuntu 18.04 bionic
number of CPUs:       6
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           :
                     : AFNI_23.1.10 'Publius Helvius Pertinax'
AFNI_version.txt     : AFNI_23.1.10, linux_ubuntu_16_64_glw_local_shared, Jun 30 2023, local
which python         :
which R              :

instances of various programs found in PATH:
    afni    : 1   (/opt/afni/install/afni)
    R       : 1   (/usr/bin/R)
    python  : 1   (/usr/bin/python3.6)
    python2 : 0 
    python3 : 1   (/usr/bin/python3.6)

** 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           :
which Xvfb           :

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        Error in readRDS(file) : 
          cannot read workspace version 3 written by R 4.3.3; need R 3.5.0 or newer
        
        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: snow!
        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 : /usr/lib/R

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /opt/user_pip_packages/lib/python3.6/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.3.4

-------------------------------- env vars --------------------------------
PATH = /opt/afni/src/../install:/opt/cmake/cmake-3.14.7-Linux-x86_64/bin:/opt/user_pip_packages/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

PYTHONPATH = 
R_LIBS = /home/sdc/R

LD_LIBRARY_PATH = /.singularity.d/libs

DYLD_LIBRARY_PATH = 
DYLD_FALLBACK_LIBRARY_PATH = 

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

--------- shell startup files ----------

   ** error: have no found abin, so please use -dir_bin
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : did not find TT_N27+tlrc

------------------------------ OS specific -------------------------------

have Ubuntu system: Ubuntu 18.04 bionic

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  missing program: afni
*  missing program: python
*  missing program: R
*  failure under initial "AFNI and related program tests"
*  missing program: tcsh
*  missing program: Xvfb
*  missing R packages (see rPkgsInstall)
*  failure running init_user_dotfiles.py -test
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)
*  possibly missing atlases

Epilogue: After trying to re-run the 3dMVM script on another Ubuntu system with 2023 AFNI and all r programs showing as installed, the script also crashed because it could not find the source statistical dataset files. We finally got it to work (including on our older AFNI system) simply by removing the quotes around the sub-brik indicators in the DataTable text file.

I see now that the 3dMVM -help file mentions perhaps dropping the quotes in prose para, but the more salient sample DataTable has the quotes.

Cheers,

Jim

Hi Jim,

Oh dear, yes that does seem like the original issue. The discussion morphed...

Note that quote are needed for sub-brick selectors on the command line, but they are inappropriate when the data table is in an external file (because the shell is not interpreting that file).

Sorry about the confusing rabbit hole, it is great that you found the problem.

  • rick

Hi Everyone,

Additional update, I was able to successfully install AFNI and all R packages on Rocky Linux 8. There were two issues.

  1. Apparently, /tmp is used when compiling some of the R packages. For security purposes, our /tmp directory is mounted with the "noexec" option. Creating an alternate $TMPDIR directory resolved this issue.

  2. The cmake package was not installed. Once installed, the remaining packages were able to install.

Hopefully this helps other Rocky Linux 8 users.

Thanks,
Eddie