AFNI install issue (Ubuntu18.04)

AFNI Message Board
1

Hi all,

I am currently having issues installing AFNI on Ubuntu 18.04. Following the steps here (https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu18.html), I get to the ‘Install AFNI binaries’ section, but encounter this error message:

– running @update.afni.binaries version 3.8, March 15, 2019
– no current AFNI package found in path…
– install dir: using default ~/abin
– any downloads will be from https://afni.nimh.nih.gov via curl -O -f

– attempting to install package linux_ubuntu_16_64 under
install dir: /root/abin…
– have install dir
deleting old temporary directory…
++ working in new temp dir, .tmp.install
++ getting install prog: curl -O -f linux_ubuntu_16_64/@update.afni.binaries …
curl -O -f https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 40307 100 40307 0 0 93519 0 --:–:-- --:–:-- --:–:-- 93519
– fixing lost permissions on @update.afni.binaries
++ using updated @update.afni.binaries, instead…

++ running: tcsh tmp.@update.afni.binaries -no_recur -package linux_ubuntu_16_64 -do_extras
– running tmp.@update.afni.binaries version 3.8, March 15, 2019
– no current AFNI package found in path…
– install dir: using default ~/abin
– any downloads will be from https://afni.nimh.nih.gov via curl -O -f

– attempting to install package linux_ubuntu_16_64 under
install dir: /root/abin…
– have install dir
deleting old temporary directory…
++ working in new temp dir, .tmp.install
– skipping update of tmp.@update.afni.binaries
++ downloading test file: curl -O -f linux_ubuntu_16_64/afni …
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 12.4M 100 12.4M 0 0 9479k 0 0:00:01 0:00:01 --:–:-- 9479k

++ update needed, installing…

++ downloading full package: curl -O -f linux_ubuntu_16_64.tgz …
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 1125M 100 1125M 0 0 33.4M 0 0:00:33 0:00:33 --:–:-- 32.0M
++ extracting package linux_ubuntu_16_64.tgz…
++ backing up current binaries to auto_backup.linux_ubuntu_16_64
deleting previous backup directory, auto_backup.linux_ubuntu_16_64 …
++ installing new binaries…
then: then/endif not found.

What’s strange is that I have used the exact same build process previously with no error. I am actually building AFNI within a Docker container, and have made no changes to the Dockerfile since my last successful build. I’ve also tried using a previously-downloaded version of linux_ubuntu_16_64.tgz in combination with the -local_package flag, but the error persists.

Does anyone have any suggestions?

Best wishes,

Richard

2

Oh, that’s my fault! Please give it one more try and let me know how it goes.

Thanks,

  • rick
3

Works like a dream now, thanks Rick!

4

Great, thanks for letting me know!

Also, Paul noted that your install directory is /root/abin. If you are installing this as root for use by others, then it is preferable to specify the binary directory, something like:

-bindir /usr/local/afni/bin

If you are the sole user on the system, then you might give your regular user sudo abilities, and do any admin steps with that. The AFNI binaries themselves can just go under the user’s ~/abin directory, without any sudo rights.

Please let me know if you have any questions on this.

  • rick