[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/

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* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-03-03 14:23 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-03-03 14:23 UTC (permalink / raw
  To: gentoo-commits

commit:     d8acffbbf1110c82aa11ddd40293d5d76c24037d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Mar  3 13:59:59 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Mar  3 13:59:59 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d8acffbb

Coot live fixes

(Portage version: 2.2.0_alpha26/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog              |    4 ++++
 sci-chemistry/coot/coot-9999.ebuild       |    5 +++--
 sci-chemistry/coot/files/9999-lidia.patch |   13 +++++++------
 3 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 954daf8..d02adf0 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Mar 2011; Justin Lecher <jlec@gentoo.org> files/9999-lidia.patch,
+  coot-9999.ebuild:
+  Coot live fixes
+
   20 Jan 2011; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Fix tests
 

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index f957107..d12f36d 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -37,10 +37,10 @@ SCIDEPS="
 
 XDEPS="
 	gnome-base/libgnomecanvas
-	gnome-base/librsvg
+	gnome-base/librsvg:2
 	media-libs/libpng
 	media-libs/freeglut
-	>=x11-libs/gtk+-2.2
+	x11-libs/gtk+:2
 	x11-libs/goocanvas
 	x11-libs/gtkglext"
 
@@ -71,6 +71,7 @@ pkg_setup() {
 }
 
 PATCHES=(
+	"${FILESDIR}"/${PV}-lidia.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-clipper.patch
 	"${FILESDIR}"/${PV}-include.patch

diff --git a/sci-chemistry/coot/files/9999-lidia.patch b/sci-chemistry/coot/files/9999-lidia.patch
index 2ac3fcc..5b5039c 100644
--- a/sci-chemistry/coot/files/9999-lidia.patch
+++ b/sci-chemistry/coot/files/9999-lidia.patch
@@ -1,16 +1,17 @@
 Index: lbg/Makefile.am
 ===================================================================
---- lbg/Makefile.am	(revision 3299)
+--- lbg/Makefile.am	(revision 3406)
 +++ lbg/Makefile.am	(working copy)
-@@ -24,6 +24,11 @@
-     lbg-search.cc some-coot-utils.cc residue-circles.cc rdkit-interface.cc \
+@@ -25,6 +25,12 @@
+     lbg-search.cc  residue-circles.cc rdkit-interface.cc \
      flev-annotations.cc
  
 +libcoot_lidia_la_LIBADD = \
 +	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
 +	$(top_builddir)/lidia-core/libcoot-lidia-core.la \
-+	$(GSL_LIBS) $(GTK_LIBS) $(GOOCANVAS_LIBS)
++	$(top_builddir)/geometry/libcoot-geometry.la \
++	$(GTK_LIBS) $(GSL_LIBS) $(GOOCANVAS_LIBS)
 +
- lidia_SOURCES = lidia-main.cc
+ lidia_SOURCES = lidia-main.cc lbg-callbacks-outer.cc
  
- # some-coot-utils.hh needed?
+ include_HEADERS = lbg.hh wmolecule.hh rdkit-interface.hh flev-annotations.hh 



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-04-29 10:05 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-04-29 10:05 UTC (permalink / raw
  To: gentoo-commits

commit:     f0c8b800774b3d554c462bd55f2901734108277a
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 28 08:39:59 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 28 08:39:59 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f0c8b800

Fixed underlinking problems

(Portage version: 2.2.0_alpha30/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog              |    4 ++++
 sci-chemistry/coot/coot-9999.ebuild       |    1 +
 sci-chemistry/coot/files/9999-gl.patch    |   10 ++++++++++
 sci-chemistry/coot/files/9999-lidia.patch |   19 +++++++++++++++----
 4 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index c44d9a6..accf687 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/9999-gl.patch,
+  files/9999-lidia.patch, coot-9999.ebuild:
+  Fixed underlinking problems
+
   28 Apr 2011; Justin Lecher <jlec@gentoo.org> -files/9999-gsl.patch,
   -files/9999-openmp.patch, -files/9999-rappermc.patch,
   -files/fix-namespace-error.patch, -files/glib.m4, -files/gtk.m4:

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index f9481c4..e8f1076 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -75,6 +75,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-clipper.patch
 	"${FILESDIR}"/${PV}-include.patch
+	"${FILESDIR}"/${PV}-gl.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/9999-gl.patch b/sci-chemistry/coot/files/9999-gl.patch
new file mode 100644
index 0000000..bbd858c
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-gl.patch
@@ -0,0 +1,10 @@
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am	(revision 3478)
++++ coot-surface/Makefile.am	(working copy)
+@@ -29,4 +29,4 @@
+ 
+ libcoot_surface_la_LIBADD = \
+ 	$(top_builddir)/surface/libccp4mg-surface.la \
+-	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) 
++	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) -lGL

diff --git a/sci-chemistry/coot/files/9999-lidia.patch b/sci-chemistry/coot/files/9999-lidia.patch
index 5b5039c..0ca154c 100644
--- a/sci-chemistry/coot/files/9999-lidia.patch
+++ b/sci-chemistry/coot/files/9999-lidia.patch
@@ -1,10 +1,10 @@
 Index: lbg/Makefile.am
 ===================================================================
---- lbg/Makefile.am	(revision 3406)
+--- lbg/Makefile.am	(revision 3478)
 +++ lbg/Makefile.am	(working copy)
-@@ -25,6 +25,12 @@
-     lbg-search.cc  residue-circles.cc rdkit-interface.cc \
-     flev-annotations.cc
+@@ -32,6 +32,12 @@
+ 	$(top_builddir)/utils/libcoot-utils.la \
+ 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) $(RDKIT_LIBS) $(GOOCANVAS_LIBS) $(GTK_LIBS)
  
 +libcoot_lidia_la_LIBADD = \
 +	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
@@ -15,3 +15,14 @@ Index: lbg/Makefile.am
  lidia_SOURCES = lidia-main.cc lbg-callbacks-outer.cc
  
  include_HEADERS = lbg.hh wmolecule.hh rdkit-interface.hh flev-annotations.hh 
+Index: lidia-core/Makefile.am
+===================================================================
+--- lidia-core/Makefile.am	(revision 3478)
++++ lidia-core/Makefile.am	(working copy)
+@@ -29,3 +29,6 @@
+ 
+ libcoot_lidia_core_la_SOURCES = lbg-molfile.cc lig-build.cc
+ 
++libcoot_lidia_core_la_LIBADD = \
++	$(top_builddir)/geometry/libcoot-geometry.la \
++	$(MMDB_LIBS)



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-04-29 10:05 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-04-29 10:05 UTC (permalink / raw
  To: gentoo-commits

commit:     1c8a1fdbc046a0feb2460af9d212ae9e7e98f7fb
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 28 08:10:39 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 28 08:10:39 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1c8a1fdb

Cleaned old patches

(Portage version: 2.2.0_alpha30/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog                       |    5 +
 sci-chemistry/coot/files/9999-gsl.patch            |   14 --
 sci-chemistry/coot/files/9999-openmp.patch         |   28 ---
 sci-chemistry/coot/files/9999-rappermc.patch       |   15 --
 sci-chemistry/coot/files/fix-namespace-error.patch |   52 -----
 sci-chemistry/coot/files/glib.m4                   |  196 -------------------
 sci-chemistry/coot/files/gtk.m4                    |  199 --------------------
 7 files changed, 5 insertions(+), 504 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index edb77b6..c44d9a6 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 Apr 2011; Justin Lecher <jlec@gentoo.org> -files/9999-gsl.patch,
+  -files/9999-openmp.patch, -files/9999-rappermc.patch,
+  -files/fix-namespace-error.patch, -files/glib.m4, -files/gtk.m4:
+  Cleaned old patches
+
   07 Mar 2011; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Correct Slots for gtk 3 introduction to tree
 

diff --git a/sci-chemistry/coot/files/9999-gsl.patch b/sci-chemistry/coot/files/9999-gsl.patch
deleted file mode 100644
index af7a405..0000000
--- a/sci-chemistry/coot/files/9999-gsl.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Index: coot-utils/Makefile.am
-===================================================================
---- coot-utils/Makefile.am	(revision 3299)
-+++ coot-utils/Makefile.am	(working copy)
-@@ -90,7 +90,8 @@
-    $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-    libcoot-map-utils.la \
-    libcoot-coord-utils.la \
--    $(top_builddir)/utils/libcoot-utils.la
-+    $(top_builddir)/utils/libcoot-utils.la \
-+	$(GSL_LIBS)
- 
- 
- noinst_PROGRAMS = test-h-bonds testshelxreader testcootutils

diff --git a/sci-chemistry/coot/files/9999-openmp.patch b/sci-chemistry/coot/files/9999-openmp.patch
deleted file mode 100644
index a239c1f..0000000
--- a/sci-chemistry/coot/files/9999-openmp.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-Index: surface/Makefile.am
-===================================================================
---- surface/Makefile.am	(revision 3299)
-+++ surface/Makefile.am	(working copy)
-@@ -1,7 +1,7 @@
- 
- INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
- 
--AM_CPPFLAGS = $(OPENMP_CFLAGS)
-+AM_CXXFLAGS = $(OPENMP_CFLAGS)
- 
- lib_LTLIBRARIES = libccp4mg-surface.la
- 
-Index: src/Makefile.am
-===================================================================
---- src/Makefile.am	(revision 3299)
-+++ src/Makefile.am	(working copy)
-@@ -417,8 +417,8 @@
- # coot_real_LDFLAGS = -static -lstdc++
- coot_real_LDFLAGS =
- 
--coot_real_LDADD =  $(OPENMP_CFLAGS)     \
--                $(COOT_EXTRA_LIBS)      \
-+coot_real_LDADD =  \
-+		$(COOT_EXTRA_LIBS)      \
- 		$(GUILE_GTK_LIBS)       \
- 		$(GUILE_LDFLAGS)	\
- 		$(CLIPPER_LIBS) 	\

diff --git a/sci-chemistry/coot/files/9999-rappermc.patch b/sci-chemistry/coot/files/9999-rappermc.patch
deleted file mode 100644
index 7b8ba03..0000000
--- a/sci-chemistry/coot/files/9999-rappermc.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Index: python/a_rapper_gui.py
-===================================================================
---- python/a_rapper_gui.py	(revision 2425)
-+++ python/a_rapper_gui.py	(working copy)
-@@ -20,8 +20,8 @@
-     home_dir = os.getenv('COOT_HOME')
- else:
-     home_dir = os.getenv('HOME')
--rapper_dir = os.path.join(os.path.normpath(home_dir), "rappermc")
--rapper_command = "rapper"
-+rapper_dir = "/usr/share/rapper"
-+rapper_command = "rappermc"
- 
- def rapper_process():
-     #needed?

diff --git a/sci-chemistry/coot/files/fix-namespace-error.patch b/sci-chemistry/coot/files/fix-namespace-error.patch
deleted file mode 100644
index 5bf8a2d..0000000
--- a/sci-chemistry/coot/files/fix-namespace-error.patch
+++ /dev/null
@@ -1,52 +0,0 @@
---- coot-utils/coot-coord-utils.cc.orig	2007-11-14 09:38:31.000000000 -0800
-+++ coot-utils/coot-coord-utils.cc	2007-11-14 09:44:50.000000000 -0800
-@@ -395,28 +395,30 @@
-    return SelHnd;
- }
- 
--std::ostream& coot::operator<< (std::ostream& s, const coot::atom_spec_t &spec) {
-+namespace coot {
-+   std::ostream& operator<< (std::ostream& s, const atom_spec_t &spec) {
- 
--   s << "[spec: ";
--   s << "\"";
--   s << spec.chain;
--   s << "\" ";
--   s << spec.resno;
--   s << " ";
--   s << "\"";
--   s << spec.insertion_code;
--   s << "\"";
--   s << " ";
--   s << "\"";
--   s  << spec.atom_name;
--   s << "\"";
--   s << " ";
--   s << "\"";
--   s << spec.alt_conf;
--   s << "\"]";
-+      s << "[spec: ";
-+      s << "\"";
-+      s << spec.chain;
-+      s << "\" ";
-+      s << spec.resno;
-+      s << " ";
-+      s << "\"";
-+      s << spec.insertion_code;
-+      s << "\"";
-+      s << " ";
-+      s << "\"";
-+      s  << spec.atom_name;
-+      s << "\"";
-+      s << " ";
-+      s << "\"";
-+      s << spec.alt_conf;
-+      s << "\"]";
- 
--   return s;
-+      return s;
- 
-+   }
- }
- 
- 

