On Tue, Nov 11, 2014 at 8:57 PM, Andreas Goetz <agoetz.sdsc.edu <mailto:agoetz.sdsc.edu>> wrote:
Hi all,
update_amber in the amber-14-with-patches branch wants to download/apply patches 14 to 19 for AmberTools, although these are in the branch (according to the log). Any idea why this happens?
Yes, I know why it happens :). updates 1 to 13 are tracked in that branch, but updates 14 to 19 are not yet. update_amber uses those files to do its bookkeeping (which also allows it to reverse certain updates upon request).
Every once in awhile I (or someone else) runs "./update_amber --update" to download and apply the patches which should just report a previously applied patch was detected and move the update into place (i.e., .patches) without making any changes.
In (what should be) rare occasions, it will catch instances where authors of some patches forgot to actually push those changes to amber14-with-patches, and it will basically point that out. In even rarer occasions, the context of a patch remains unchanged after it is applied, so it can continue to apply multiple times, so whoever updates the database of tracked patches needs to be mindful of that.
In this particular case, it seems that update.16 was never actually added to the amber14-with-patches branch, so I'll take this opportunity to remind people that create patches to follow
http://ambermd.org/pmwiki/index.php/Main/BugFixCreationInstructions <
http://ambermd.org/pmwiki/index.php/Main/BugFixCreationInstructions> to help keep our updating mechanism working well.
In any case, this all should be fixed now:
[swails.Robin ~/amber (amber14-with-patches) ]$ ./update_amber --check
Checking for available patches online. This may take a few seconds...
Available AmberTools 14 patches:
No patches available
Available Amber 14 patches:
No patches available
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 11 2014 - 19:00:02 PST
