Hi Scott,
On Wed, Jul 27, 2011 at 2:10 AM, Scott Brozell <sbrozell.rci.rutgers.edu>wrote:
> Hi,
>
> On Tue, Jun 28, 2011 at 12:34:04AM -0600, Jason Swails wrote:
> > On Mon, Jun 27, 2011 at 8:15 PM, Scott Brozell <sbrozell.rci.rutgers.edu
> >wrote:
> > > On Mon, Jun 27, 2011 at 09:58:45PM +0000, B. Lachele Foley wrote:
> > > > I am working on adding to this page: http://ambermd.org/ubuntu.html
> > >
> > > I thought that i had worked on that page, but
> > > there are only 2 log entries and I didnt do either.
> > >
> > > > The page says that earlier versions of amber needed bison or byacc.
> I
> > > got an install to go pretty well without any such (Ubuntu 10.04.2 LTS
> --
> > > Lucid Lynx outfitted to be an LTSP server).
> > > >
> > > > Does that give anyone reason for concern? The test results are
> below.
> > > Details upon request.
> > > >
> > >
> > > Probably not. grepping the Makefiles shows that a yacc is used.
> > > But in configure there is
> > > YACC= \$(BINDIR)/yacc
> > >
> > > There are no useful comments in the logs on yacc.
> >
> > bison was at one point necessary for Amber on Ubuntu. There was a line
> that
> > bison would interpret correctly, but the amber-provided yacc would not.
> It
> > was actually you (Scott) that caught the cause of this issue, and Dave
> that
> > checked in the fix (back in the CVS days from the look of the message
> log).
> ^^^^^^^^^^^
>
> Jason, what log exactly are you viewing and how did you get that log ?
>
See the thread that I linked in my last email. The log you're looking for
won't be in amber_web, it'll be in the main amber repo. Here it is:
commit a89dd8dfbcd9ba0ad0a7fc7944f054e58cb783a9
Author: case <case>
Date: Wed Mar 10 16:19:41 2010 +0000
comment out expect line, doesn't seem to work for Amber's yacc
If it was the days of git, the Author would be Dave with his full email
(most likely).
>
> When i did a git log of amber_web/ubuntu.html i got:
> ----
> commit 505e9de6cbe5258e34102278d62d39ee6cd47782
> Author: Jason Swails <jason.swails.gmail.com>
> Date: Wed Jan 5 11:35:45 2011 -0500
>
> Update Ubuntu instructions -- bz2 and libbz2 must be installed from
> aptitude for cpptraj to work fully, so I added this to the list of
> packages that should be installed.
>
> commit fa453eb884ff8403171e099b9457de606d57e6d3
> Author: David A. Case <case.biomaps.rutgers.edu>
> Date: Thu May 13 22:05:47 2010 -0400
>
> initial repo on 5/13/10
> ----
>
> As you can see there is no mention of bison/yacc...
> I really miss being able to read old (cvs) logs.
> I put a lot of clues in my logs so that i could remember what i did
> and why. There have always been too many bosses/projects/programs
> to keep that in my head.
>
The amber tree retained the CVS logs, but amber_web apparently did not
(probably since Dave didn't migrate all of the files over).
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Thu Jul 28 2011 - 09:00:22 PDT