diff --git a/sci-chemistry/coot/files/glib.m4 b/sci-chemistry/coot/files/glib.m4
deleted file mode 100644
index b3c632b..0000000
--- a/sci-chemistry/coot/files/glib.m4
+++ /dev/null
@@ -1,196 +0,0 @@
-# Configure paths for GLIB
-# Owen Taylor     97-11-3
-
-dnl AM_PATH_GLIB([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]])
-dnl Test for GLIB, and define GLIB_CFLAGS and GLIB_LIBS, if "gmodule" or 
-dnl gthread is specified in MODULES, pass to glib-config
-dnl
-AC_DEFUN([AM_PATH_GLIB],
-[dnl 
-dnl Get the cflags and libraries from the glib-config script
-dnl
-AC_ARG_WITH(glib-prefix,[  --with-glib-prefix=PFX   Prefix where GLIB is installed (optional)],
-            glib_config_prefix="$withval", glib_config_prefix="")
-AC_ARG_WITH(glib-exec-prefix,[  --with-glib-exec-prefix=PFX Exec prefix where GLIB is installed (optional)],
-            glib_config_exec_prefix="$withval", glib_config_exec_prefix="")
-AC_ARG_ENABLE(glibtest, [  --disable-glibtest       Do not try to compile and run a test GLIB program],
-		    , enable_glibtest=yes)
-
-  if test x$glib_config_exec_prefix != x ; then
-     glib_config_args="$glib_config_args --exec-prefix=$glib_config_exec_prefix"
-     if test x${GLIB_CONFIG+set} != xset ; then
-        GLIB_CONFIG=$glib_config_exec_prefix/bin/glib-config
-     fi
-  fi
-  if test x$glib_config_prefix != x ; then
-     glib_config_args="$glib_config_args --prefix=$glib_config_prefix"
-     if test x${GLIB_CONFIG+set} != xset ; then
-        GLIB_CONFIG=$glib_config_prefix/bin/glib-config
-     fi
-  fi
-
-  for module in . $4
-  do
-      case "$module" in
-         gmodule) 
-             glib_config_args="$glib_config_args gmodule"
-         ;;
-         gthread) 
-             glib_config_args="$glib_config_args gthread"
-         ;;
-      esac
-  done
-
-  AC_PATH_PROG(GLIB_CONFIG, glib-config, no)
-  min_glib_version=ifelse([$1], ,0.99.7,$1)
-  AC_MSG_CHECKING(for GLIB - version >= $min_glib_version)
-  no_glib=""
-  if test "$GLIB_CONFIG" = "no" ; then
-    no_glib=yes
-  else
-    GLIB_CFLAGS=`$GLIB_CONFIG $glib_config_args --cflags`
-    GLIB_LIBS=`$GLIB_CONFIG $glib_config_args --libs`
-    glib_config_major_version=`$GLIB_CONFIG $glib_config_args --version | \
-           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
-    glib_config_minor_version=`$GLIB_CONFIG $glib_config_args --version | \
-           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
-    glib_config_micro_version=`$GLIB_CONFIG $glib_config_args --version | \
-           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
-    if test "x$enable_glibtest" = "xyes" ; then
-      ac_save_CFLAGS="$CFLAGS"
-      ac_save_LIBS="$LIBS"
-      CFLAGS="$CFLAGS $GLIB_CFLAGS"
-      LIBS="$GLIB_LIBS $LIBS"
-dnl
-dnl Now check if the installed GLIB is sufficiently new. (Also sanity
-dnl checks the results of glib-config to some extent
-dnl
-      rm -f conf.glibtest
-      AC_TRY_RUN([
-#include <glib.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-int 
-main ()
-{
-  int major, minor, micro;
-  char *tmp_version;
-
-  system ("touch conf.glibtest");
-
-  /* HP/UX 9 (%@#!) writes to sscanf strings */
-  tmp_version = g_strdup("$min_glib_version");
-  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
-     printf("%s, bad version string\n", "$min_glib_version");
-     exit(1);
-   }
-
-  if ((glib_major_version != $glib_config_major_version) ||
-      (glib_minor_version != $glib_config_minor_version) ||
-      (glib_micro_version != $glib_config_micro_version))
-    {
-      printf("\n*** 'glib-config --version' returned %d.%d.%d, but GLIB (%d.%d.%d)\n", 
-             $glib_config_major_version, $glib_config_minor_version, $glib_config_micro_version,
-             glib_major_version, glib_minor_version, glib_micro_version);
-      printf ("*** was found! If glib-config was correct, then it is best\n");
-      printf ("*** to remove the old version of GLIB. You may also be able to fix the error\n");
-      printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n");
-      printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n");
-      printf("*** required on your system.\n");
-      printf("*** If glib-config was wrong, set the environment variable GLIB_CONFIG\n");
-      printf("*** to point to the correct copy of glib-config, and remove the file config.cache\n");
-      printf("*** before re-running configure\n");
-    } 
-  else if ((glib_major_version != GLIB_MAJOR_VERSION) ||
-	   (glib_minor_version != GLIB_MINOR_VERSION) ||
-           (glib_micro_version != GLIB_MICRO_VERSION))
-    {
-      printf("*** GLIB header files (version %d.%d.%d) do not match\n",
-	     GLIB_MAJOR_VERSION, GLIB_MINOR_VERSION, GLIB_MICRO_VERSION);
-      printf("*** library (version %d.%d.%d)\n",
-	     glib_major_version, glib_minor_version, glib_micro_version);
-    }
-  else
-    {
-      if ((glib_major_version > major) ||
-        ((glib_major_version == major) && (glib_minor_version > minor)) ||
-        ((glib_major_version == major) && (glib_minor_version == minor) && (glib_micro_version >= micro)))
-      {
-        return 0;
-       }
-     else
-      {
-        printf("\n*** An old version of GLIB (%d.%d.%d) was found.\n",
-               glib_major_version, glib_minor_version, glib_micro_version);
-        printf("*** You need a version of GLIB newer than %d.%d.%d. The latest version of\n",
-	       major, minor, micro);
-        printf("*** GLIB is always available from ftp://ftp.gtk.org.\n");
-        printf("***\n");
-        printf("*** If you have already installed a sufficiently new version, this error\n");
-        printf("*** probably means that the wrong copy of the glib-config shell script is\n");
-        printf("*** being found. The easiest way to fix this is to remove the old version\n");
-        printf("*** of GLIB, but you can also set the GLIB_CONFIG environment to point to the\n");
-        printf("*** correct copy of glib-config. (In this case, you will have to\n");
-        printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n");
-        printf("*** so that the correct libraries are found at run-time))\n");
-      }
-    }
-  return 1;
-}
-],, no_glib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
-       CFLAGS="$ac_save_CFLAGS"
-       LIBS="$ac_save_LIBS"
-     fi
-  fi
-  if test "x$no_glib" = x ; then
-     AC_MSG_RESULT(yes)
-     ifelse([$2], , :, [$2])     
-  else
-     AC_MSG_RESULT(no)
-     if test "$GLIB_CONFIG" = "no" ; then
-       echo "*** The glib-config script installed by GLIB could not be found"
-       echo "*** If GLIB was installed in PREFIX, make sure PREFIX/bin is in"
-       echo "*** your path, or set the GLIB_CONFIG environment variable to the"
-       echo "*** full path to glib-config."
-     else
-       if test -f conf.glibtest ; then
-        :
-       else
-          echo "*** Could not run GLIB test program, checking why..."
-          CFLAGS="$CFLAGS $GLIB_CFLAGS"
-          LIBS="$LIBS $GLIB_LIBS"
-          AC_TRY_LINK([
-#include <glib.h>
-#include <stdio.h>
-],      [ return ((glib_major_version) || (glib_minor_version) || (glib_micro_version)); ],
-        [ echo "*** The test program compiled, but did not run. This usually means"
-          echo "*** that the run-time linker is not finding GLIB or finding the wrong"
-          echo "*** version of GLIB. If it is not finding GLIB, you'll need to set your"
-          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
-          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
-          echo "*** is required on your system"
-	  echo "***"
-          echo "*** If you have an old version installed, it is best to remove it, although"
-          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"
-          echo "***"
-          echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that"
-          echo "*** came with the system with the command"
-          echo "***"
-          echo "***    rpm --erase --nodeps gtk gtk-devel" ],
-        [ echo "*** The test program failed to compile or link. See the file config.log for the"
-          echo "*** exact error that occured. This usually means GLIB was incorrectly installed"
-          echo "*** or that you have moved GLIB since it was installed. In the latter case, you"
-          echo "*** may want to edit the glib-config script: $GLIB_CONFIG" ])
-          CFLAGS="$ac_save_CFLAGS"
-          LIBS="$ac_save_LIBS"
-       fi
-     fi
-     GLIB_CFLAGS=""
-     GLIB_LIBS=""
-     ifelse([$3], , :, [$3])
-  fi
-  AC_SUBST(GLIB_CFLAGS)
-  AC_SUBST(GLIB_LIBS)
-  rm -f conf.glibtest
-])

diff --git a/sci-chemistry/coot/files/gtk.m4 b/sci-chemistry/coot/files/gtk.m4
deleted file mode 100644
index beb1859..0000000
--- a/sci-chemistry/coot/files/gtk.m4
+++ /dev/null
@@ -1,199 +0,0 @@
-# Configure paths for GTK+
-# Owen Taylor     97-11-3
-AC_DEFUN([GTK_AC_DIVERT_BEFORE_HELP],
-[ifdef([m4_divert_text], [m4_divert_text([NOTICE],[$1])],
-       [ifdef([AC_DIVERT], [AC_DIVERT([NOTICE],[$1])],
-              [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)dnl
-$1
-AC_DIVERT_POP()])])])
-dnl AM_PATH_GTK([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]])
-dnl Test for GTK, and define GTK_CFLAGS and GTK_LIBS
-dnl
-AC_DEFUN([AM_PATH_GTK],
-[dnl 
-dnl Get the cflags and libraries from the gtk-config script
-dnl
-AC_ARG_WITH(gtk-prefix,[  --with-gtk-prefix=PFX   Prefix where GTK is installed (optional)],
-            gtk_config_prefix="$withval", gtk_config_prefix="")
-AC_ARG_WITH(gtk-exec-prefix,[  --with-gtk-exec-prefix=PFX Exec prefix where GTK is installed (optional)],
-            gtk_config_exec_prefix="$withval", gtk_config_exec_prefix="")
-AC_ARG_ENABLE(gtktest, [  --disable-gtktest       Do not try to compile and run a test GTK program],
-		    , enable_gtktest=yes)
-
-  for module in . $4
-  do
-      case "$module" in
-         gthread) 
-             gtk_config_args="$gtk_config_args gthread"
-         ;;
-      esac
-  done
-
-  if test x$gtk_config_exec_prefix != x ; then
-     gtk_config_args="$gtk_config_args --exec-prefix=$gtk_config_exec_prefix"
-     if test x${GTK_CONFIG+set} != xset ; then
-        GTK_CONFIG=$gtk_config_exec_prefix/bin/gtk-config
-     fi
-  fi
-  if test x$gtk_config_prefix != x ; then
-     gtk_config_args="$gtk_config_args --prefix=$gtk_config_prefix"
-     if test x${GTK_CONFIG+set} != xset ; then
-        GTK_CONFIG=$gtk_config_prefix/bin/gtk-config
-     fi
-  fi
-
-  AC_PATH_PROG(GTK_CONFIG, gtk-config, no)
-  min_gtk_version=ifelse([$1], ,0.99.7,$1)
-  AC_MSG_CHECKING(for GTK - version >= $min_gtk_version)
-  no_gtk=""
-  if test "$GTK_CONFIG" = "no" ; then
-    no_gtk=yes
-  else
-    GTK_CFLAGS=`$GTK_CONFIG $gtk_config_args --cflags`
-    GTK_LIBS=`$GTK_CONFIG $gtk_config_args --libs`
-    gtk_config_major_version=`$GTK_CONFIG $gtk_config_args --version | \
-           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'`
-    gtk_config_minor_version=`$GTK_CONFIG $gtk_config_args --version | \
-           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'`
-    gtk_config_micro_version=`$GTK_CONFIG $gtk_config_args --version | \
-           sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'`
-    if test "x$enable_gtktest" = "xyes" ; then
-      ac_save_CFLAGS="$CFLAGS"
-      ac_save_LIBS="$LIBS"
-      CFLAGS="$CFLAGS $GTK_CFLAGS"
-      LIBS="$GTK_LIBS $LIBS"
-dnl
-dnl Now check if the installed GTK is sufficiently new. (Also sanity
-dnl checks the results of gtk-config to some extent
-dnl
-      rm -f conf.gtktest
-      AC_TRY_RUN([
-#include <gtk/gtk.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-int 
-main ()
-{
-  int major, minor, micro;
-  char *tmp_version;
-
-  system ("touch conf.gtktest");
-
-  /* HP/UX 9 (%@#!) writes to sscanf strings */
-  tmp_version = g_strdup("$min_gtk_version");
-  if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, &micro) != 3) {
-     printf("%s, bad version string\n", "$min_gtk_version");
-     exit(1);
-   }
-
-  if ((gtk_major_version != $gtk_config_major_version) ||
-      (gtk_minor_version != $gtk_config_minor_version) ||
-      (gtk_micro_version != $gtk_config_micro_version))
-    {
-      printf("\n*** 'gtk-config --version' returned %d.%d.%d, but GTK+ (%d.%d.%d)\n", 
-             $gtk_config_major_version, $gtk_config_minor_version, $gtk_config_micro_version,
-             gtk_major_version, gtk_minor_version, gtk_micro_version);
-      printf ("*** was found! If gtk-config was correct, then it is best\n");
-      printf ("*** to remove the old version of GTK+. You may also be able to fix the error\n");
-      printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n");
-      printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n");
-      printf("*** required on your system.\n");
-      printf("*** If gtk-config was wrong, set the environment variable GTK_CONFIG\n");
-      printf("*** to point to the correct copy of gtk-config, and remove the file config.cache\n");
-      printf("*** before re-running configure\n");
-    } 
-#if defined (GTK_MAJOR_VERSION) && defined (GTK_MINOR_VERSION) && defined (GTK_MICRO_VERSION)
-  else if ((gtk_major_version != GTK_MAJOR_VERSION) ||
-	   (gtk_minor_version != GTK_MINOR_VERSION) ||
-           (gtk_micro_version != GTK_MICRO_VERSION))
-    {
-      printf("*** GTK+ header files (version %d.%d.%d) do not match\n",
-	     GTK_MAJOR_VERSION, GTK_MINOR_VERSION, GTK_MICRO_VERSION);
-      printf("*** library (version %d.%d.%d)\n",
-	     gtk_major_version, gtk_minor_version, gtk_micro_version);
-    }
-#endif /* defined (GTK_MAJOR_VERSION) ... */
-  else
-    {
-      if ((gtk_major_version > major) ||
-        ((gtk_major_version == major) && (gtk_minor_version > minor)) ||
-        ((gtk_major_version == major) && (gtk_minor_version == minor) && (gtk_micro_version >= micro)))
-      {
-        return 0;
-       }
-     else
-      {
-        printf("\n*** An old version of GTK+ (%d.%d.%d) was found.\n",
-               gtk_major_version, gtk_minor_version, gtk_micro_version);
-        printf("*** You need a version of GTK+ newer than %d.%d.%d. The latest version of\n",
-	       major, minor, micro);
-        printf("*** GTK+ is always available from ftp://ftp.gtk.org.\n");
-        printf("***\n");
-        printf("*** If you have already installed a sufficiently new version, this error\n");
-        printf("*** probably means that the wrong copy of the gtk-config shell script is\n");
-        printf("*** being found. The easiest way to fix this is to remove the old version\n");
-        printf("*** of GTK+, but you can also set the GTK_CONFIG environment to point to the\n");
-        printf("*** correct copy of gtk-config. (In this case, you will have to\n");
-        printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n");
-        printf("*** so that the correct libraries are found at run-time))\n");
-      }
-    }
-  return 1;
-}
-],, no_gtk=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"])
-       CFLAGS="$ac_save_CFLAGS"
-       LIBS="$ac_save_LIBS"
-     fi
-  fi
-  if test "x$no_gtk" = x ; then
-     AC_MSG_RESULT(yes)
-     ifelse([$2], , :, [$2])     
-  else
-     AC_MSG_RESULT(no)
-     if test "$GTK_CONFIG" = "no" ; then
-       echo "*** The gtk-config script installed by GTK could not be found"
-       echo "*** If GTK was installed in PREFIX, make sure PREFIX/bin is in"
-       echo "*** your path, or set the GTK_CONFIG environment variable to the"
-       echo "*** full path to gtk-config."
-     else
-       if test -f conf.gtktest ; then
-        :
-       else
-          echo "*** Could not run GTK test program, checking why..."
-          CFLAGS="$CFLAGS $GTK_CFLAGS"
-          LIBS="$LIBS $GTK_LIBS"
-          AC_TRY_LINK([
-#include <gtk/gtk.h>
-#include <stdio.h>
-],      [ return ((gtk_major_version) || (gtk_minor_version) || (gtk_micro_version)); ],
-        [ echo "*** The test program compiled, but did not run. This usually means"
-          echo "*** that the run-time linker is not finding GTK or finding the wrong"
-          echo "*** version of GTK. If it is not finding GTK, you'll need to set your"
-          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
-          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
-          echo "*** is required on your system"
-	  echo "***"
-          echo "*** If you have an old version installed, it is best to remove it, although"
-          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"
-          echo "***"
-          echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that"
-          echo "*** came with the system with the command"
-          echo "***"
-          echo "***    rpm --erase --nodeps gtk gtk-devel" ],
-        [ echo "*** The test program failed to compile or link. See the file config.log for the"
-          echo "*** exact error that occured. This usually means GTK was incorrectly installed"
-          echo "*** or that you have moved GTK since it was installed. In the latter case, you"
-          echo "*** may want to edit the gtk-config script: $GTK_CONFIG" ])
-          CFLAGS="$ac_save_CFLAGS"
-          LIBS="$ac_save_LIBS"
-       fi
-     fi
-     GTK_CFLAGS=""
-     GTK_LIBS=""
-     ifelse([$3], , :, [$3])
-  fi
-  AC_SUBST(GTK_CFLAGS)
-  AC_SUBST(GTK_LIBS)
-  rm -f conf.gtktest
-])



