Thanks, unfortunately it still didn't work.

1. In the sources list I changed things as you said (with the actual url and not the hyperlink). Here is the output:

grep -H cran /etc/apt/sources.list

/etc/apt/sources.list:#deb [cran.cnr.berkeley.edu] rebecca/
/etc/apt/sources.list:#deb [cran.cnr.berkeley.edu] rebecca/
/etc/apt/sources.list:#deb [cran.cnr.berkeley.edu] rebecca/
/etc/apt/sources.list:#deb [cran.cnr.berkeley.edu] rebecca/
/etc/apt/sources.list:#deb [cran.cnr.berkeley.edu] rebecca/
/etc/apt/sources.list:#deb [cran.cnr.berkeley.edu] rebecca/
/etc/apt/sources.list:deb [cran.cnr.berkeley.edu] trusty/

Should the commented lines be in the output?

2. Updated R, I see this:

rPkgsInstall -pkgs ALL -update

This package has been installed on the computer: afex
This package has been installed on the computer: phia
This package has been installed on the computer: brm

However, in the system check they still don't exist.

afni_system_check.py -check_all

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!


Perhaps the following output from the updating command might help - this appeared right before the announcement of successful installation (I get this kind of error for many packages there other than afex):
* installing *source* package ‘afex’ ...
** package ‘afex’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Warning: S3 methods ‘print.curl_handle’, ‘print.curl_multi’, ‘print.form_data’, ‘print.form_file’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) :
shared object ‘curl.so’ not found
ERROR: lazy loading failed for package ‘afex’
* removing ‘/home/galit/R/afex’
* restoring previous ‘/home/galit/R/afex’

And in addition this message also appears:

The downloaded source packages are in
‘/tmp/RtmpUqDXzp/downloaded_packages’

Many thanks again for all the help!