I'm trying to download AFNI on my PC (windows os) and am running into some issues. If anyone can help that would be much appreciated!
Here is the "please fix" message I got when running the check-all:
just be aware:
login shell 'bash', but our code examples use 'tcsh'
missing R packages (see rPkgsInstall)
dot file test : want 1 modifications across 3 files:
And here is the complete code output:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 6.6.87.2-microsoft-standard-WSL2
version: #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025
distribution: ubuntu 24.04 Noble Numbat
number of CPUs: 8
user: emtar
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/emtar/abin/afni
afni version : Precompiled binary linux_ubuntu_24_64: Sep 17 2025
: AFNI_25.2.13 'Gordian I'
AFNI_version.txt : AFNI_25.2.13, linux_ubuntu_24_64, Sep 17 2025, official
which python : /usr/bin/python
python version : 3.12.3
which R : /usr/bin/R
R version : R version 4.3.3 (x86_64-pc-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/emtar/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.12)
python2 : 0
python3 : 1 (/usr/bin/python3.12)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
build_afni.py : success
uber_subject.py : success
3dMVM : success
rPkgsInstall : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
tcsh version : 6.24.10
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: gamm4!
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.6.3
++ module loaded: flask
module file : /usr/lib/python3/dist-packages/flask/__init__.py
flask version : 3.0.2
++ module loaded: flask_cors
module file : /usr/lib/python3/dist-packages/flask_cors/__init__.py
flask_cors version : 4.0.0
-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Program Files/Eclipse Adoptium/jdk-11.0.27.6-hotspot/bin:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program Files/dotnet/:/mnt/c/Users/emtar/AppData/Local/Programs/Python/Python313/Scripts/:/mnt/c/Users/emtar/AppData/Local/Programs/Python/Python313/:/mnt/c/Users/emtar/AppData/Local/Programs/Python/Launcher/:/mnt/c/Users/emtar/AppData/Local/Microsoft/WindowsApps:/snap/bin:/home/emtar/abin
PYTHONPATH =
R_LIBS = /home/emtar/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
CC =
HOMEBREW_PREFIX =
----------------------------- 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 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (1031G Avail)
top history: ...d GroupAna_cases/gen_datatables/ggc_dt_commands.tcsh
data dir : found AFNI_data7 under $HOME
top history: ...025 [PT/RCR]: init with do_ scripts and sub-000 data
data dir : found AFNI_demos under $HOME
top history: 22 May 2025 [taylorp]: update subject QC directories
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 $HOME
atlas : found TT_N27+tlrc under /home/emtar/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.8.3 (amd64)
which git : /usr/bin/git
git version : git version 2.43.0
which gcc : /usr/bin/gcc
gcc version : gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
have Ubuntu system: ubuntu 24.04 Noble Numbat
have Ubuntu afni : Precompiled binary linux_ubuntu_24_64: Sep 17 2025
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* dot file test : want 1 modifications across 3 files:
I tried downloading the R packages another way and that didn't seem to work. Here is the code for that:
emtar@TarlowInsp15-2:~$ rPkgsInstall -pkgs ALL
Installing package into ‘/home/emtar/R’
(as ‘lib’ is unspecified)
++ Note: @ 18:36:57
This package has been installed on the computer: gamm4
Warning message:
package ‘gamm4’ is not available for this version of R
‘gamm4’ version 0.2-7 is in the repositories but depends on R (>= 4.4.0)
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
Then I tried following the advice given in another discussion post (Fail to install R packages) and after making a mistake with the username and then fixing it I got this:
emtar@TarlowInsp15-2:~$ sudo apt-get remove -y r-base r-base-core r-base-dev
mv /home/liubingyu/R /home/liubingyu/R_old_backup
mkdir /home/emtar/R
[sudo] password for emtar:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Package 'r-base' is not installed, so not removed
The following packages were automatically installed and are no longer required:
libauthen-sasl-perl libclone-perl libdata-dump-perl libencode-locale-perl libfile-basedir-perl
libfile-desktopentry-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libhtml-form-perl
libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl
libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libllvm19 liblwp-mediatypes-perl
liblwp-protocol-https-perl libmailtools-perl libncurses-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libreadline-dev libtie-ixhash-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl
libwww-robotrules-perl libx11-protocol-perl libxcb-shape0 libxml-parser-perl libxml-twig-perl
libxml-xpathengine-perl libxxf86dga1 perl-openssl-defaults r-doc-html unzip x11-utils xdg-utils zip
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth
r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial
r-cran-survival r-recommended
0 upgraded, 0 newly installed, 18 to remove and 16 not upgraded.
