afni.nimh.nih.gov
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:
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
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
| December 31, 2019 02:03PM | |
Hi,
I have followed the installation guide for Ubuntu 18.04, however, four libraries continue to be missing "afex", "phia", "brms", and "metafor". I see from the message board history that user alfarmer8 had the same issue a couple of months ago, and I'm wondering whether a solution was found. Thank you, and happy new year!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.0.0-37-generic
version: #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019
distribution: elementary 5.1 hera
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/pereanez/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 27 2019
: AFNI_19.3.18 'Nero'
AFNI_version.txt : AFNI_19.3.18, linux_ubuntu_16_64, Dec 27 2019
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/pereanez/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: brms!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/pereanez/abin
PYTHONPATH =
R_LIBS = /home/pereanez/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
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/pereanez/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.12 (amd64)
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .profile
* missing R packages (see rPkgsInstall)
I have followed the installation guide for Ubuntu 18.04, however, four libraries continue to be missing "afex", "phia", "brms", and "metafor". I see from the message board history that user alfarmer8 had the same issue a couple of months ago, and I'm wondering whether a solution was found. Thank you, and happy new year!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.0.0-37-generic
version: #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 UTC 2019
distribution: elementary 5.1 hera
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/pereanez/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 27 2019
: AFNI_19.3.18 'Nero'
AFNI_version.txt : AFNI_19.3.18, linux_ubuntu_16_64, Dec 27 2019
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/pereanez/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: brms!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/pereanez/abin
PYTHONPATH =
R_LIBS = /home/pereanez/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
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/pereanez/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.12 (amd64)
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .profile
* missing R packages (see rPkgsInstall)
