Hello,
What is the best way to install AFNI on AlmaLinux 8? The Red Hat Linux instructions I found are for RHEL/CentOS 7. Will these work with AlmaLinux 8?
Thanks,
Eddie
Hi Eddie,
We have a more compatible package for Rocky 8, with instructions and 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
Note that those instructions are for a build machine. You should be able to remove -devel from those package names.
But other than the admin instructions, you can follow the same steps, just use package linux_rocky_8 instead of linux_centos_7_64.
- rick
Hi Rick,
Thanks for providing these instructions. I was able to install the binaries, but received errors when running rPkgsInstall. Below is the output from the afni system check.
Can you please help me troubleshoot?
Thanks,
Eddie
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Linux
release: 4.18.0-477.27.1.el8_8.x86_64
version: #1 SMP Wed Sep 20 15:55:39 UTC 2023
distribution: Rocky Linux 8.8 Green Obsidian
number of CPUs: 6
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/eddie/abin/afni
afni version : Precompiled binary linux_rocky_8: Oct 12 2023
: AFNI_23.3.01 'Septimius Severus'
AFNI_version.txt : AFNI_23.3.01, linux_rocky_8, Oct 12 2023, official
which python : /usr/bin/python
python version : 3.6.8
which R : /usr/bin/R
R version : R version 4.3.1 (x86_64-redhat-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/eddie/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/libexec/platform-python3.6)
python2 : 0
python3 : 1 (/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 : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: gamm4!
These packages are not installed on the computer: brms!
R RHOME : /usr/lib64/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/lib64/python3.6/site-packages/matplotlib/pyplot.py
matplotlib version : 3.0.3
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/opt/puppetlabs/bin:/opt/puppetlabs/bin:/home/eddie/abin
PYTHONPATH =
R_LIBS = /home/eddie/R
LD_LIBRARY_PATH =
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 ----------
-- 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 2 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
------------------------------ 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/eddie/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: =========================
- missing program: Xvfb
- missing R packages (see rPkgsInstall)
- dot file test : want 1 modifications across 2 files:
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
Hi Rick,
I attempted to install AFNI on a different Rocky Linux 8 workstation and continue to get several errors. Below is my out.ASC.txt. Can you please help troubleshoot?
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Linux
release: 4.18.0-477.27.1.el8_8.x86_64
version: #1 SMP Wed Sep 20 15:55:39 UTC 2023
distribution: Rocky Linux 8.8 Green Obsidian
number of CPUs: 6
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/idas-admin/abin/afni
afni version : Precompiled binary linux_rocky_8: Nov 7 2023
: AFNI_23.3.07 'Septimius Severus'
AFNI_version.txt : AFNI_23.3.07, linux_rocky_8, Nov 07 2023, official
which python : /usr/bin/python
python version : 3.6.8
which R : /usr/bin/R
R version : R version 4.3.2 (x86_64-redhat-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/idas-admin/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/libexec/platform-python3.6)
python2 : 0
python3 : 1 (/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 :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: 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 : /usr/lib64/python3.6/site-packages/matplotlib/pyplot.py
matplotlib version : 3.0.3
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/opt/puppetlabs/bin:/opt/puppetlabs/bin:/usr/local/cuda-12.2/bin:/home/idas-admin/abin:/usr/local/cuda-12.2/bin:/home/idas-admin/abin
PYTHONPATH =
R_LIBS = /home/idas-admin/R
LD_LIBRARY_PATH =
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 ----------
-- 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)
dot file test : want 1 modifications across 2 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
------------------------------ 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/idas-admin/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: =========================
* AFNI programs show FAILURE
* missing program: Xvfb
* missing R packages (see rPkgsInstall)
* dot file test : want 1 modifications across 2 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
Thanks,
Eddie
Hi Eddie,
The most important thing you are missing (well, depending on your needs) is probably Xvfb. An admin user should install that package (xorg-x11-server-Xvfb), though they might want to review the packages in our install instructions: OS_notes.linux_rocky_8.txt. That list would imply the x11 packages.
The R_LIBS directory might need to be filled by admin owner, but if you can write there, consider running:
rPkgsInstall -pkgs ALL
If you get those 2 things done, you will be in good shape. We can ponder the apsearch bit if you would like to.
- rick
Hi Rick,
I was able to install Xvfb.
The same R packages failed to install when using rPkgsInstall -pkgs ALL. If these packages aren't required for typical AFNI use, I'll just ignore them. I'm installing AFNI for another user and I am not very familiar with those packages.
Thanks,
Eddie
Sure. Those R libraries are needed for most of Gang's group analysis programs. So it depends on whether you want to use them. If it seems like you want the R libraries, I would be happy to help more directly with that. Just let me know.
- rick
We are interested in using those programs. Please help install the R libraries. Thanks!
I will send you a private message...
- rick