On Mon, 2014-03-10 at 12:32 -0300, George Tzotzos wrote:
> I’m trying to recompile Amber12.
>
> Applying the patches results in:
>
> Warning: AMBERHOME [None] differs from expected [/Users/3i521409/Programs/amber12].
> No changes will be made until this is fixed
>
> SetupError: Making changes has been disabled because AMBERHOME is not set correctly or the updater has been moved from AMBERHOME.
>
> However, the environment is set up correctly as shown below.
>
> $ env | grep AMBERHOME
> AMBERHOME=/Users/3i521409/Programs/amber12/
>
> Any suggestions will be extremely helpful
Whatever you're doing to run the configure script is launching the
configure script in a shell that has lost your environment. The stdlib
functions used to extract environment variables is well-defined in
Python. So if update_amber indicates that AMBERHOME is not set, then I
assure you that AMBERHOME is not set by the running configure script
(you can verify this by putting the command "env | grep AMBERHOME"
before the update checking command in $AMBERHOME/configure). In this
case, knowing *exactly* how you configured your environment and called
the configure script is critical to debugging your problem.
The most common reason I've seen for this type of environment confusion
is the use of "sudo" which in many cases launches a shell that does not
inherit the original shell's environment. This can be fixed in one of
the following ways.
1) Do not use sudo. Change directory ownership and execute every
command as a normal user.
2) Same as 1
3) Same as 1
4) ...
...
100) Use "sudo -E" instead so the root shell that sudo spawns inherits
the parent shell's environment.
(If it wasn't apparent, I strongly discourage the use of approach 100).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 10 2014 - 10:00:04 PDT