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-05-28 11:50 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-05-28 11:50 UTC (permalink / raw
  To: gentoo-commits

commit:     55eb436710074770a07f4822d28117a12f6db822
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat May 28 10:42:56 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat May 28 10:42:56 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=55eb4367

Cleaned for current HEAD

(Portage version: 2.2.0_alpha37/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog                |    4 +++
 sci-chemistry/coot/coot-9999.ebuild         |    1 -
 sci-chemistry/coot/files/9999-clipper.patch |    9 ------
 sci-chemistry/coot/files/9999-lidia.patch   |   37 ++++++++------------------
 4 files changed, 16 insertions(+), 35 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 07b2eb3..61ad2d8 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  28 May 2011; Justin Lecher <jlec@gentoo.org> -files/9999-clipper.patch,
+  files/9999-lidia.patch, coot-9999.ebuild:
+  Cleaned for current HEAD
+
   02 May 2011; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Fix x11-libs/goocanvas SLOT
 

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 67b679f..bfeee1e 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -73,7 +73,6 @@ pkg_setup() {
 PATCHES=(
 	"${FILESDIR}"/${PV}-lidia.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
-	"${FILESDIR}"/${PV}-clipper.patch
 	"${FILESDIR}"/${PV}-include.patch
 	"${FILESDIR}"/${PV}-gl.patch
 	)

diff --git a/sci-chemistry/coot/files/9999-clipper.patch b/sci-chemistry/coot/files/9999-clipper.patch
deleted file mode 100644
index e3f028f..0000000
--- a/sci-chemistry/coot/files/9999-clipper.patch
+++ /dev/null
@@ -1,9 +0,0 @@
-Index: lidia-core/Makefile.am
-===================================================================
---- lidia-core/Makefile.am	(revision 3299)
-+++ lidia-core/Makefile.am	(working copy)
-@@ -23,3 +23,4 @@
- 
- libcoot_lidia_core_la_SOURCES = lbg-molfile.cc lig-build.cc
- 
-+libcoot_lidia_core_la_LIBADD = $(CLIPPER_LIBS)

diff --git a/sci-chemistry/coot/files/9999-lidia.patch b/sci-chemistry/coot/files/9999-lidia.patch
index 0ca154c..2076513 100644
--- a/sci-chemistry/coot/files/9999-lidia.patch
+++ b/sci-chemistry/coot/files/9999-lidia.patch
@@ -1,28 +1,15 @@
-Index: lbg/Makefile.am
-===================================================================
---- lbg/Makefile.am	(revision 3478)
-+++ lbg/Makefile.am	(working copy)
-@@ -32,6 +32,12 @@
- 	$(top_builddir)/utils/libcoot-utils.la \
- 	$(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) $(RDKIT_LIBS) $(GOOCANVAS_LIBS) $(GTK_LIBS)
- 
-+libcoot_lidia_la_LIBADD = \
-+	$(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+	$(top_builddir)/lidia-core/libcoot-lidia-core.la \
-+	$(top_builddir)/geometry/libcoot-geometry.la \
-+	$(GTK_LIBS) $(GSL_LIBS) $(GOOCANVAS_LIBS)
+ lidia-core/Makefile.am |    4 ++++
+ 1 files changed, 4 insertions(+), 0 deletions(-)
+
+diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
+index 17d468d..78bf054 100644
+--- a/lidia-core/Makefile.am
++++ b/lidia-core/Makefile.am
+@@ -34,3 +34,7 @@ libcoot_lidia_core_la_SOURCES = lbg-molfile.cc lig-build.cc
+ # test_molfile_SOURCES: test-molfile.cc
+ 
+ # test_molfile_LDADD: libcoot-lidia-core.la
 +
- lidia_SOURCES = lidia-main.cc lbg-callbacks-outer.cc
- 
- include_HEADERS = lbg.hh wmolecule.hh rdkit-interface.hh flev-annotations.hh 
-Index: lidia-core/Makefile.am
-===================================================================
---- lidia-core/Makefile.am	(revision 3478)
-+++ lidia-core/Makefile.am	(working copy)
-@@ -29,3 +29,6 @@
- 
- libcoot_lidia_core_la_SOURCES = lbg-molfile.cc lig-build.cc
- 
 +libcoot_lidia_core_la_LIBADD = \
 +	$(top_builddir)/geometry/libcoot-geometry.la \
-+	$(MMDB_LIBS)
++	$(MMDB_LIBS) $(CLIPPER_LIBS)



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-06-02  8:39 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-06-02  8:39 UTC (permalink / raw
  To: gentoo-commits

commit:     065a95be5ffc0c5b37c5f7b6b8aa89271247ab12
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun  2 08:39:46 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun  2 08:39:46 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=065a95be

Fixes for latest HEAD

(Portage version: 2.2.0_alpha37/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog              |    4 ++++
 sci-chemistry/coot/coot-9999.ebuild       |    1 +
 sci-chemistry/coot/files/9999-align.patch |   29 +++++++++++++++++++++++++++++
 3 files changed, 34 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 61ad2d8..30aec2f 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/9999-align.patch,
+  coot-9999.ebuild:
+  Fixes for latest HEAD
+
   28 May 2011; Justin Lecher <jlec@gentoo.org> -files/9999-clipper.patch,
   files/9999-lidia.patch, coot-9999.ebuild:
   Cleaned for current HEAD

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index bfeee1e..c6c8953 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -75,6 +75,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-include.patch
 	"${FILESDIR}"/${PV}-gl.patch
+	"${FILESDIR}"/${PV}-align.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/9999-align.patch b/sci-chemistry/coot/files/9999-align.patch
new file mode 100644
index 0000000..17e5787
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-align.patch
@@ -0,0 +1,29 @@
+Index: src/c-interface-mutate.cc
+===================================================================
+--- src/c-interface-mutate.cc	(revision 3528)
++++ src/c-interface-mutate.cc	(working copy)
+@@ -292,7 +292,9 @@
+   PyObject *r = Py_False;
+    if (is_valid_model_molecule(imol)) {
+       std::pair<bool, std::string> p = 
+-	 graphics_info_t::molecules[imol].find_terminal_residue_type(chain_id, resno);
++	 graphics_info_t::molecules[imol].find_terminal_residue_type(chain_id, resno,
++																					graphics_info_t::alignment_wgap,
++																					graphics_info_t::alignment_wspace);
+       if (p.first) {
+ 	 r = PyString_FromString(p.second.c_str());
+       }
+Index: src/c-interface-validate.cc
+===================================================================
+--- src/c-interface-validate.cc	(revision 3528)
++++ src/c-interface-validate.cc	(working copy)
+@@ -1653,7 +1653,8 @@
+ 
+    if (is_valid_model_molecule(imol)) {
+       std::pair<bool, std::vector<coot::chain_mutation_info_container_t> > ar = 
+-      	 graphics_info_t::molecules[imol].residue_mismatches();
++      	 graphics_info_t::molecules[imol].residue_mismatches(graphics_info_t::alignment_wgap,
++																				graphics_info_t::alignment_wspace);
+       if (ar.first)
+ 	r = PyList_New(0);
+       for (unsigned int ir=0; ir<ar.second.size(); ir++) {



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-06-15 20:50 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-06-15 20:50 UTC (permalink / raw
  To: gentoo-commits

commit:     df5c5e7ff841c1a20bb841e5c4da4dc398cfe9bc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 15 15:24:51 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 15 15:24:51 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=df5c5e7f

Updated to current HEAD

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog              |    4 ++++
 sci-chemistry/coot/coot-9999.ebuild       |    1 -
 sci-chemistry/coot/files/9999-align.patch |   29 -----------------------------
 3 files changed, 4 insertions(+), 30 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 30aec2f..2d688c2 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jun 2011; Justin Lecher <jlec@gentoo.org> -files/9999-align.patch,
+  coot-9999.ebuild:
+  Updated to current HEAD
+
   02 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/9999-align.patch,
   coot-9999.ebuild:
   Fixes for latest HEAD

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index c6c8953..bfeee1e 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -75,7 +75,6 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-include.patch
 	"${FILESDIR}"/${PV}-gl.patch
-	"${FILESDIR}"/${PV}-align.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/9999-align.patch b/sci-chemistry/coot/files/9999-align.patch
deleted file mode 100644
index 17e5787..0000000
--- a/sci-chemistry/coot/files/9999-align.patch
+++ /dev/null
@@ -1,29 +0,0 @@
-Index: src/c-interface-mutate.cc
-===================================================================
---- src/c-interface-mutate.cc	(revision 3528)
-+++ src/c-interface-mutate.cc	(working copy)
-@@ -292,7 +292,9 @@
-   PyObject *r = Py_False;
-    if (is_valid_model_molecule(imol)) {
-       std::pair<bool, std::string> p = 
--	 graphics_info_t::molecules[imol].find_terminal_residue_type(chain_id, resno);
-+	 graphics_info_t::molecules[imol].find_terminal_residue_type(chain_id, resno,
-+																					graphics_info_t::alignment_wgap,
-+																					graphics_info_t::alignment_wspace);
-       if (p.first) {
- 	 r = PyString_FromString(p.second.c_str());
-       }
-Index: src/c-interface-validate.cc
-===================================================================
---- src/c-interface-validate.cc	(revision 3528)
-+++ src/c-interface-validate.cc	(working copy)
-@@ -1653,7 +1653,8 @@
- 
-    if (is_valid_model_molecule(imol)) {
-       std::pair<bool, std::vector<coot::chain_mutation_info_container_t> > ar = 
--      	 graphics_info_t::molecules[imol].residue_mismatches();
-+      	 graphics_info_t::molecules[imol].residue_mismatches(graphics_info_t::alignment_wgap,
-+																				graphics_info_t::alignment_wspace);
-       if (ar.first)
- 	r = PyList_New(0);
-       for (unsigned int ir=0; ir<ar.second.size(); ir++) {



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-06-29 13:32 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-06-29 13:32 UTC (permalink / raw
  To: gentoo-commits

commit:     767b48f97d415ca52c9aa904172fc1e24f5d5533
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 29 13:32:19 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jun 29 13:32:19 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=767b48f9

Imported changes from tree

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog                       |    5 ++
 sci-chemistry/coot/coot-9999.ebuild                |   46 ++++++++++----------
 sci-chemistry/coot/files/9999-clipper-config.patch |   17 +++++++
 sci-chemistry/coot/files/9999-mmdb-config.patch    |   18 ++++++++
 sci-chemistry/coot/files/9999-test.patch           |   16 +++++++
 sci-chemistry/coot/metadata.xml                    |    8 ++--
 6 files changed, 83 insertions(+), 27 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 2d688c2..c4d7981 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Jun 2011; Justin Lecher <jlec@gentoo.org>
+  +files/9999-clipper-config.patch, +files/9999-mmdb-config.patch,
+  coot-9999.ebuild, +files/9999-test.patch, metadata.xml:
+  Imported changes from tree
+
   15 Jun 2011; Justin Lecher <jlec@gentoo.org> -files/9999-align.patch,
   coot-9999.ebuild:
   Updated to current HEAD

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 5561140..ecb5ff0 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI="3"
+EAPI=3
 
