Quote
ptaylor
Are you using precompiled binaries, or building on your own system (I'm guessing the latter, from the version info)?
I was using an fmriprep singularity image. I realized the version was old, so I built my own singularity container using @update.afni.binaries to install afni. This is the version I am using now:
Precompiled binary linux_ubuntu_16_64: Dec 2 2022 (Version AFNI_22.3.07 'Lucius Verus')
Here is the output of `afni_system_check.py -check_all` now:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 3.10.0-1160.15.2.el7.x86_64
version: #1 SMP Wed Feb 3 15:06:38 UTC 2021
distribution: Ubuntu 22.04.1 LTS
number of CPUs: 56
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /opt/afni/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 2 2022
: AFNI_22.3.07 'Lucius Verus'
AFNI_version.txt : AFNI_22.3.07, linux_ubuntu_16_64, Dec 02 2022
which python : /usr/local/miniconda/bin/python
python version : 3.10.8
which R : /usr/bin/R
R version : R version 4.1.2 (2021-11-01) -- "Bird Hippie"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/opt/afni/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/local/miniconda/bin/python3.10)
python2 : 0
python3 : 2
/usr/local/miniconda/bin/python3.10
/usr/bin/python3.10
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
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: paran!
These packages are not installed on the computer: brms!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /usr/local/miniconda/lib/python3.10/site-packages/matplotlib/pyplot.py
matplotlib version : 3.6.2
-------------------------------- env vars --------------------------------
PATH = /usr/local/miniconda/bin:/opt/workbench/bin_linux64:/opt/fsl-v6.0.6.1/share/fsl/bin:/opt/fsl-v6.0.6.1/share/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/afni
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /opt/workbench/lib_linux64::/.singularity.d/libs
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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 /opt/afni
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.8 (amd64)
have Ubuntu system: Ubuntu 22.04.1 LTS
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Dec 2 2022
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* please run: "suma -update_env" for .sumarc
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
The update fixed the problem I was having.
Edited 1 time(s). Last edit at 12/31/2022 02:28AM by heffjos.
