From 1639fbdaa00e3a3f8bd4c4f0e9386bf0d73a6cde Mon Sep 17 00:00:00 2001
From: Justin Lecher <jlec@gentoo.org>
Date: Wed, 2 Oct 2013 08:49:15 +0200
Subject: sci-chemistry/coot: Update patch for HEAD

Package-Manager: portage-2.2.7
---
 sci-chemistry/coot/ChangeLog           |  3 ++
 sci-chemistry/coot/files/9999-pc.patch | 52 ++++++++++++++++------------------
 2 files changed, 28 insertions(+), 27 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 2d2b7c315..d1c958455 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Oct 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
+  Update patch for HEAD
+
   21 Sep 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
   Adjust pc patch for latest head
 
diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 2f97194e2..7f8553215 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -262,7 +262,9 @@ index 7734f09..c58fe1d 100644
  
  libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \
 diff --git a/ccp4mg-utils/mmut/Makefile.am b/ccp4mg-utils/mmut/Makefile.am
-index d0651db..d4e0bf8 100755
+old mode 100755
+new mode 100644
+index d0651db..d4e0bf8
 --- a/ccp4mg-utils/mmut/Makefile.am
 +++ b/ccp4mg-utils/mmut/Makefile.am
 @@ -70,9 +70,9 @@ INCLUDES = \
@@ -279,7 +281,9 @@ index d0651db..d4e0bf8 100755
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am
-index a7e68b5..e26a6c8 100755
+old mode 100755
+new mode 100644
+index a7e68b5..e26a6c8
 --- a/ccp4mg-utils/pygl/Makefile.am
 +++ b/ccp4mg-utils/pygl/Makefile.am
 @@ -108,9 +108,9 @@ INCLUDES = \
@@ -296,7 +300,9 @@ index a7e68b5..e26a6c8 100755
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am
-index 399f453..3d2ff55 100755
+old mode 100755
+new mode 100644
+index 399f453..3d2ff55
 --- a/ccp4mg-utils/util/Makefile.am
 +++ b/ccp4mg-utils/util/Makefile.am
 @@ -73,9 +73,9 @@ INCLUDES = \
@@ -799,35 +805,27 @@ index de8ab65..4c1b418 100644
  
  ])
 diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4
-index 30fdcb9..3e4c0c6 100644
+index e2494a5..cf96688 100644
 --- a/macros/goo-canvas.m4
 +++ b/macros/goo-canvas.m4
-@@ -36,9 +36,9 @@ if test x$goocanvas_prefix != x; then
+@@ -35,7 +35,7 @@ if test x$goocanvas_prefix != x; then
+   # SGI compiler CC (CXX=CC) needs -lm to link maths library, but 
    # GCC c++ does not.
    #
-   if test -e $goocanvas_prefix/lib/libgoocanvas.la ; then
--    GOOCANVAS_LDOPTS="$goocanvas_prefix/lib/libgoocanvas.la"
-+    GOOCANVAS_LIBS="$goocanvas_prefix/lib/libgoocanvas.la"
-   else
--    GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas"
-+    GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas"
-   fi
+-  GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas"
++  GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas"
+ 
  else
    # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig)
-@@ -57,19 +57,19 @@ else
+@@ -54,15 +54,15 @@ else
      break;;
    esac
-   if test -e /usr/lib/libgoocanvas.la ; then
--    GOOCANVAS_LDOPTS="libgoocanvas.la"
-+    GOOCANVAS_LIBS="libgoocanvas.la"
+   if test -z "${PKG_CONFIG}"; then
+-     GOOCANVAS_LDOPTS="-lgoocanvas"
++     GOOCANVAS_LIBS="-lgoocanvas"
    else
-     if test -z "${PKG_CONFIG}"; then
--      GOOCANVAS_LDOPTS="-lgoocanvas"
-+      GOOCANVAS_LIBS="-lgoocanvas"
-     else
--      GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
-+      GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
-     fi
+-     GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
++     GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
    fi
  fi
  
@@ -836,9 +834,9 @@ index 30fdcb9..3e4c0c6 100644
 -LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
 +LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
  CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
- #
- # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
-@@ -95,7 +95,7 @@ AC_MSG_RESULT($have_goocanvas)
+ 
+ 
+@@ -96,7 +96,7 @@ AC_MSG_RESULT($have_goocanvas)
  if test x$have_goocanvas = xyes; then
  
   GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
@@ -1028,7 +1026,7 @@ index af5276b..d0ab482 100644
  	$(GLOB_CFLAGS)                 \
  	$(CURL_CFLAGS)                 
 diff --git a/surface/Makefile.am b/surface/Makefile.am
-index 8cb8432..d82e6ff 100644
+index 3de5953..2461f58 100644
 --- a/surface/Makefile.am
 +++ b/surface/Makefile.am
 @@ -1,5 +1,5 @@
-- 
cgit v1.2.3-65-gdbad