 PYTHON_DEPEND="2"
 
@@ -23,16 +23,17 @@ SRC_URI="test? ( http://www.biop.ox.ac.uk/coot/devel/greg-data.tar.gz )"
 SLOT="0"
 LICENSE="GPL-3"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="test"
+IUSE="+openmp test"
 
 SCIDEPS="
 	>=sci-libs/ccp4-libs-6.1
 	>=sci-libs/clipper-20090520
 	>=sci-libs/coot-data-2
 	>=sci-libs/gsl-1.3
-	sci-libs/mmdb
+	>=sci-libs/mmdb-1.23
+	<sci-libs/monomer-db-1
 	sci-chemistry/reduce
-	sci-chemistry/refmac
+	<sci-chemistry/refmac-5.6
 	sci-chemistry/probe"
 
 XDEPS="
@@ -67,14 +68,20 @@ DEPEND="${RDEPEND}
 S="${WORKDIR}"
 
 pkg_setup() {
+	if use openmp; then
+		tc-has-openmp || die "Please use an OPENMP capable compiler"
+	fi
 	python_set_active_version 2
 }
 
 PATCHES=(
+	"${FILESDIR}"/${PV}-clipper-config.patch
 	"${FILESDIR}"/${PV}-lidia.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-include.patch
 	"${FILESDIR}"/${PV}-gl.patch
+	"${FILESDIR}"/${PV}-mmdb-config.patch
+	"${FILESDIR}"/${PV}-test.patch
 	)
 
 src_unpack() {
@@ -85,12 +92,6 @@ src_unpack() {
 src_prepare() {
 	base_src_prepare
 
-	# Link against single-precision fftw
-	sed -i \
-		-e "s:\}fftw:}sfftw:g" \
-		-e "s:\}rfftw:}srfftw:g" \
-		"${S}"/macros/clipper.m4
-
 	cat >> src/svn-revision.cc <<- EOF
 	extern "C" {
 	int svn_revision() {
@@ -107,17 +108,15 @@ src_configure() {
 	# Yes, this is broken behavior.
 	econf \
 		--includedir='${prefix}/include/coot' \
-		--with-gtkcanvas-prefix="${EPREFIX}"/usr \
-		--with-clipper-prefix="${EPREFIX}"/usr \
-		--with-mmdb-prefix="${EPREFIX}"/usr \
-		--with-ssmlib-prefix="${EPREFIX}"/usr \
-		--with-gtkgl-prefix="${EPREFIX}"/usr \
+		--with-gtkcanvas-prefix="${EPREFIX}/usr" \
+		--with-ssmlib-prefix="${EPREFIX}/usr" \
+		--with-gtkgl-prefix="${EPREFIX}/usr" \
 		--with-guile \
-		--with-python="${EPREFIX}"/usr \
+		--with-python="${EPREFIX}/usr" \
 		--with-guile-gtk \
 		--with-gtk2 \
 		--with-pygtk \
-		--enable-openmp
+		$(use_enable openmp)
 }
 
 src_compile() {
@@ -133,16 +132,16 @@ src_test() {
 	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
 	export COOT_SCHEME_DIR="${S}/scheme/"
 	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps"
-	export COOT_DATA_DIR="${S}"
-	export COOT_PYTHON_DIR="${S}/python"
+	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
+	export COOT_DATA_DIR="${S}/"
+	export COOT_PYTHON_DIR="${S}/python/"
 	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr
-	export CCP4_SCR="${T}"/coot_test
+	export PYTHONHOME="${EPREFIX}"/usr/
+	export CCP4_SCR="${T}"/coot_test/
 	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
 	export SYMINFO="${S}/syminfo.lib"
 
-	export COOT_TEST_DATA_DIR="${S}"/data/greg-data
+	export COOT_TEST_DATA_DIR="${S}"/data/greg-data/
 
 	cat > command-line-greg.scm <<- EOF
 	(use-modules (ice-9 greg))
@@ -169,4 +168,5 @@ src_test() {
 	einfo "SYMINFO ${SYMINFO}"
 
 	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
 }

diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch
new file mode 100644
index 0000000..311b5e8
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-clipper-config.patch
@@ -0,0 +1,17 @@
+ macros/clipper.m4 |    3 +++
+ 1 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/macros/clipper.m4 b/macros/clipper.m4
+index 0bf087a..d0e8b6b 100644
+--- a/macros/clipper.m4
++++ b/macros/clipper.m4
+@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
+         ;;
+ esac
+ 
++CLIPPER_CXXFLAGS=`clipper-config --cflags`
++CLIPPER_LDOPTS=`clipper-config --libs`
++
+ AC_MSG_CHECKING([for Clipper])
+ 
+ 	LIBS="$save_LIBS $CLIPPER_LDOPTS"

diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
new file mode 100644
index 0000000..1d7cbd4
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-mmdb-config.patch
@@ -0,0 +1,18 @@
+ macros/mmdb.m4 |    4 ++++
+ 1 files changed, 4 insertions(+), 0 deletions(-)
+
+diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
+index b477597..d05cf66 100644
+--- a/macros/mmdb.m4
++++ b/macros/mmdb.m4
+@@ -86,6 +86,10 @@ else
+  ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+ 
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
++ac_MMDB_LDOPTS="${MMDB_LIBS}"
++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
++
+ AC_MSG_CHECKING([for MMDB])
+ 
+ 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"

diff --git a/sci-chemistry/coot/files/9999-test.patch b/sci-chemistry/coot/files/9999-test.patch
new file mode 100644
index 0000000..8cb79e6
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-test.patch
@@ -0,0 +1,16 @@
+ src/testing.cc |    4 +++-
+ 1 files changed, 3 insertions(+), 1 deletions(-)
+
+diff --git a/src/testing.cc b/src/testing.cc
+index f767bf6..097b9b9 100644
+--- a/src/testing.cc
++++ b/src/testing.cc
+@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) {
+    const char *c = getenv("COOT_TEST_DATA_DIR");
+    if (c) {
+       dd = c;
++      dd += "/";
++      dd += file_name;
+    } else { 
+       const char *d = getenv("HOME");
+       if (d) {

diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
index d7156cf..702e073 100644
--- a/sci-chemistry/coot/metadata.xml
+++ b/sci-chemistry/coot/metadata.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+	<herd>sci</herd>
+	<maintainer>
+		<email>sci@gentoo.org</email>
+	</maintainer>
 	<maintainer>
 		<email>jlec@gentoo.org</email>
 		<name>Justin Lecher</name>



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-07-16 13:45 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-07-16 13:45 UTC (permalink / raw
  To: gentoo-commits

commit:     d098e9d60d0ea751eee13de02cff23e54cc84d45
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jul 15 18:15:53 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jul 15 18:15:53 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d098e9d6

Mmdb fix

(Portage version: 2.2.0_alpha45/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog                    |    3 +++
 sci-chemistry/coot/files/9999-mmdb-config.patch |   20 ++++++++++----------
 2 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index c4d7981..50444a3 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Jul 2011; Justin Lecher <jlec@gentoo.org> files/9999-mmdb-config.patch:
+  Mmdb fix
+
   29 Jun 2011; Justin Lecher <jlec@gentoo.org>
   +files/9999-clipper-config.patch, +files/9999-mmdb-config.patch,
   coot-9999.ebuild, +files/9999-test.patch, metadata.xml:

diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
index 1d7cbd4..b3b66ab 100644
--- a/sci-chemistry/coot/files/9999-mmdb-config.patch
+++ b/sci-chemistry/coot/files/9999-mmdb-config.patch
@@ -1,18 +1,18 @@
- macros/mmdb.m4 |    4 ++++
- 1 files changed, 4 insertions(+), 0 deletions(-)
-
-diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
-index b477597..d05cf66 100644
---- a/macros/mmdb.m4
-+++ b/macros/mmdb.m4
-@@ -86,6 +86,10 @@ else
+Index: macros/mmdb.m4
+===================================================================
+--- macros/mmdb.m4	(revision 3579)
++++ macros/mmdb.m4	(working copy)
+@@ -86,8 +86,12 @@
   ac_MMDB_LDOPTS="-lmmdb -lm"
  fi
  
+-AC_MSG_CHECKING([for MMDB])
 +PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
 +ac_MMDB_LDOPTS="${MMDB_LIBS}"
 +ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
-+
- AC_MSG_CHECKING([for MMDB])
  
++AC_MSG_CHECKING([for CISPEP in MMDB])
++
  	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
+ 	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
+ 	#



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-07-16 13:45 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-07-16 13:45 UTC (permalink / raw
  To: gentoo-commits

commit:     a42c9e88010b8d397ad5629cb48308d8f8c85fa9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 16 13:45:33 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jul 16 13:45:33 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a42c9e88

Adopt to unbundled ssm

(Portage version: 2.2.0_alpha45/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog            |    4 ++
 sci-chemistry/coot/coot-9999.ebuild     |    3 +-
 sci-chemistry/coot/files/9999-ssm.patch |   56 +++++++++++++++++++++++++++++++
 3 files changed, 62 insertions(+), 1 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 50444a3..7f7c6e4 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Jul 2011; Justin Lecher <jlec@gentoo.org> +files/9999-ssm.patch,
+  coot-9999.ebuild:
+  Adopt to unbundled ssm
+
   15 Jul 2011; Justin Lecher <jlec@gentoo.org> files/9999-mmdb-config.patch:
   Mmdb fix
 

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index ecb5ff0..93859d2 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -31,6 +31,7 @@ SCIDEPS="
 	>=sci-libs/coot-data-2
 	>=sci-libs/gsl-1.3
 	>=sci-libs/mmdb-1.23
+	sci-libs/ssm
 	<sci-libs/monomer-db-1
 	sci-chemistry/reduce
 	<sci-chemistry/refmac-5.6
@@ -82,6 +83,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-gl.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-test.patch
+	"${FILESDIR}"/${PV}-ssm.patch
 	)
 
 src_unpack() {
@@ -109,7 +111,6 @@ src_configure() {
 	econf \
 		--includedir='${prefix}/include/coot' \
 		--with-gtkcanvas-prefix="${EPREFIX}/usr" \
-		--with-ssmlib-prefix="${EPREFIX}/usr" \
 		--with-gtkgl-prefix="${EPREFIX}/usr" \
 		--with-guile \
 		--with-python="${EPREFIX}/usr" \

diff --git a/sci-chemistry/coot/files/9999-ssm.patch b/sci-chemistry/coot/files/9999-ssm.patch
new file mode 100644
index 0000000..c801da7
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-ssm.patch
@@ -0,0 +1,56 @@
+ macros/mmdb-ssm.m4 |   42 +-----------------------------------------
+ 1 files changed, 1 insertions(+), 41 deletions(-)
+
+diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
+index 1937a16..6ef547c 100644
+--- a/macros/mmdb-ssm.m4
++++ b/macros/mmdb-ssm.m4
+@@ -22,47 +22,7 @@
+ AC_DEFUN([AM_WITH_MMDBSSM],
+ [AC_PROVIDE([AM_USE_MMDBSSM])
+ 
+-
+-AC_ARG_WITH(ssmlib-prefix, 
+-	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
+-	[ with_ssmlib_prefix="$withval" ],
+- with_ssmlib_prefix="")
+-
+-AC_MSG_CHECKING([for SSMLib])
+-
+-if test x$with_ssmlib_prefix != x; then
+-
+-   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
+-   MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+-
+-ac_mmdb_dirs='
+-.
+-include
+-include/ssm
+-include/mmdb
+-lib
+-src
+-lib/src
+-lib/src/mmdb'
+-
+-   for ac_dir in $ac_mmdb_dirs; do
+-      if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
+-         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
+-         break
+-      fi
+-   done
+-
+-  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
+-  
+-else 
+-
+-   MMDBSSM_CXXFLAGS=""
+-   MMDBSSM_LIBS=""
+-   with_ssmlib_prefix=no 
+-
+-fi
+-
+-AC_MSG_RESULT([$with_ssmlib_prefix])
++PKG_CHECK_MODULES([MMDBSSM],[ssm])
+ 
+ AC_SUBST(MMDBSSM_CXXFLAGS)
+ AC_SUBST(MMDBSSM_LIBS)



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2011-10-11 20:50 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2011-10-11 20:50 UTC (permalink / raw
  To: gentoo-commits

commit:     31f73020c2fad31dd8beb989bcaeb20915761549
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Oct  6 20:42:07 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Oct  6 20:42:07 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=31f73020

Add png15 support and don't build static libs

(Portage version: 2.2.0_alpha62/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-chemistry/coot/ChangeLog                   |    4 +++
 sci-chemistry/coot/coot-9999.ebuild            |    2 +
 sci-chemistry/coot/files/9999-libpng-1.5.patch |   29 ++++++++++++++++++++++++
 3 files changed, 35 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 7f7c6e4..164b64e 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Oct 2011; Justin Lecher <jlec@gentoo.org> +files/9999-libpng-1.5.patch,
+  coot-9999.ebuild:
+  Add png15 support and don't build static libs
+
   16 Jul 2011; Justin Lecher <jlec@gentoo.org> +files/9999-ssm.patch,
   coot-9999.ebuild:
   Adopt to unbundled ssm

