Installation error

Dear All,

I am new to this forum. I have installed afni recently with some minor error. Please see the message pasted below and let me know what should I do (see the highlighted message)?

Thanks in advance
Ramesh

-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.13.0-21-generic
version: #24-Ubuntu SMP Mon Dec 18 17:29:16 UTC 2017
distribution: Ubuntu 17.10 artful
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /opt/afni/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 22 2017
: AFNI_17.3.09
AFNI_version.txt : AFNI_17.3.09, linux_ubuntu_16_64, Dec 22 2017
which python : /usr/bin/python
python version : 2.7.14
which R : /usr/bin/R
R version : R version 3.4.2 (2017-09-28) – “Short Summer”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/opt/afni/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 : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.19: 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 : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/c3d-1.1.0-Linux-gcc64/bin:/home/rb/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/afni:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/cuda-9.0/bin

PYTHONPATH =
R_LIBS = /home/rb/R

LD_LIBRARY_PATH = :/usr/local/cuda-9.0/lib64

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH = /opt/afni

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /opt/afni

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.5.1 (amd64)

have Ubuntu system: Ubuntu 17.10 artful
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Dec 22 2017

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

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • AFNI programs show FAILURE
  • insufficient data for AFNI bootcamp

Hi, Ramesh-

Welcome to the forum.

I will note that the installation instructions are listed for “Ubuntu 16.04 and higher”… but so far I haven’t tried anything as modern as 17.10-- so we’re in slightly uncharted territory here! What is the output of the following:


find /usr/lib -name "libgsl*"

?

–pt

Hi Ramesh,

Are you sure you have installed that package? I do
not think there is a change in the name:

sudo apt-get install -y gsl-bin

If that makes a difference, you might want to review
that first part of the install instructions, to be sure.

  • rick

Hi,
Thanks for your reply.
Out put from terminal

$ find /usr/lib -name “libgsl*”
/usr/lib/x86_64-linux-gnu/libgsl.so.23.0.0
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0.0.0
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0
/usr/lib/x86_64-linux-gnu/libgslcblas.a
/usr/lib/x86_64-linux-gnu/libgsl.so.23
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgsl.a

Dear Rick & Ptaylor,

Happy Christmas.

Please see the output from terminal.

$ find /usr/lib -name “libgsl*”
/usr/lib/x86_64-linux-gnu/libgsl.so.23.0.0
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0.0.0
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0
/usr/lib/x86_64-linux-gnu/libgslcblas.a
/usr/lib/x86_64-linux-gnu/libgsl.so.23
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgsl.a

I have tried this command also.
sudo apt-get install -y gsl-bin
It says, latest version is already exits.

Thanks
Ramesh

Hi, Ramesh-

We’re not certain, but can you try making the following soft link:


sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0

… and then rerun the system check?

Thanks,
pt

Dear Ptaylor,

Thank your for your suggestion. It is successful. The last letter in the script i used 19 instead of zero. I am just pasting last lines which I need to fix. It is asking to install python qut4 but I have already installed it. Please help to fix the issue.

Thanks
Ramesh

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

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • insufficient data for AFNI bootcamp
  • consider running: apt-get install python-qt4

Can you copy/paste the terminal output message from running (after you put in your password):


sudo apt-get install python-qt4

?

Then, what happens if you run:


uber_subject.py

? Does a GUI open up (-> good) or do you get error messages (-> bad)?

–pt

Dear Ptaylor,

Please see the attached error report.

[b]$ sudo apt-get install python-qt4
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-qt4 is already the newest version (4.11.4+dfsg-2build2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

$ uber_subject.py

**** failed to import PyQt4.QtGui ****

PyQt4 must be installed to run the uber_subject.py GUI
→ see the output of: uber_subject.py -help_install[/b]

Should I install different version of python-qt4?

Ramesh

Hi, Ramesh–

If you just type:


python --version

and


python -c "from PyQt4 import QtCore"

what do you get?

–pt

And it is worth noting that PyQ4 is only required for a couple supplementary GUI things, ones that don’t really get used that much (programs starting with uber_*). So, while it would be good to sort this out, it shouldn’t stop you from getting on with using AFNI+SUMA for your analyses.

-pt

Dear Ptylor,

Wish you a happy new year 2018

I reinstalled python qt4. Still I am facing the same problem.
Please help me to find out the solution.

Thanks
Ramesh

rb@rb:~$ python --version
Python 2.7.14 :: Anaconda custom (64-bit)

rb@rb:~$ python -c “from PyQt4 import QtCore”
Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named PyQt4

rb@rb:~$ sudo apt-get install python-qt4
[sudo] password for rb:
Reading package lists… Done
Building dependency tree
Reading state information… Done
python-qt4 is already the newest version (4.11.4+dfsg-2build2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

rb@rb:~$ uber_subject.py

**** failed to import PyQt4.QtGui ****

PyQt4 must be installed to run the uber_subject.py GUI
→ see the output of: uber_subject.py -help_install

Hi Ramesh,

The apt-get install will help in a normal environment, but you are
choosing to use conda, instead. If you are going to run python out
of conda, then you will need to install pyqt4 there, e.g.

conda install pyqt=4.11.4
  • rick

Dear Ptylor, & Rick,

Thank you very much for your help.

Wishing you happy new year.

I hope I have shorted out all the issues. Now I can begin my work. Please see the out from


afni_system_check.py -check_all 

Please have a look and let me know if I have to short out further.
Thanks
Ramesh
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.13.0-21-generic
version: #24-Ubuntu SMP Mon Dec 18 17:29:16 UTC 2017
distribution: debian stretch/sid
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /opt/afni/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 22 2017
: AFNI_17.3.09
AFNI_version.txt : AFNI_17.3.09, linux_ubuntu_16_64, Dec 22 2017
which python : /home/rb/anaconda2/bin/python
python version : 2.7.14
which R : /usr/bin/R
R version : R version 3.4.2 (2017-09-28) – “Short Summer”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/opt/afni/afni)
R : 1 (/usr/bin/R)
python : 2
/home/rb/anaconda2/bin/python2.7
/usr/bin/python2.7
python2 : 2
/home/rb/anaconda2/bin/python2.7
/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

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /home/rb/anaconda2/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/MATLAB/R2017b/bin:/home/rb/anaconda2/bin:/usr/local/c3d-1.1.0-Linux-gcc64/bin:/home/rb/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/afni:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/cuda-9.0/bin

PYTHONPATH =
R_LIBS = /home/rb/R

LD_LIBRARY_PATH = :/usr/local/cuda-9.0/lib64

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH = /opt/afni

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /opt/afni

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.5.1 (amd64)

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

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • insufficient data for AFNI bootcamp

Hi, Ramesh-

Yep, looks good.

–pt

Hi, again, Ramesh-

Just a quick other note: I see that you don’t have the Bootcamp dataset downloaded. That is OK, but there is really a lot of useful stuff in their – example scripts and the afni_handouts/ directory with a lot of descriptive PDFs. In addition to the online helps and programs helps, it is a very useful resource (as well as the Message Board).

–pt

Thank you Ptaylor,

Sure I will download bootcamp.

Thanks
Ramesh