AFNI UBUNTU 20.04 R PKGs not installing/ PyQT4 issue

Hi there,

I’m reattemtping to install afni on UBUNTU 20.04 (using the “quick setup”): lmerTest, phia and afex won’t install, and I can’t seem to install them manually. Output from -check_all is below. On a different note, I previously tried to install and could not figure out a PyQT4 issue: “check for partial installation of PyQT4” needed to launch Does anyone have any suggestions on the next procedural steps I should take to load all the necessary python packages needed for, [i]after[i] running quick setup?

Might be a shot in the dark, but would be really useful to have for exploratory analyses and not having it is bugging me.

Any help would be appreciated!!!

-Sam -check_all -------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.13.0-27-generic
version: #29~20.04.1-Ubuntu SMP Fri Jan 14 00:32:30 UTC 2022
distribution: ubuntu 20.04 focal
number of CPUs: 4
apparent login shell: bash (current shell is tcsh)
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/klei0742/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Jan 18 2022
: AFNI_22.0.03 ‘Hadrian’
AFNI_version.txt : AFNI_22.0.03, linux_ubuntu_16_64, Jan 18 2022
which python : /usr/bin/python
python version : 3.8.10
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 (/home/klei0742/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.8)
python2 : 0
python3 : 1 (/usr/bin/python3.8)

** have python3 but not python2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : 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: lmerTest!

R RHOME : /usr/lib/R

checking for $HOME files…
.afnirc : found
.sumarc : found
.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/lib/python3/dist-packages/matplotlib/
matplotlib version : 3.1.2

-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/klei0742/abin:/home/klei0742/abin

R_LIBS = /home/klei0742/R


------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (248176M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_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/klei0742/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.6 (amd64)

have Ubuntu system: ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Jan 18 2022

========================= summary, please fix: =========================

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • missing R packages (see rPkgsInstall)

Hi Sam,

Dealing with those R packages is a bit tricky, and pyqt4 is not directly available under Ubuntu 20.
So the first question is whether you actually want to use the few programs that depend on those packages.
Are you really hoping to use any of the uber_* programs?

It might be worth not worrying about until you actually run into a program that they are needed for.

  • rick

Ah, that’s helpful re: PyQt4. Thanks!