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 93859d2..c3f3455 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -84,6 +84,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-test.patch
 	"${FILESDIR}"/${PV}-ssm.patch
+	"${FILESDIR}"/${PV}-libpng-1.5.patch
 	)
 
 src_unpack() {
@@ -109,6 +110,7 @@ src_configure() {
 	# All the --with's are used to activate various parts.
 	# Yes, this is broken behavior.
 	econf \
+		--disable-static \
 		--includedir='${prefix}/include/coot' \
 		--with-gtkcanvas-prefix="${EPREFIX}/usr" \
 		--with-gtkgl-prefix="${EPREFIX}/usr" \

diff --git a/sci-chemistry/coot/files/9999-libpng-1.5.patch b/sci-chemistry/coot/files/9999-libpng-1.5.patch
new file mode 100644
index 0000000..bddd251
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-libpng-1.5.patch
@@ -0,0 +1,29 @@
+--- ccp4mg-utils/ppmutil.cc
++++ ccp4mg-utils/ppmutil.cc
+@@ -2494,15 +2494,21 @@
+ 
+   pixels = new unsigned char[width*height*colourspace];
+ 
++  png_colorp palette;
++  int num_trans;
++#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
++  png_bytep trans_alpha;
++#endif
++
+   for (int i=0; i<height; i++){
+     if(color_type==PNG_COLOR_TYPE_PALETTE){
+       for (int j=0; j<width; j++){
+-        pixels[i*width*colourspace+j*colourspace] = png_ptr->palette[row_pointers[i][j]].red;
+-        pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green;
+-        pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue;
+-        if(row_pointers[i][j]<png_ptr->num_trans){
++        pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red;
++        pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green;
++        pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue;
++        if(row_pointers[i][j]<num_trans){
+ #if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
+-         pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]];
++         pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
+ #else
+          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
+ #endif



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2012-02-27  7:29 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2012-02-27  7:29 UTC (permalink / raw
  To: gentoo-commits

commit:     a8123cc7b89c5ab45e3b19f82a6f242aaacb2ed0
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 27 07:29:24 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Feb 27 07:29:24 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a8123cc7

Cleaned old patches, added goocanvas config option

(Portage version: 2.2.0_alpha89/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/coot/ChangeLog                |    8 ++++++++
 sci-chemistry/coot/coot-9999.ebuild         |    5 +----
 sci-chemistry/coot/files/9999-include.patch |   12 ------------
 sci-chemistry/coot/files/9999-lidia.patch   |   15 ---------------
 4 files changed, 9 insertions(+), 31 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index b097d5b..1508087 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  27 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/9999-include.patch,
+  -files/9999-lidia.patch, coot-9999.ebuild:
+  Cleaned old patches, added goocanvas config option
+
+  25 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/9999-include.patch,
+  -files/9999-lidia.patch, coot-9999.ebuild:
+  Cleaned old patches, added goocanvas config option
+
   14 Jan 2012; Justin Lecher <jlec@gentoo.org> -Manifest, -Manifest:
   Dropped Manifest
 

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index dd204d0..ec0fe56 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -81,9 +81,7 @@ pkg_setup() {
 
 PATCHES=(
 	"${FILESDIR}"/${PV}-clipper-config.patch
-	"${FILESDIR}"/${PV}-lidia.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
-	"${FILESDIR}"/${PV}-include.patch
 	"${FILESDIR}"/${PV}-gl.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-test.patch
@@ -113,8 +111,7 @@ src_configure() {
 	# Yes, this is broken behavior.
 	local myeconfargs=(
 		--includedir='${prefix}/include/coot'
-		--with-gtkcanvas-prefix="${EPREFIX}/usr"
-		--with-gtkgl-prefix="${EPREFIX}/usr"
+		--with-goocanvas-prefix="${EPREFIX}/usr"
 		--with-guile
 		--with-python="${EPREFIX}/usr"
 		--with-guile-gtk

diff --git a/sci-chemistry/coot/files/9999-include.patch b/sci-chemistry/coot/files/9999-include.patch
deleted file mode 100644
index 3076663..0000000
--- a/sci-chemistry/coot/files/9999-include.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Index: lbg/Makefile.am
-===================================================================
---- lbg/Makefile.am	(revision 3219)
-+++ lbg/Makefile.am	(working copy)
-@@ -2,6 +2,7 @@
- lib_LTLIBRARIES=libcoot-lidia.la
- 
- INCLUDES = \
-+	-I$(top_srcdir)/coot-utils \
- 	-I$(top_srcdir)/lidia-core \
- 	-I$(top_srcdir)/geometry \
- 	-I$(top_srcdir)/utils \

diff --git a/sci-chemistry/coot/files/9999-lidia.patch b/sci-chemistry/coot/files/9999-lidia.patch
deleted file mode 100644
index 2076513..0000000
--- a/sci-chemistry/coot/files/9999-lidia.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- lidia-core/Makefile.am |    4 ++++
- 1 files changed, 4 insertions(+), 0 deletions(-)
-
-diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 17d468d..78bf054 100644
---- a/lidia-core/Makefile.am
-+++ b/lidia-core/Makefile.am
-@@ -34,3 +34,7 @@ libcoot_lidia_core_la_SOURCES = lbg-molfile.cc lig-build.cc
- # test_molfile_SOURCES: test-molfile.cc
- 
- # test_molfile_LDADD: libcoot-lidia-core.la
-+
-+libcoot_lidia_core_la_LIBADD = \
-+	$(top_builddir)/geometry/libcoot-geometry.la \
-+	$(MMDB_LIBS) $(CLIPPER_LIBS)



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2012-03-21 11:20 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2012-03-21 11:20 UTC (permalink / raw
  To: gentoo-commits

commit:     cff4c2d27310f3f1b94ff5dfc493adbac6a8eecc
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Mar 16 11:20:22 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Mar 16 11:20:22 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cff4c2d2

Drop gl and test patch -> included upstream

(Portage version: 2.2.0_alpha90/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/coot/ChangeLog             |    4 ++++
 sci-chemistry/coot/coot-9999.ebuild      |   11 +++++++----
 sci-chemistry/coot/files/9999-gl.patch   |   10 ----------
 sci-chemistry/coot/files/9999-test.patch |   16 ----------------
 4 files changed, 11 insertions(+), 30 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 1508087..d281af2 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Mar 2012; Justin Lecher <jlec@gentoo.org> -files/9999-gl.patch,
+  -files/9999-test.patch, coot-9999.ebuild:
+  Drop gl and test patch -> included upstream
+
   27 Feb 2012; Justin Lecher <jlec@gentoo.org> -files/9999-include.patch,
   -files/9999-lidia.patch, coot-9999.ebuild:
   Cleaned old patches, added goocanvas config option

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index ec0fe56..f5bd086 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -5,6 +5,7 @@
 EAPI=4
 
 PYTHON_DEPEND="2"
+
 AUTOTOOLS_AUTORECONF="true"
 
 inherit autotools-utils python subversion toolchain-funcs versionator
@@ -25,6 +26,8 @@ LICENSE="GPL-3"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="+openmp static-libs test"
 
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
 SCIDEPS="
 	>=sci-libs/ccp4-libs-6.1
 	>=sci-libs/clipper-20090520
@@ -69,8 +72,6 @@ DEPEND="${RDEPEND}
 
 S="${WORKDIR}"
 
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
 pkg_setup() {
 	if use openmp; then
 		tc-has-openmp || die "Please use an OPENMP capable compiler"
@@ -82,9 +83,7 @@ pkg_setup() {
 PATCHES=(
 	"${FILESDIR}"/${PV}-clipper-config.patch
 	"${FILESDIR}"/${PV}-goocanvas.patch
-	"${FILESDIR}"/${PV}-gl.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
-	"${FILESDIR}"/${PV}-test.patch
 	"${FILESDIR}"/${PV}-ssm.patch
 	"${FILESDIR}"/${PV}-libpng-1.5.patch
 	)
@@ -95,6 +94,10 @@ src_unpack() {
 }
 
 src_prepare() {
+	sed \
+		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
+		-i configure.in || die
+
 	autotools-utils_src_prepare
 
 	cat >> src/svn-revision.cc <<- EOF

diff --git a/sci-chemistry/coot/files/9999-gl.patch b/sci-chemistry/coot/files/9999-gl.patch
deleted file mode 100644
index bbd858c..0000000
--- a/sci-chemistry/coot/files/9999-gl.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-Index: coot-surface/Makefile.am
-===================================================================
---- coot-surface/Makefile.am	(revision 3478)
-+++ coot-surface/Makefile.am	(working copy)
-@@ -29,4 +29,4 @@
- 
- libcoot_surface_la_LIBADD = \
- 	$(top_builddir)/surface/libccp4mg-surface.la \
--	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) 
-+	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) -lGL

diff --git a/sci-chemistry/coot/files/9999-test.patch b/sci-chemistry/coot/files/9999-test.patch
deleted file mode 100644
index 8cb79e6..0000000
--- a/sci-chemistry/coot/files/9999-test.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/testing.cc |    4 +++-
- 1 files changed, 3 insertions(+), 1 deletions(-)
-
-diff --git a/src/testing.cc b/src/testing.cc
-index f767bf6..097b9b9 100644
---- a/src/testing.cc
-+++ b/src/testing.cc
-@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) {
-    const char *c = getenv("COOT_TEST_DATA_DIR");
-    if (c) {
-       dd = c;
-+      dd += "/";
-+      dd += file_name;
-    } else { 
-       const char *d = getenv("HOME");
-       if (d) {



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2012-04-25 15:26 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2012-04-25 15:26 UTC (permalink / raw
  To: gentoo-commits

commit:     d858ac3b7a4d7f28e524ddaf398a3c39532e7907
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 25 15:24:24 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Apr 25 15:24:24 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d858ac3b

sci-chemistry/coot: Drop libpng-1.5 patch, included upstream

(Portage version: 2.2.0_alpha101/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/coot/ChangeLog                   |    7 +++++
 sci-chemistry/coot/coot-9999.ebuild            |    1 -
 sci-chemistry/coot/files/9999-libpng-1.5.patch |   29 ------------------------
 3 files changed, 7 insertions(+), 30 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index d281af2..0b2d8a9 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  25 Apr 2012; Justin Lecher <jlec@gentoo.org> -files/9999-libpng-1.5.patch,
+  coot-9999.ebuild:
+  Drop libpng-1.5 patch, included upstream
+
+  25 Apr 2012; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
+  Add fix for >glib-2.32
+
   16 Mar 2012; Justin Lecher <jlec@gentoo.org> -files/9999-gl.patch,
   -files/9999-test.patch, coot-9999.ebuild:
   Drop gl and test patch -> included upstream

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index f5bd086..fc6ca94 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -85,7 +85,6 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-ssm.patch
-	"${FILESDIR}"/${PV}-libpng-1.5.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/9999-libpng-1.5.patch b/sci-chemistry/coot/files/9999-libpng-1.5.patch
deleted file mode 100644
index bddd251..0000000
--- a/sci-chemistry/coot/files/9999-libpng-1.5.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- ccp4mg-utils/ppmutil.cc
-+++ ccp4mg-utils/ppmutil.cc
-@@ -2494,15 +2494,21 @@
- 
-   pixels = new unsigned char[width*height*colourspace];
- 
-+  png_colorp palette;
-+  int num_trans;
-+#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
-+  png_bytep trans_alpha;
-+#endif
-+
-   for (int i=0; i<height; i++){
-     if(color_type==PNG_COLOR_TYPE_PALETTE){
-       for (int j=0; j<width; j++){
--        pixels[i*width*colourspace+j*colourspace] = png_ptr->palette[row_pointers[i][j]].red;
--        pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green;
--        pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue;
--        if(row_pointers[i][j]<png_ptr->num_trans){
-+        pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red;
-+        pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green;
-+        pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue;
-+        if(row_pointers[i][j]<num_trans){
- #if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
--         pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]];
-+         pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
- #else
-          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
- #endif



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2012-06-14 12:11 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2012-06-14 12:11 UTC (permalink / raw
  To: gentoo-commits

commit:     3bdd9d0c7138075bded9befe7eb76591dfd9b8af
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 14 12:11:08 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 14 12:11:08 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3bdd9d0c

sci-chemistry/coot: Fix for gcc-4.7

(Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/coot/ChangeLog                   |    4 ++
 sci-chemistry/coot/coot-9999.ebuild            |    1 +
 sci-chemistry/coot/files/coot-9999-gcc47.patch |   47 ++++++++++++++++++++++++
 3 files changed, 52 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 0b2d8a9..6facbcb 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Jun 2012; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+  +files/coot-9999-gcc47.patch:
+  Fix for gcc-4.7
+
   25 Apr 2012; Justin Lecher <jlec@gentoo.org> -files/9999-libpng-1.5.patch,
   coot-9999.ebuild:
   Drop libpng-1.5 patch, included upstream

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index fc6ca94..87215ab 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -85,6 +85,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-ssm.patch
+	"${FILESDIR}"/${P}-gcc47.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/coot-9999-gcc47.patch b/sci-chemistry/coot/files/coot-9999-gcc47.patch
new file mode 100644
index 0000000..465923a
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-gcc47.patch
@@ -0,0 +1,47 @@
+Index: utils/coot-utils.cc
+===================================================================
+--- utils/coot-utils.cc	(revision 4235)
++++ utils/coot-utils.cc	(working copy)
+@@ -28,6 +28,7 @@
+ #include <stdexcept> // for string_to_int.
+ #include <sstream>   // ditto.
+ #include <cstdio>    // 20090806 Justin Lecher says we need this on Gentoo 
++#include <unistd.h>
+ 
+ #include "coot-sysdep.h"
+ #if defined _MSC_VER
+Index: coot-utils/coot-coord-utils.cc
+===================================================================
+--- coot-utils/coot-coord-utils.cc	(revision 4235)
++++ coot-utils/coot-coord-utils.cc	(working copy)
+@@ -196,7 +196,7 @@
+       clipper::Coord_frac cf = coot::util::shift_to_origin(mol);
+       clipper::Coord_orth co = cf.coord_orth(csp.first);
+       for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
+-	 int imod = 1;
++//	 int imod = 1;
+ 	 CModel *model_p = mol->GetModel(imod);
+ 	 CChain *chain_p;
+ 	 int nchains = model_p->GetNumberOfChains();
+@@ -2779,7 +2779,7 @@
+    short int whole_res_flag = 1;
+ 
+    for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) {
+-     int imod = 1;
++//     int imod = 1;
+      CModel *model_p = mol_in->GetModel(imod);
+      CModel *new_model_p = new CModel;
+      int nchains = model_p->GetNumberOfChains();
+Index: src/molecule-class-info-residues.cc
+===================================================================
+--- src/molecule-class-info-residues.cc	(revision 4235)
++++ src/molecule-class-info-residues.cc	(working copy)
+@@ -145,7 +145,7 @@
+ 
+    int r = 0;
+    for(int imod = 1; imod<=atom_sel.mol->GetNumberOfModels(); imod++) {
+-      int imod = 1;
++//      int imod = 1;
+       CModel *model_p = atom_sel.mol->GetModel(imod);
+       CChain *chain_p;
+       // run over chains of the existing mol



