AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
ptaylor
September 22, 2021 08:35AM
Dear AFNI Gurus-

I followed the main installation instructions here for AFNI on a fresh, new Ubuntu 20.04 OS:
[afni.nimh.nih.gov]
But I am missing the "brms" package for R. How can I install it?

Here is my system check output: 
-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Linux
release:              5.11.0-34-generic
version:              #36~20.04.1-Ubuntu SMP Fri Aug 27 08:06:32 UTC 2021
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/ptaylor/afni_build/src/linux_ubuntu_16_64_glw_local_shared/afni
afni version         : Precompiled binary linux_ubuntu_16_64_glw_local_shared: Sep 21 2021 
                     : AFNI_21.2.07 'Nerva'
AFNI_version.txt     : AFNI_21.2.07, linux_ubuntu_16_64_glw_local_shared, Sep 21 2021
which python         : /home/ptaylor/miniconda3/envs/py37_afni_jup_sph/bin/python
python version       : 3.7.9
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/ptaylor/afni_build/src/linux_ubuntu_16_64_glw_local_shared/afni)
    R       : 1   (/usr/bin/R)
    python  : 2 
      /home/ptaylor/miniconda3/envs/py37_afni_jup_sph/bin/python3.7
      /usr/bin/python3.8
    python2 : 1   (/usr/bin/python2.7)
    python3 : 2 
      /home/ptaylor/miniconda3/envs/py37_afni_jup_sph/bin/python3.7
      /usr/bin/python3.8


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: brms!
        

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 : /home/ptaylor/miniconda3/envs/py37_afni_jup_sph/lib/python3.7/site-packages/matplotlib/pyplot.py

-------------------------------- env vars --------------------------------
PATH = /home/ptaylor/miniconda3/envs/py37_afni_jup_sph/bin:/home/ptaylor/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ptaylor/afni_build/src/linux_ubuntu_16_64_glw_local_shared

PYTHONPATH = 
R_LIBS = /home/ptaylor/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: ...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    : did not find TT_N27+tlrc

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


=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  missing R packages (see rPkgsInstall)
*  possibly missing atlases

Grazie,
pt
Reply Quote
RSS
Subject Author Posted

how to install brms on Ubuntu 20.04?

ptaylor September 22, 2021 08:35AM

Re: how to install brms on Ubuntu 20.04?

gang September 22, 2021 06:37PM

Re: how to install brms on Ubuntu 20.04?

ptaylor September 23, 2021 12:56PM

Re: how to install brms on Ubuntu 20.04?

gang September 23, 2021 02:27PM