After this operation, 72.9 MB disk space will be freed.
(Reading database ... 105339 files and directories currently installed.)
Removing r-recommended (4.3.3-2build2) ...
Removing r-cran-rpart (4.1.23-1build1) ...
Removing r-cran-survival (3.5-8-1) ...
Removing r-cran-codetools (0.2-19-1) ...
Removing r-cran-spatial (7.3-17-1build1) ...
Removing r-base-dev (4.3.3-2build2) ...
Removing r-cran-boot (1.3-30-1) ...
Removing r-cran-class (7.3-22-2build1) ...
Removing r-cran-cluster (2.1.6-1build1) ...
Removing r-cran-foreign (0.8.86-1build1) ...
Removing r-cran-kernsmooth (2.23-22-1build1) ...
Removing r-cran-mgcv (1.9-1-1) ...
Removing r-cran-nlme (3.1.164-1build1) ...
Removing r-cran-matrix (1.6-5-1) ...
Removing r-cran-lattice (0.22-5-1build1) ...
Removing r-cran-mass (7.3-60.0.1-1) ...
Removing r-cran-nnet (7.3-19-2build1) ...
Removing r-base-core (4.3.3-2build2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for man-db (2.12.0-4build2) ...
Processing triggers for desktop-file-utils (0.27-2build1) ...
mv: cannot stat '/home/liubingyu/R': No such file or directory
mkdir: cannot create directory ‘/home/emtar/R’: File exists
emtar@TarlowInsp15-2:~$ sudo apt-get remove -y r-base r-base-core r-base-dev
mv /home/emtar/R /home/emtar/R_old_backup
mkdir /home/emtar/R
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Package 'r-base' is not installed, so not removed
Package 'r-base-core' is not installed, so not removed
Package 'r-base-dev' is not installed, so not removed
The following packages were automatically installed and are no longer required:
libauthen-sasl-perl libclone-perl libdata-dump-perl libencode-locale-perl libfile-basedir-perl
libfile-desktopentry-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libhtml-form-perl
libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl
libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libllvm19 liblwp-mediatypes-perl
liblwp-protocol-https-perl libmailtools-perl libncurses-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libreadline-dev libtie-ixhash-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl
libwww-robotrules-perl libx11-protocol-perl libxcb-shape0 libxml-parser-perl libxml-twig-perl
libxml-xpathengine-perl libxxf86dga1 perl-openssl-defaults r-doc-html unzip x11-utils xdg-utils zip
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
emtar@TarlowInsp15-2:~$ sudo echo "" >> /etc/apt/sources.list
sudo echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list
sudo echo "" >> /etc/apt/sources.list
-bash: /etc/apt/sources.list: Permission denied
-bash: /etc/apt/sources.list: Permission denied
-bash: /etc/apt/sources.list: Permission denied
login shell 'bash', but our code examples use 'tcsh'
This is just a comment for you to be aware of, in case you try copy+pasting from a script into your terminal. It's not an error message, so there isn't actually anything to fix.
missing R packages (see rPkgsInstall)
This one occurs because theere is one R package (gamm4) that is not available in the R ver 4.3.*, and only in 4.4.* and higher. Sigh. If you wanted, you could try to update your R version, but that package actually is not used in many AFNI programs (I believe only 3dMSS at present, which is a fairly particular use case), so I don't think it is likely worth worrying about at present. I would just wait until you actually need that program before going through the hassle of an R update. (I guess R ver 4.5.1 actually has many sub-package issues, at present, as well, so it would be worth avoiding those til those are sorted.)
dot file test : want 1 modifications across 3 files:
This refers to how your shell setup files look across different shells. Based on the "shell startup files" subsection of the system check output there (and thanks for copy+pasting the full thing for clarity!), I think it is just that if you switched your default shell to 'csh', you might not have auto-completion of AFNI program options (which the program "apsearch" generates/makes use of). So, I think if things are working reasonably well at present, you are probably also set there.