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2012-07-04  7:43 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2012-07-04  7:43 UTC (permalink / raw
  To: gentoo-commits

commit:     fcac9ab8d559c154577fde4b0a73ad3f207efcfa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul  3 15:31:04 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jul  3 15:31:04 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fcac9ab8

sci-chemistry/coot: Gcc-4.7 support included upstream

(Portage version: 2.2.0_alpha115/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/coot/ChangeLog                   |    4 ++
 sci-chemistry/coot/coot-9999.ebuild            |    1 -
 sci-chemistry/coot/files/coot-9999-gcc47.patch |   47 ------------------------
 3 files changed, 4 insertions(+), 48 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 6facbcb..38e7315 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Jul 2012; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+  -files/coot-9999-gcc47.patch:
+  Gcc-4.7 support included upstream
+
   14 Jun 2012; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
   +files/coot-9999-gcc47.patch:
   Fix for gcc-4.7

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 87215ab..fc6ca94 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -85,7 +85,6 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-ssm.patch
-	"${FILESDIR}"/${P}-gcc47.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/coot-9999-gcc47.patch b/sci-chemistry/coot/files/coot-9999-gcc47.patch
deleted file mode 100644
index 465923a..0000000
--- a/sci-chemistry/coot/files/coot-9999-gcc47.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-Index: utils/coot-utils.cc
-===================================================================
---- utils/coot-utils.cc	(revision 4235)
-+++ utils/coot-utils.cc	(working copy)
-@@ -28,6 +28,7 @@
- #include <stdexcept> // for string_to_int.
- #include <sstream>   // ditto.
- #include <cstdio>    // 20090806 Justin Lecher says we need this on Gentoo 
-+#include <unistd.h>
- 
- #include "coot-sysdep.h"
- #if defined _MSC_VER
-Index: coot-utils/coot-coord-utils.cc
-===================================================================
---- coot-utils/coot-coord-utils.cc	(revision 4235)
-+++ coot-utils/coot-coord-utils.cc	(working copy)
-@@ -196,7 +196,7 @@
-       clipper::Coord_frac cf = coot::util::shift_to_origin(mol);
-       clipper::Coord_orth co = cf.coord_orth(csp.first);
-       for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
--	 int imod = 1;
-+//	 int imod = 1;
- 	 CModel *model_p = mol->GetModel(imod);
- 	 CChain *chain_p;
- 	 int nchains = model_p->GetNumberOfChains();
-@@ -2779,7 +2779,7 @@
-    short int whole_res_flag = 1;
- 
-    for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) {
--     int imod = 1;
-+//     int imod = 1;
-      CModel *model_p = mol_in->GetModel(imod);
-      CModel *new_model_p = new CModel;
-      int nchains = model_p->GetNumberOfChains();
-Index: src/molecule-class-info-residues.cc
-===================================================================
---- src/molecule-class-info-residues.cc	(revision 4235)
-+++ src/molecule-class-info-residues.cc	(working copy)
-@@ -145,7 +145,7 @@
- 
-    int r = 0;
-    for(int imod = 1; imod<=atom_sel.mol->GetNumberOfModels(); imod++) {
--      int imod = 1;
-+//      int imod = 1;
-       CModel *model_p = atom_sel.mol->GetModel(imod);
-       CChain *chain_p;
-       // run over chains of the existing mol



^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2013-06-02 16:48 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2013-06-02 16:48 UTC (permalink / raw
  To: gentoo-commits

commit:     eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  2 16:42:24 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun  2 16:42:24 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb7653c7

sci-chemistry/coot: Update pc patches

Package-Manager: portage-2.2.0_alpha177

---
 sci-chemistry/coot/ChangeLog                       |    5 +
 sci-chemistry/coot/coot-9999.ebuild                |   20 +-
 sci-chemistry/coot/files/9999-clipper-config.patch |   17 -
 sci-chemistry/coot/files/9999-goocanvas.patch      |   25 -
 sci-chemistry/coot/files/9999-mmdb-config.patch    |   18 -
 sci-chemistry/coot/files/9999-pc.patch             | 1040 ++++++++++++++++++++
 sci-chemistry/coot/files/9999-ssm.patch            |   56 --
 7 files changed, 1054 insertions(+), 127 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index c729ace..2bbf002 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jun 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+  -files/9999-clipper-config.patch, -files/9999-goocanvas.patch,
+  -files/9999-mmdb-config.patch, +files/9999-pc.patch, -files/9999-ssm.patch:
+  Update pc patches
+
   02 Jun 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Fix PYTHON() -> ${EPYTHON} for new eclasses
 

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 4a7ee55..c8831ad 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -37,9 +37,9 @@ SCIDEPS="
 	>=sci-libs/gsl-1.3
 	>=sci-libs/mmdb-1.23
 	sci-libs/ssm
-	<sci-libs/monomer-db-1
+	sci-libs/monomer-db
 	sci-chemistry/reduce
-	<sci-chemistry/refmac-5.6
+	sci-chemistry/refmac
 	sci-chemistry/probe"
 
 XDEPS="
@@ -82,21 +82,19 @@ pkg_setup() {
 	python-single-r1_pkg_setup
 }
 
-PATCHES=(
-	"${FILESDIR}"/${PV}-clipper-config.patch
-	"${FILESDIR}"/${PV}-goocanvas.patch
-	"${FILESDIR}"/${PV}-mmdb-config.patch
-	"${FILESDIR}"/${PV}-ssm.patch
-	)
+PATCHES=( "${FILESDIR}"/${PV}-pc.patch	)
 
 src_unpack() {
 	subversion_src_unpack
-	use test && unpack ${A}
+	if use test; then
+		unpack ${A}
+		ln -sf . "${S}"/coot-ccp4
+	fi
 }
 
 src_prepare() {
 	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${PYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
+		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
 		-i configure.in || die
 
 	autotools-utils_src_prepare
@@ -128,7 +126,7 @@ src_configure() {
 
 src_compile() {
 	autotools-utils_src_compile
-	python_fix_shebang "${S}"/src/coot_gtk2.py "${S}"/python-tests/coot_unittest.py
+	python_fix_shebang "${S}"/src/coot_gtk2.py
 	cp "${S}"/src/coot_gtk2.py python/coot.py || die
 }
 

diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch
deleted file mode 100644
index 311b5e8..0000000
--- a/sci-chemistry/coot/files/9999-clipper-config.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- macros/clipper.m4 |    3 +++
- 1 files changed, 3 insertions(+), 0 deletions(-)
-
-diff --git a/macros/clipper.m4 b/macros/clipper.m4
-index 0bf087a..d0e8b6b 100644
---- a/macros/clipper.m4
-+++ b/macros/clipper.m4
-@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
-         ;;
- esac
- 
-+CLIPPER_CXXFLAGS=`clipper-config --cflags`
-+CLIPPER_LDOPTS=`clipper-config --libs`
-+
- AC_MSG_CHECKING([for Clipper])
- 
- 	LIBS="$save_LIBS $CLIPPER_LDOPTS"

diff --git a/sci-chemistry/coot/files/9999-goocanvas.patch b/sci-chemistry/coot/files/9999-goocanvas.patch
deleted file mode 100644
index ce0d4a0..0000000
--- a/sci-chemistry/coot/files/9999-goocanvas.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Index: macros/goo-canvas.m4
-===================================================================
---- macros/goo-canvas.m4	(revision 3307)
-+++ macros/goo-canvas.m4	(working copy)
-@@ -56,9 +56,9 @@
-   fi
- fi
- 
--AC_MSG_CHECKING([for Goocanvas])
-+PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
- 
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
- #
- # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
-@@ -76,7 +76,7 @@
- if test x$have_goocanvas = xyes; then
- 
-  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
- 
- ifelse([$1], , :, [$1])
- 

diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
deleted file mode 100644
index b3b66ab..0000000
--- a/sci-chemistry/coot/files/9999-mmdb-config.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Index: macros/mmdb.m4
-===================================================================
---- macros/mmdb.m4	(revision 3579)
-+++ macros/mmdb.m4	(working copy)
-@@ -86,8 +86,12 @@
-  ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
- 
--AC_MSG_CHECKING([for MMDB])
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
-+ac_MMDB_LDOPTS="${MMDB_LIBS}"
-+ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
- 
-+AC_MSG_CHECKING([for CISPEP in MMDB])
-+
- 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
- 	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
- 	#

