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 afni_system_check.py -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 Uber_Subject.py. Does anyone have any suggestions on the next procedural steps I should take to load all the necessary python packages needed for Uber_Subject.py, [i]after[i] running quick setup?
Might be a shot in the dark, but Uber_Subject.py would be really useful to have for exploratory analyses and not having it is bugging me.
Any help would be appreciated!!!
-Sam
afni_system_check.py -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
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: 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/pyplot.py
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
PYTHONPATH =
R_LIBS = /home/klei0742/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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)