I just ran the check-all command and a few new failures came up. Are they any cause for concern?
just be aware: login shell 'bash', but our code examples use 'tcsh'
missing program: R
failure under initial "AFNI and related program tests"
AFNI programs show FAILURE
missing binary library: libR.so
missing R packages (see rPkgsInstall)
dot file test : want 1 modifications across 3 files:
Here's the full thing:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 6.6.87.2-microsoft-standard-WSL2
version: #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025
distribution: ubuntu 24.04 Noble Numbat
number of CPUs: 8
user: emtar
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/emtar/abin/afni
afni version : Precompiled binary linux_ubuntu_24_64: Sep 17 2025
: AFNI_25.2.13 'Gordian I'
AFNI_version.txt : AFNI_25.2.13, linux_ubuntu_24_64, Sep 17 2025, official
which python : /usr/bin/python
python version : 3.12.3
which R :
instances of various programs found in PATH:
afni : 1 (/home/emtar/abin/afni)
R : 0
python : 1 (/usr/bin/python3.12)
python2 : 0
python3 : 1 (/usr/bin/python3.12)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
build_afni.py : success
uber_subject.py : success
3dMVM : FAILURE
R: Command not found.
rPkgsInstall : FAILURE
R: Command not found.
** missing binary library 'libR.so' in program R_io.so
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
tcsh version : 6.24.10
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.
R RHOME : R: Command not found.
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.6.3
++ module loaded: flask
module file : /usr/lib/python3/dist-packages/flask/__init__.py
flask version : 3.0.2
++ module loaded: flask_cors
module file : /usr/lib/python3/dist-packages/flask_cors/__init__.py
flask_cors version : 4.0.0
-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Program Files/Eclipse Adoptium/jdk-11.0.27.6-hotspot/bin:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program Files/dotnet/:/mnt/c/Users/emtar/AppData/Local/Programs/Python/Python313/Scripts/:/mnt/c/Users/emtar/AppData/Local/Programs/Python/Python313/:/mnt/c/Users/emtar/AppData/Local/Programs/Python/Launcher/:/mnt/c/Users/emtar/AppData/Local/Microsoft/WindowsApps:/snap/bin:/home/emtar/abin
PYTHONPATH =
R_LIBS = /home/emtar/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
CC =
HOMEBREW_PREFIX =
----------------------------- 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 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (1031G Avail)
top history: ...d GroupAna_cases/gen_datatables/ggc_dt_commands.tcsh
data dir : found AFNI_data7 under $HOME
top history: ...025 [PT/RCR]: init with do_ scripts and sub-000 data
data dir : found AFNI_demos under $HOME
top history: 22 May 2025 [taylorp]: update subject QC directories
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 $HOME
atlas : found TT_N27+tlrc under /home/emtar/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.8.3 (amd64)
which git : /usr/bin/git
git version : git version 2.43.0
which gcc : /usr/bin/gcc
gcc version : gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
have Ubuntu system: ubuntu 24.04 Noble Numbat
have Ubuntu afni : Precompiled binary linux_ubuntu_24_64: Sep 17 2025
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing program: R
* failure under initial "AFNI and related program tests"
* AFNI programs show FAILURE
* missing binary library: libR.so
* missing R packages (see rPkgsInstall)
* dot file test : want 1 modifications across 3 files:
I think I removed it when trying to install the missing R package (gamm4). I posted the code I put in and the output I got for it at the end of my initial post.
I'm posting it here again:
rPkgsInstall -pkgs ALL
Installing package into ‘/home/emtar/R’
(as ‘lib’ is unspecified)
++ Note: @ 18:36:57
This package has been installed on the computer: gamm4
Warning message:
package ‘gamm4’ is not available for this version of R
‘gamm4’ version 0.2-7 is in the repositories but depends on R (>= 4.4.0)
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
emtar@TarlowInsp15-2:~$ sudo apt-get remove -y r-base r-base-core r-base-dev
mv /home/liubingyu/R /home/liubingyu/R_old_backup
mkdir /home/emtar/R
[sudo] password for emtar:
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Package 'r-base' is not installed, so not removed
The following packages were automatically installed and are no longer required:
libauthen-sasl-perl libclone-perl libdata-dump-perl libencode-locale-perl libfile-basedir-perl
libfile-desktopentry-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libhtml-form-perl
libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl
libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libllvm19 liblwp-mediatypes-perl
liblwp-protocol-https-perl libmailtools-perl libncurses-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libreadline-dev libtie-ixhash-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl
libwww-robotrules-perl libx11-protocol-perl libxcb-shape0 libxml-parser-perl libxml-twig-perl
libxml-xpathengine-perl libxxf86dga1 perl-openssl-defaults r-doc-html unzip x11-utils xdg-utils zip
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth
r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial
r-cran-survival r-recommended
0 upgraded, 0 newly installed, 18 to remove and 16 not upgraded.