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
new file mode 100644
index 0000000..a6bc18e
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -0,0 +1,1040 @@
+Index: ChangeLog
+===================================================================
+--- ChangeLog	(revision 4651)
++++ ChangeLog	(working copy)
+@@ -1959,7 +1959,7 @@
+ 2005-01-29  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
+ 
+ 	* macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in
+-	MMDBSSM_CXXFLAGS [Oops].  Hopefully fixes problems spotted by Joel
++	MMDBSSM_CFLAGS [Oops].  Hopefully fixes problems spotted by Joel
+ 	Bard and Joseph Toth.
+ 
+ 	* src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add
+@@ -2252,14 +2252,14 @@
+ 
+ 2004-11-20  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
+ 
+-	* coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for
++	* coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for
+ 	coot-close.cc usage].
+ 
+ 2004-11-19  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
+ 
+-	* sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS
++	* sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS
+ 
+-	* analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS
++	* analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS
+ 
+ 2004-11-16  Paul Emsley  <emsley@localhost>
+ 
+@@ -2269,7 +2269,7 @@
+  
+ 2004-11-15  Paul Emsley  <emsley@localhost>
+ 
+-	* coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks 
++	* coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks 
+           Joseph Toth].
+ 
+ 	* surface/CXXSphereNode.h: removed the ; again!
+Index: analysis/Makefile.am
+===================================================================
+--- analysis/Makefile.am	(revision 4651)
++++ analysis/Makefile.am	(working copy)
+@@ -11,8 +11,8 @@
+ 	-I$(top_srcdir)/coot-utils   	\
+ 	-I$(top_srcdir)/mini-mol   	\
+ 	-I$(top_srcdir)/utils   	\
+-	$(CLIPPER_CXXFLAGS)		\
+-	$(MMDB_CXXFLAGS)
++	$(CLIPPER_CFLAGS)		\
++	$(MMDB_CFLAGS)
+ 
+ libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc 
+ 
+Index: angles/Makefile.am
+===================================================================
+--- angles/Makefile.am	(revision 4651)
++++ angles/Makefile.am	(working copy)
+@@ -6,7 +6,7 @@
+ 
+ include_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS)
+ 
+ libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h  \
+ 	AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc
+Index: auxil/catcheck/Makefile.am
+===================================================================
+--- auxil/catcheck/Makefile.am	(revision 4651)
++++ auxil/catcheck/Makefile.am	(working copy)
+@@ -1,7 +1,7 @@
+ 
+ EXTRA_DIST = Makefile.simple
+ 
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
+ 
+ check_PROGRAMS = catcheck
+ 
+Index: auxil/catcheck/Makefile.simple
+===================================================================
+--- auxil/catcheck/Makefile.simple	(revision 4651)
++++ auxil/catcheck/Makefile.simple	(working copy)
+@@ -1,17 +1,17 @@
+ 
+-# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
++# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
+ 
+ 
+ BASE = /home/paule/autobuild/Linux-kalypso-pre-release
+-CLIPPER_CXXFLAGS = -I$(BASE)/include
+-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
++CLIPPER_CFLAGS = -I$(BASE)/include
++MMDB_CFLAGS = -I$(BASE)/include/mmdb
+ 
+ CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
+ 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ 	-lclipper-core -lccp4c -L$(BASE)/lib \
+ 	-L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+ 
+ catcheck: catcheck.cc catcheck.hh
+Index: auxil/rama/Makefile.am
+===================================================================
+--- auxil/rama/Makefile.am	(revision 4651)
++++ auxil/rama/Makefile.am	(working copy)
+@@ -1,7 +1,7 @@
+ 
+ EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm
+ 
+-INCLUDES =  $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES =  $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ 
+ 
+ check_PROGRAMS = rama-data rama-doughnut 
+Index: auxil/rama/Makefile.simple
+===================================================================
+--- auxil/rama/Makefile.simple	(revision 4651)
++++ auxil/rama/Makefile.simple	(working copy)
+@@ -1,12 +1,12 @@
+ 
+-CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
++CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
+ 
+ CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
+ 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ 	-lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
+ 	-L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+ 
+ rama-data: rama-data.cc
+Index: auxil/sec-str/Makefile.am
+===================================================================
+--- auxil/sec-str/Makefile.am	(revision 4651)
++++ auxil/sec-str/Makefile.am	(working copy)
+@@ -1,6 +1,6 @@
+ 
+ EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
+ 
+ #check_PROGRAMS = sec-str-dist-check
+ 
+Index: auxil/sec-str/Makefile.simple
+===================================================================
+--- auxil/sec-str/Makefile.simple	(revision 4651)
++++ auxil/sec-str/Makefile.simple	(working copy)
+@@ -1,27 +1,27 @@
+ 
+-#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
++#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
+ 
+ #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
+ #	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ #	-lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
+ #	-L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
+ 
+-#INCLUDES = $(CLIPPER_CXXFLAGS)
++#INCLUDES = $(CLIPPER_CFLAGS)
+ #LDLIBS = $(CLIPPER_LIBS)
+ 
+ 
+ # 
+ 
+ BASE = /home/paule/autobuild/Linux-kalypso-pre-release
+-CLIPPER_CXXFLAGS = -I$(BASE)/include
+-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
++CLIPPER_CFLAGS = -I$(BASE)/include
++MMDB_CFLAGS = -I$(BASE)/include/mmdb
+ 
+ CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
+ 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ 	-lclipper-core -lccp4c -L$(BASE)/lib \
+ 	-L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+ 
+ sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh
+Index: auxil/strand-analysis/Makefile.am
+===================================================================
+--- auxil/strand-analysis/Makefile.am	(revision 4651)
++++ auxil/strand-analysis/Makefile.am	(working copy)
+@@ -3,8 +3,8 @@
+ 
+ 
+ INCLUDES = -I$(top_srcdir)/auxil/sec-str \
+-	$(MMDB_CXXFLAGS) 	         \
+-	$(CLIPPER_CXXFLAGS) 		
++	$(MMDB_CFLAGS) 	         \
++	$(CLIPPER_CFLAGS) 		
+ 
+ 
+ check_PROGRAMS = 
+Index: auxil/strand-analysis/Makefile.simple
+===================================================================
+--- auxil/strand-analysis/Makefile.simple	(revision 4651)
++++ auxil/strand-analysis/Makefile.simple	(working copy)
+@@ -2,13 +2,13 @@
+ 
+ CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based
+ 
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include
++CLIPPER_CFLAGS = -I$(CLIPPER)/include
+ 
+ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \
+ 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ 	-lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm
+ 
+-INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS)
++INCLUDES = -I../sec-str $(CLIPPER_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+ 
+ .cc:
+Index: auxil/vectors/Makefile.am
+===================================================================
+--- auxil/vectors/Makefile.am	(revision 4651)
++++ auxil/vectors/Makefile.am	(working copy)
+@@ -1,6 +1,6 @@
+ 
+ EXTRA_DIST = Makefile.simple diff-vec.cc
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+ check_PROGRAMS = 
+ 
+ #diff_vec_SOURCES = diff-vec.cc
+Index: build/Makefile.am
+===================================================================
+--- build/Makefile.am	(revision 4651)
++++ build/Makefile.am	(working copy)
+@@ -24,8 +24,8 @@
+ 
+ INCLUDES =  \
+ 	-I$(top_srcdir)/angles \
+-	$(CLIPPER_CXXFLAGS) \
+-	$(MMDB_CXXFLAGS)
++	$(CLIPPER_CFLAGS) \
++	$(MMDB_CFLAGS)
+ 
+ noinst_PROGRAMS = testcabuild
+ 
+Index: ccp4mg-utils/Makefile.am
+===================================================================
+--- ccp4mg-utils/Makefile.am	(revision 4651)
++++ ccp4mg-utils/Makefile.am	(working copy)
+@@ -25,7 +25,7 @@
+ EXTRA_DIST = convert.sh get-new-utils.sh
+ 
+ INCLUDES =  \
+-	$(MMDB_CXXFLAGS) \
++	$(MMDB_CFLAGS) \
+ 	$(LIBPNG_CFLAGS)
+ 
+ libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \
+Index: ccp4mg-utils/mmut/Makefile.am
+===================================================================
+--- ccp4mg-utils/mmut/Makefile.am	(revision 4651)
++++ ccp4mg-utils/mmut/Makefile.am	(working copy)
+@@ -70,9 +70,9 @@
+ 	$(LIBGLADE_CFLAGS)		\
+ 	@GTK_CFLAGS@ 			\
+ 	$(GLUT_CFLAGS)			\
+-	$(MMDBSSM_CXXFLAGS) 		\
+-	$(MMDB_CXXFLAGS) 		\
+-	$(CLIPPER_CXXFLAGS) 		
++	$(MMDBSSM_CFLAGS) 		\
++	$(MMDB_CFLAGS) 		\
++	$(CLIPPER_CFLAGS) 		
+ 
+ #	$(WITH_SCRIPT_CFLAGS) 
+ 
+Index: ccp4mg-utils/pygl/Makefile.am
+===================================================================
+--- ccp4mg-utils/pygl/Makefile.am	(revision 4651)
++++ ccp4mg-utils/pygl/Makefile.am	(working copy)
+@@ -108,9 +108,9 @@
+ 	$(LIBGLADE_CFLAGS)		\
+ 	@GTK_CFLAGS@ 			\
+ 	$(GLUT_CFLAGS)			\
+-	$(MMDBSSM_CXXFLAGS) 		\
+-	$(MMDB_CXXFLAGS) 		\
+-	$(CLIPPER_CXXFLAGS) 		
++	$(MMDBSSM_CFLAGS) 		\
++	$(MMDB_CFLAGS) 		\
++	$(CLIPPER_CFLAGS) 		
+ 
+ #	$(WITH_SCRIPT_CFLAGS) 
+ 
+Index: ccp4mg-utils/util/Makefile.am
+===================================================================
+--- ccp4mg-utils/util/Makefile.am	(revision 4651)
++++ ccp4mg-utils/util/Makefile.am	(working copy)
+@@ -73,9 +73,9 @@
+ 	$(LIBGLADE_CFLAGS)		\
+ 	@GTK_CFLAGS@ 			\
+ 	$(GLUT_CFLAGS)			\
+-	$(MMDBSSM_CXXFLAGS) 		\
+-	$(MMDB_CXXFLAGS) 		\
+-	$(CLIPPER_CXXFLAGS) 		
++	$(MMDBSSM_CFLAGS) 		\
++	$(MMDB_CFLAGS) 		\
++	$(CLIPPER_CFLAGS) 		
+ 
+ #	$(WITH_SCRIPT_CFLAGS) 
+ 
+Index: configure.in
+===================================================================
+--- configure.in	(revision 4651)
++++ configure.in	(working copy)
+@@ -108,14 +108,18 @@
+ 
+ 
+ dnl Check for MMDB.
+-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)])
+ 
+-AM_WITH_MMDBSSM
++PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM])
+ AM_WITH_CCP4SRS
+ 
+ dnl Check for Clipper.  we exit if clipper is not found.
+ #
+-AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
++PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [
++  CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS])
++  ], [
++  AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
++  ])
+ 
+ # we set default coot_guile to true
+ coot_guile=true
+@@ -189,11 +193,15 @@
+ 
+ dnl =========================== GooCanvas ================================
+ 
+-AM_PATH_GOOCANVAS
+-# give something for the preprocessor to chew on...
+-if test "$GOOCANVAS_CFLAGS" != "" ; then
+-   GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
+-fi
++PKG_CHECK_MODULES([GOOCANVAS], [goocanvas],
++	[GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)],
++	[
++		AM_PATH_GOOCANVAS
++		# give something for the preprocessor to chew on...
++		if test "$GOOCANVAS_CFLAGS" != "" ; then
++   		GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
++		fi
++	])
+ 
+ AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ],
+  coot_enterprise_additions="true",
+Index: coords/Makefile.am
+===================================================================
+--- coords/Makefile.am	(revision 4651)
++++ coords/Makefile.am	(working copy)
+@@ -34,7 +34,7 @@
+ 	-I$(top_srcdir)/compat     \
+ 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(RDKIT_CXXFLAGS) 		\
+-	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ 
+ AM_CXXFLAGS = \
+ 	-DPKGDATADIR='"$(pkgdatadir)"' \
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am	(revision 4651)
++++ coot-surface/Makefile.am	(working copy)
+@@ -21,7 +21,7 @@
+ INCLUDES = -I$(top_srcdir)/surface \
+            -I$(top_srcdir)/coot-utils \
+            -I$(top_srcdir)/mini-mol \
+-	$(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
++	$(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
+ 
+ lib_LTLIBRARIES = libcoot-surface.la
+ 
+Index: coot-utils/Makefile.am
+===================================================================
+--- coot-utils/Makefile.am	(revision 4651)
++++ coot-utils/Makefile.am	(working copy)
+@@ -38,8 +38,8 @@
+ 	-I$(top_srcdir)/geometry	\
+ 	-I$(top_srcdir)/compat		\
+ 	-I$(top_srcdir)/mini-mol	\
+-	$(CLIPPER_CXXFLAGS) 		\
+-	$(MMDB_CXXFLAGS) 		\
++	$(CLIPPER_CFLAGS) 		\
++	$(MMDB_CFLAGS) 		\
+ 	$(GSL_CFLAGS)			\
+ 	$(WITH_GUILE_CFLAGS)		\
+ 	$(WITH_PYTHON_CFLAGS)
+Index: cootaneer/Makefile.am
+===================================================================
+--- cootaneer/Makefile.am	(revision 4651)
++++ cootaneer/Makefile.am	(working copy)
+@@ -20,7 +20,7 @@
+ EXTRA_DIST = 		\
+ 	cootaneer-llk-2.40.dat
+ 
+-INCLUDES = 	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
++INCLUDES = 	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
+ 
+ cootaneer_demo_SOURCES = cootaneer-demo.cpp
+ 
+Index: cootilus/Makefile.am
+===================================================================
+--- cootilus/Makefile.am	(revision 4651)
++++ cootilus/Makefile.am	(working copy)
+@@ -20,7 +20,7 @@
+ EXTRA_DIST = 		\
+ 	nautilus_lib.pdb
+ 
+-INCLUDES = 	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
++INCLUDES = 	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
+ 
+ cootilus_demo_SOURCES = cootilus-demo.cpp
+ 
+Index: db-main/Makefile.am
+===================================================================
+--- db-main/Makefile.am	(revision 4651)
++++ db-main/Makefile.am	(working copy)
+@@ -6,7 +6,7 @@
+ 	-DDATADIR='"$(datadir)"'
+ 
+ INCLUDES = -I$(top_srcdir)/utils -I$(top_srcdir)/coot-utils -I$(top_srcdir)/mini-mol \
+-   $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++   $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+ 
+ include_HEADERS = db-main.hh db-strands.hh
+ 
+Index: db-main/Makefile.simple
+===================================================================
+--- db-main/Makefile.simple	(revision 4651)
++++ db-main/Makefile.simple	(working copy)
+@@ -19,7 +19,7 @@
+ MCCP4   = $(HOME)/crystal
+ 
+ CXX = g++
+-MMDB_CXXFLAGS = -I$(MMDB)/include 
++MMDB_CFLAGS = -I$(MMDB)/include 
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
+ 
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
+@@ -28,9 +28,9 @@
+ 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
+ 
+ MCCP4_CFLAGS = -I$(MCCP4)/include
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
+ 
+ CXXFLAGS = -g $(INCLUDES)
+ LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) 
+@@ -44,4 +44,4 @@
+ db-main.o: db-main.cc db-main.hh
+ 
+ testmmdbbits: testmmdbbits.cc
+-	$(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@
++	$(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@
+Index: density-contour/Makefile.am
+===================================================================
+--- density-contour/Makefile.am	(revision 4651)
++++ density-contour/Makefile.am	(working copy)
+@@ -20,7 +20,7 @@
+ 
+ COORD_INCLUDES = -I$(top_srcdir)/coords
+ 
+-INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS) 
++INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS) 
+ 
+ lib_LTLIBRARIES = libcoot-isosurface.la
+ 
+Index: geometry/Makefile.am
+===================================================================
+--- geometry/Makefile.am	(revision 4651)
++++ geometry/Makefile.am	(working copy)
