I am trying to install AFNI on Ubuntu 20.04 LTS. I followed all instructions found
here. I was getting some warnings/errors throughout, for example with libxm4 (libXm.so.4) not being installed -- which that alone seems to lead to major errors (e.g. suma -update_env won't work, AFNI won't open, etc.). I have a .txt. file with the output from
afni_system_check.py that I can email, but I have also posted it below.
From the summary I am also unsure what "login shell 'bash', trusting user to translate code examples from 'tcsh'" means I need to do (my normal shell is bash, although tcsh is installed). I will also install miniconda 2.7 to fix that requirement. I am unsure on what is wrong with the R installation given I followed all the steps and that seemed to go fine. I cannot run the suma command, but I did run the suggested apsearch command.
Thank you so much for the help!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.4.0-31-generic
version: #35-Ubuntu SMP Thu May 7 20:20:34 UTC 2020
distribution: debian bullseye/sid
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/keith/abin/afni
afni version : afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
:
AFNI_version.txt : AFNI_20.1.13, linux_ubuntu_16_64, Jun 03 2020
which python : /home/keith/miniconda3/bin/python
python version : 3.7.6
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/keith/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/home/keith/miniconda3/bin/python3.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/home/keith/miniconda3/bin/python3.7
/usr/bin/python3.8
testing ability to start various programs...
afni : FAILURE
afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
suma : FAILURE
suma: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
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 : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/keith/miniconda3/bin:/home/keith/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/keith/abin
PYTHONPATH =
R_LIBS = /home/keith/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
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/keith/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.2ubuntu0.1 (amd64)
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* have python version 3.7.6, some programs need 2.7.x
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
