rPkgsInstall -pkgs ALL command not found

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1

rPkgsInstall -pkgs ALL command not found

I am getting this error ,When I give above command on CentOS 7. Please guide me where to check and how to fix this.

Thank you.
-Shiva

2

Please provide the output of:


afni_system_check.py -check_all

–pt

3

When I run that, I got the reply like bash: afni_system_check.py -check_all: command not found

4

As per your other post, I don’t think you have refreshed your terminal by sourcing shell RC file-- in your case, it appeared to be a bash shell, so by doing:


source ~/.bashrc

Or, you could try opening a new terminal.

–pt

5

Hi,

I followed the link [afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_Fed_RH.html]

sudo yum install -y epel-release
sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc
PyQt4 R-devel netpbm-progs gnome-tweak-tool ed
libpng12 xorg-x11-server-Xvfb firefox
sudo yum update -y

cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries
tcsh @update.afni.binaries -package linux_centos_7_64 -do_extras

export R_LIBS=$HOME/R
mkdir $R_LIBS
echo ‘setenv R_LIBS ~/R’ >> ~/.cshrc
echo ‘export R_LIBS=$HOME/R’ >> ~/.bashrc
. ~/.bashrc

complete the all above steps without errors

when I run rPkgsInstall -pkgs ALL , I am getting the error.

6

Hi,

I am sorry, I signed out completely and signed back in… still same error.

7

When you log back in, are you logged in as root? Or as a separate user?

You can type “whoami” in a terminal to see who you are on the machine.

–pt

8

Is your user account login as “root”? If not, “cd” should take you to your user home directory, and your abin would be put there (not in /root/, where, again, it probably should not live).

–pt

9

Hi Taylor,

I have only three accounts on the machine

  1. root login
  2. shiva ( i have sudo privileges)
  3. imt

I am trying the installation using my account i.e shiva

Thank you.

10

Then I wonder if the problem is having abin under /root/ while you are logged in as a different user.

I think the abin under root should be removed (and be VERY careful if you use wildcards to do this!!! one reason not to put abin under /root…).

Then follow the normal AFNI setup instructions, and install/put abin under your home directory (probably /home/shiva):


cd
curl -O [https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries](https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries)
tcsh @update.afni.binaries -package linux_centos_7_64 -do_extras

In doing the above command, after “cd”, you can type “pwd” to make sure you really are in your home directory-- “pwd” tells you your present working directory-- before doing the next commands.

–pt

11

Thank you Taylor for clarification. I will follow your instruction. I will try to do fresh installation and will get you back.

Thank you
Shiva