After this operation, 72.9 MB disk space will be freed.
(Reading database ... 105339 files and directories currently installed.)
Removing r-recommended (4.3.3-2build2) ...
Removing r-cran-rpart (4.1.23-1build1) ...
Removing r-cran-survival (3.5-8-1) ...
Removing r-cran-codetools (0.2-19-1) ...
Removing r-cran-spatial (7.3-17-1build1) ...
Removing r-base-dev (4.3.3-2build2) ...
Removing r-cran-boot (1.3-30-1) ...
Removing r-cran-class (7.3-22-2build1) ...
Removing r-cran-cluster (2.1.6-1build1) ...
Removing r-cran-foreign (0.8.86-1build1) ...
Removing r-cran-kernsmooth (2.23-22-1build1) ...
Removing r-cran-mgcv (1.9-1-1) ...
Removing r-cran-nlme (3.1.164-1build1) ...
Removing r-cran-matrix (1.6-5-1) ...
Removing r-cran-lattice (0.22-5-1build1) ...
Removing r-cran-mass (7.3-60.0.1-1) ...
Removing r-cran-nnet (7.3-19-2build1) ...
Removing r-base-core (4.3.3-2build2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for man-db (2.12.0-4build2) ...
Processing triggers for desktop-file-utils (0.27-2build1) ...
mv: cannot stat '/home/liubingyu/R': No such file or directory
mkdir: cannot create directory ‘/home/emtar/R’: File exists
emtar@TarlowInsp15-2:~$ sudo apt-get remove -y r-base r-base-core r-base-dev
mv /home/emtar/R /home/emtar/R_old_backup
mkdir /home/emtar/R
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Package 'r-base' is not installed, so not removed
Package 'r-base-core' is not installed, so not removed
Package 'r-base-dev' is not installed, so not removed
The following packages were automatically installed and are no longer required:
libauthen-sasl-perl libclone-perl libdata-dump-perl libencode-locale-perl libfile-basedir-perl
libfile-desktopentry-perl libfile-listing-perl libfile-mimeinfo-perl libfont-afm-perl libhtml-form-perl
libhtml-format-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl
libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libio-html-perl
libio-socket-ssl-perl libio-stringy-perl libipc-system-simple-perl libllvm19 liblwp-mediatypes-perl
liblwp-protocol-https-perl libmailtools-perl libncurses-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libreadline-dev libtie-ixhash-perl libtimedate-perl libtry-tiny-perl liburi-perl libwww-perl
libwww-robotrules-perl libx11-protocol-perl libxcb-shape0 libxml-parser-perl libxml-twig-perl
libxml-xpathengine-perl libxxf86dga1 perl-openssl-defaults r-doc-html unzip x11-utils xdg-utils zip
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded.
emtar@TarlowInsp15-2:~$ sudo echo "" >> /etc/apt/sources.list
sudo echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list
sudo echo "" >> /etc/apt/sources.list
-bash: /etc/apt/sources.list: Permission denied
-bash: /etc/apt/sources.list: Permission denied
-bash: /etc/apt/sources.list: Permission denied
Your original setup seemed good, which was what Paul was suggesting.
Ubuntu 24 comes with R 4.3.3 which is too old for gamm4. But gamm4 is needed only for the program 3dMSS. Do you definitely need that program? If not, it is not a problem.
So if 3dMSS is not important to you, which is probably the case, then please reinstall the R packages:
That's perfect. I've got the R packages back on and I most likely won't need the 3dMSS program.
Thanks for the help!
-Eli
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.