Re: amber-developers: gleap/sleap issues

From: David A. Case <>
Date: Wed, 24 Oct 2007 21:57:03 -0700

On Wed, Oct 24, 2007, Mengjuei Hsieh wrote:
> It seem that the current makefile for src/gleap needs some revisions,
> first of all, it includes ../config.h, which should be ../
> config_amber.h now.

This is not the correct solution, although I would understand that it's not
obvious to anyone but me... :-)

You need to run amber10/src/configure_at first (which creates
amber10/src/config.h), then the Makefile should work.

sleap/gleap are now part of amber_tools, and (currently) are configured via
"configure_at" and are compiled via amber10/src/Makefile_at. Please see
amber10/README_at for more info.

Sometime soon, the "configure" and "configure_at" scripts will be merged (we
hope!) into a single unified script. Until then, see if the info in README_at

> Also the make clean rule for src/gleap doesn't remove *.a files.

I'll take a look at this.

> In sleap's own repository of readline, the readline/xmalloc.h is
> trying to include readline/readline/rlstdc.h, which may need to be
> taken care of. In some operating systems, gcc -I. get to read the
> rlstdc.h without problem, but that's not the case in my linux fc6 and
> macosx.

My recommendation is to change amber10/src/gleap/freelib/readline/xmalloc.h
as follows:

c.h 4 May 2007 17:49:11 -0000 1.1
--- xmalloc.h 25 Oct 2007 00:13:35 -0000
*** 23,33 ****
  #if !defined (_XMALLOC_H_)
  #define _XMALLOC_H_
! #if defined (READLINE_LIBRARY)
! # include "rlstdc.h"
! #else
! # include <readline/rlstdc.h>
! #endif
  #ifndef PTR_T
--- 23,29 ----
  #if !defined (_XMALLOC_H_)
  #define _XMALLOC_H_
! #include "rlstdc.h"
  #ifndef PTR_T

Mengjeui: would this change fix things for you?
Wei: is there a reason not to do this?

...thanks for the input....dave

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |
Received on Sun Oct 28 2007 - 06:07:17 PDT
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