Hi all!
I'm trying to run AFNI within a Docker container. I start the container with this command: "docker run -it --rm afni/afni:latest". Although I can use the viewer just fine, few other things seem to work. When I run "afni_system_check.py -check_all", I get the following output:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.19.104-microsoft-standard
version: #1 SMP Wed Feb 19 06:37:35 UTC 2020
distribution: Ubuntu 18.04 bionic
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /opt/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: May 22 2020
: AFNI_20.1.07 'Otho'
AFNI_version.txt : AFNI_20.1.07, linux_ubuntu_16_64, May 22 2020
which python : /usr/bin/python
python version : 2.7.17
which R : /usr/bin/R
R version : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/opt/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)
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: 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
checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python2.7/dist-packages/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /opt/abin:/cmake/cmake-3.14.7-Linux-x86_64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under /opt/src/afni/doc/misc_scripts
top history: NONE FOUND
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
which apt-get : /usr/local/bin/apt-get
apt-get version : apt 1.6.12 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: May 22 2020
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* 'afni' executable is owned by root
* missing R packages (see rPkgsInstall)
* please run: cp /opt/abin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
* possibly missing atlases
I don't think I launched the container wrong. I'm wondering if the container itself wasn't built correctly. What might I be doing wrong?
Ben
Edited 1 time(s). Last edit at 09/17/2020 10:25AM by veliebm.