+@@ -29,7 +29,7 @@
+ 	   -I$(top_srcdir)/mini-mol   \
+ 	   -I$(top_srcdir)/coot-utils \
+ 	   -I$(top_srcdir)/compat     \
+-	 $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS)
++	 $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS)
+ 
+ AM_CXXFLAGS = \
+ 	-DDATADIR='"$(datadir)"'       \
+Index: geometry/Makefile.simple
+===================================================================
+--- geometry/Makefile.simple	(revision 4651)
++++ geometry/Makefile.simple	(working copy)
+@@ -46,7 +46,7 @@
+ 
+ 
+ CXX = g++
+-MMDB_CXXFLAGS = -I$(MMDB)/include 
++MMDB_CFLAGS = -I$(MMDB)/include 
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
+ 
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
+@@ -55,9 +55,9 @@
+ 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
+ 
+ MCCP4_CFLAGS = -I$(MCCP4)/include
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords 
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords 
+ 
+ top_srcdir = ..
+ 
+Index: high-res/Makefile.am
+===================================================================
+--- high-res/Makefile.am	(revision 4651)
++++ high-res/Makefile.am	(working copy)
+@@ -36,8 +36,8 @@
+ 	-I$(top_srcdir)/coot-utils   \
+ 	-I$(top_srcdir)/lidia-core   \
+ 	-I$(top_srcdir)/compat       \
+-	$(MMDB_CXXFLAGS)  \
+-	$(CLIPPER_CXXFLAGS)
++	$(MMDB_CFLAGS)  \
++	$(CLIPPER_CFLAGS)
+ 
+ libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
+ 	sequence-assignment.cc
+Index: ideal/Makefile.am
+===================================================================
+--- ideal/Makefile.am	(revision 4651)
++++ ideal/Makefile.am	(working copy)
+@@ -37,11 +37,11 @@
+ 	-I$(top_srcdir)/coot-utils \
+ 	-I$(top_srcdir)/mini-mol   \
+ 	-I$(top_srcdir)/geometry   \
+-	$(CLIPPER_CXXFLAGS)        \
+-	$(MMDB_CXXFLAGS)
++	$(CLIPPER_CFLAGS)        \
++	$(MMDB_CFLAGS)
+ 
+ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \
+-     $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS) 
++     $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS) 
+ AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS)
+ 
+ 
+Index: ideal/Makefile.simple
+===================================================================
+--- ideal/Makefile.simple	(revision 4651)
++++ ideal/Makefile.simple	(working copy)
+@@ -44,7 +44,7 @@
+ 
+ 
+ CXX = g++
+-MMDB_CXXFLAGS = -I$(MMDB)/include 
++MMDB_CFLAGS = -I$(MMDB)/include 
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
+ 
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
+@@ -53,9 +53,9 @@
+ 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
+ 
+ MCCP4_CFLAGS = -I$(MCCP4)/include
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
+ 
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \
+ 	-I$(top_srcdir)/coords  \
+ 	-I$(top_srcdir)/geometry
+ 
+Index: lbg/Makefile.am
+===================================================================
+--- lbg/Makefile.am	(revision 4651)
++++ lbg/Makefile.am	(working copy)
+@@ -11,7 +11,7 @@
+         $(GSL_CFLAGS) \
+         $(GOOCANVAS_CFLAGS) \
+         $(GTK_CFLAGS) \
+-	$(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
++	$(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
+ 	$(COOT_WINDOWS_CFLAGS) \
+ 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(RDKIT_CXXFLAGS) \
+Index: lbg/Makefile.simple
+===================================================================
+--- lbg/Makefile.simple	(revision 4651)
++++ lbg/Makefile.simple	(working copy)
+@@ -24,11 +24,11 @@
+ MMDB=$(CRYST)
+ # MMDB=$(HOME)/test/mmdb
+ 
+-MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb
++MMDB_CFLAGS=-I$(MMDB)/include/mmdb
+ MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la
+ 
+ CLIPPER=$(CRYST)
+-CLIPPER_CXXFLAGS=-I$(CLIPPER)/include
++CLIPPER_CFLAGS=-I$(CLIPPER)/include
+ CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \
+         $(CLIPPER)/lib/librfftw.la \
+         $(CLIPPER)/lib/libfftw.la
+@@ -40,7 +40,7 @@
+ LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la
+ 
+ 
+-CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \
++CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \
+     -I$(top_srcdir)/compat
+ 
+ lbg:  lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
+Index: lidia-core/Makefile.am
+===================================================================
+--- lidia-core/Makefile.am	(revision 4651)
++++ lidia-core/Makefile.am	(working copy)
+@@ -22,7 +22,7 @@
+ 
+ #  20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t
+ # simple
+-#INCLUDES = $(CLIPPER_CXXFLAGS)
++#INCLUDES = $(CLIPPER_CFLAGS)
+ #
+ INCLUDES = \
+ 	 -I$(top_srcdir)/geometry       \
+@@ -31,7 +31,7 @@
+ 	 -I$(top_srcdir)/utils          \
+ 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(RDKIT_CXXFLAGS) 		\
+-        $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++        $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ 
+ libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \
+ 	cod-types.cc
+Index: ligand/Makefile.am
+===================================================================
+--- ligand/Makefile.am	(revision 4651)
++++ ligand/Makefile.am	(working copy)
+@@ -36,7 +36,7 @@
+ 	-I$(top_srcdir)/db-main \
+ 	$(COOT_GSL_FLAGS)		\
+ 	$(GSL_CFLAGS)			\
+-	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
++	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
+ 
+ include_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \
+ 	chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh        \
+Index: macros/clipper.m4
+===================================================================
+--- macros/clipper.m4	(revision 4651)
++++ macros/clipper.m4	(working copy)
+@@ -56,7 +56,7 @@
+  #
+  # should use clipper-config --cflags
+  #
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/include"
++ CLIPPER_CFLAGS="-I$clipper_prefix/include"
+  # -I$clipper_prefix/cctbx
+  
+  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
+@@ -75,7 +75,7 @@
+  #
+  ccp4c=ccp4c
+ 
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
++ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
+  # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
+ 
+ 
+@@ -102,8 +102,8 @@
+  # this needs to be 'configured' - typically either s or blank.
+  fftw_pre=
+ 
+- CLIPPER_CXXFLAGS="$CCP4_CFLAGS"
+- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
++ CLIPPER_CFLAGS="$CCP4_CFLAGS"
++ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
+ fi
+ 
+ # BL: workaround needed for new MinGW
+@@ -113,17 +113,17 @@
+ case $ac_cv_build_alias in
+         # BL says:: same as for cygwin in mingw
+         MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*)
+-                CLIPPER_LDOPTS=$CLIPPER_LDOPTS
++                CLIPPER_LIBS=$CLIPPER_LIBS
+ 	;; 
+ 	*)
+-		CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread"
++		CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread"
+         ;;
+ esac
+ 
+ AC_MSG_CHECKING([for Clipper])
+ 
+-	LIBS="$save_LIBS $CLIPPER_LDOPTS"
+-	CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
++	LIBS="$save_LIBS $CLIPPER_LIBS"
++	CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
+ 	# AC_TRY_LINK uses the c compiler, so we will temporarily 
+ 	# reassign $CC to the c++ compiler.
+  	#
+@@ -140,7 +140,7 @@
+ 
+  LIBS="$saved_LIBS"
+  CFLAGS="$saved_CFLAGS"
+- CLIPPER_LIBS="$CLIPPER_LDOPTS"
++ CLIPPER_LIBS="$CLIPPER_LIBS"
+  ifelse([$1], , :, [$1])
+ 
+ else
+@@ -148,12 +148,12 @@
+  LIBS="$saved_LIBS"
+  CFLAGS="$saved_CFLAGS"
+  CLIPPER_LIBS=""
+- CLIPPER_CXXFLAGS=""
++ CLIPPER_CFLAGS=""
+  ifelse([$2], , :, [$2])
+ 
+ fi
+ 
+-AC_SUBST(CLIPPER_CXXFLAGS)
++AC_SUBST(CLIPPER_CFLAGS)
+ AC_SUBST(CLIPPER_LIBS)
+ 
+ ])
+Index: macros/clipper.m4.old
+===================================================================
+--- macros/clipper.m4.old	(revision 4651)
++++ macros/clipper.m4.old	(working copy)
+@@ -34,7 +34,7 @@
+  # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
+  # when clipper and dependencies get installed.
+  #  
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
++ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
+ # -I$clipper_prefix/cctbx
+  
+  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
+@@ -45,20 +45,20 @@
+  # HACK! FIXME
+  # added lz, we should have proper autoconf check for this.
+  #
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
++ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
+ else
+  # the compiler looks in the "standard" places for clipper.  In real life,
+  # it would be quite unlikely that clipper would be installed in /usr/include, 
+  # /usr/lib etc. so this code will not usually find the right dependencies.
+- CLIPPER_CXXFLAGS=""
+- CLIPPER_LDOPTS=""
++ CLIPPER_CFLAGS=""
++ CLIPPER_LIBS=""
+ fi
+ 
+ AC_MSG_CHECKING([for Clipper])
+ 
+-	LIBS="$save_LIBS $CLIPPER_LDOPTS"
+-	CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
++	LIBS="$save_LIBS $CLIPPER_LIBS"
++	CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
+ 	# AC_TRY_LINK uses the c compiler, so we will temporarily 
+ 	# reassign $CC to the c++ compiler.
+  	#
+@@ -72,7 +72,7 @@
+ 
+  LIBS="$saved_LIBS"
+  CFLAGS="$saved_CFLAGS"
+- CLIPPER_LIBS="$CLIPPER_LDOPTS"
++ CLIPPER_LIBS="$CLIPPER_LIBS"
+  ifelse([$1], , :, [$1])
+ 
+ else
+@@ -80,12 +80,12 @@
+  LIBS="$saved_LIBS"
+  CFLAGS="$saved_CFLAGS"
+  CLIPPER_LIBS=""
+- CLIPPER_CXXFLAGS=""
++ CLIPPER_CFLAGS=""
+  ifelse([$2], , :, [$2])
+ 
+ fi
+ 
+-AC_SUBST(CLIPPER_CXXFLAGS)
++AC_SUBST(CLIPPER_CFLAGS)
+ AC_SUBST(CLIPPER_LIBS)
+ 
+ ])
+Index: macros/goo-canvas.m4
+===================================================================
+--- macros/goo-canvas.m4	(revision 4651)
++++ macros/goo-canvas.m4	(working copy)
+@@ -36,9 +36,9 @@
+   # 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$goocanvas_prefix/lib -lgoocanvas"
+   fi
+ else
+   # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig)
+@@ -57,19 +57,19 @@
+     break;;
+   esac
+   if test -e /usr/lib/libgoocanvas.la ; then
+-    GOOCANVAS_LDOPTS="libgoocanvas.la"
++    GOOCANVAS_LIBS="libgoocanvas.la"
+   else
+     if test -z "${PKG_CONFIG}"; then
+-      GOOCANVAS_LDOPTS="-lgoocanvas"
++      GOOCANVAS_LIBS="-lgoocanvas"
+     else
+-      GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
++      GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
+     fi
+   fi
+ fi
+ 
+ AC_MSG_CHECKING([for Goocanvas])
+ 
+-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
+ CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
+ #
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
+@@ -95,7 +95,7 @@
+ if test x$have_goocanvas = xyes; then
+ 
+  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
+- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
+ 
+ ifelse([$1], , :, [$1])
+ 
+Index: macros/mmdb-ssm.m4
+===================================================================
+--- macros/mmdb-ssm.m4	(revision 4651)
++++ macros/mmdb-ssm.m4	(working copy)
+@@ -32,7 +32,7 @@
+ 
+ if test x$with_ssmlib_prefix != x; then
+ 
+-   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
++   MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
+    MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+ 
+ ac_mmdb_dirs='
+@@ -47,16 +47,16 @@
+ 
+    for ac_dir in $ac_mmdb_dirs; do
+       if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
+-         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
++         ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/$ac_dir"
+          break
+       fi
+    done
+ 
+-  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
++  MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
+   
+ else 
+ 
+-   MMDBSSM_CXXFLAGS=""
++   MMDBSSM_CFLAGS=""
+    MMDBSSM_LIBS=""
+    with_ssmlib_prefix=no 
+ 
+@@ -64,6 +64,6 @@
+ 
+ AC_MSG_RESULT([$with_ssmlib_prefix])
+ 
+-AC_SUBST(MMDBSSM_CXXFLAGS)
++AC_SUBST(MMDBSSM_CFLAGS)
+ AC_SUBST(MMDBSSM_LIBS)
+ ])
+Index: macros/mmdb.m4
+===================================================================
+--- macros/mmdb.m4	(revision 4651)
++++ macros/mmdb.m4	(working copy)
+@@ -55,7 +55,7 @@
+ 	# --with-mmdb=/some/thing
+ 	#
+ 
+- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like
++ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like
+  # when MMDB and dependencies get installed - we infact, include both
+  # directories.
+  #  
+@@ -69,7 +69,7 @@
+ lib/src/mmdb'
+ for ac_dir in $ac_mmdb_dirs; do
+    if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then
+-      ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir"
++      ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir"
+       break
+    fi
+ done
+@@ -82,14 +82,14 @@
+  # the compiler looks in the "standard" places for MMDB.  In real life,
+  # it would be quite unlikely that MMDB would be installed in /usr/include, 
+  # /usr/lib etc. so this code will not usually find the right dependencies.
+- ac_MMDB_CXXFLAGS=""
++ ac_MMDB_CFLAGS=""
+  ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+ 
+ AC_MSG_CHECKING([for MMDB])
+ 
+ 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
+-	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
++	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS"
+ 	#
+ 	# AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
+ 	# temporarily reassign $CC to the c++ compiler.
+@@ -118,7 +118,7 @@
+     CLINKR_FLAG=-DMMDB_WITHOUT_LINKR
+  fi
+  CXXFLAGS="$saved_CXXFLAGS"
+- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
++ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
+  MMDB_LIBS="$ac_MMDB_LDOPTS"
+ ifelse([$1], , :, [$1])
+ 
+@@ -134,12 +134,12 @@
+  LIBS="$saved_LIBS"
+  CXXFLAGS="$saved_CXXFLAGS"
+  MMDB_LIBS=""
+- MMDB_CXXFLAGS=""
++ MMDB_CFLAGS=""
+  ifelse([$2], , :, [$2])
+ 
+ fi
+ 
+-AC_SUBST(MMDB_CXXFLAGS)
++AC_SUBST(MMDB_CFLAGS)
+ AC_SUBST(MMDB_LIBS)
+ 
+ ])
+Index: mini-mol/Makefile.am
+===================================================================
+--- mini-mol/Makefile.am	(revision 4651)
++++ mini-mol/Makefile.am	(working copy)
+@@ -25,8 +25,8 @@
+ INCLUDES =  \
+ 	-I$(top_srcdir)/coot-utils \
+ 	-I$(top_srcdir)/compat \
+-	$(CLIPPER_CXXFLAGS)    \
+-	$(MMDB_CXXFLAGS)
++	$(CLIPPER_CFLAGS)    \
++	$(MMDB_CFLAGS)
+ 
+ AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
+ 
+Index: protein_db/Makefile.am
+===================================================================
+--- protein_db/Makefile.am	(revision 4651)
++++ protein_db/Makefile.am	(working copy)
+@@ -19,7 +19,7 @@
+ 
+ lib_LTLIBRARIES=libcoot-protein-db.la
+ 
+-INCLUDES= $(CLIPPER_CXXFLAGS)  $(MMDB_CXXFLAGS)
++INCLUDES= $(CLIPPER_CFLAGS)  $(MMDB_CFLAGS)
+ 
+ include_HEADERS=protein_db.h  protein_db_utils.h rna_db.h
+ 
+Index: sequence-view/Makefile.am
+===================================================================
+--- sequence-view/Makefile.am	(revision 4651)
++++ sequence-view/Makefile.am	(working copy)
+@@ -55,9 +55,9 @@
+ 	-I$(top_srcdir)/analysis	\
+ 	-I$(top_srcdir)/cootaneer	\
+ 	-I$(top_srcdir)/src     	\
+-	$(CLIPPER_CXXFLAGS) 		\
+-	$(MMDB_CXXFLAGS) 		\
+-	$(MMDBSSM_CXXFLAGS) 		\
++	$(CLIPPER_CFLAGS) 		\
++	$(MMDB_CFLAGS) 		\
++	$(MMDBSSM_CFLAGS) 		\
+ 	$(GLUT_CFLAGS)			\
+ 	$(CANVAS_CFLAGS) 		\
+ 	$(GTKGL_CONTEXT_CFLAGS)		\
+Index: skeleton/Makefile.am
+===================================================================
+--- skeleton/Makefile.am	(revision 4651)
++++ skeleton/Makefile.am	(working copy)
+@@ -28,7 +28,7 @@
+           -I$(top_srcdir)/angles     \
+           -I$(top_srcdir)/coot-utils \
+ 	  -I$(top_srcdir)/compat     \
+-	 $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
++	 $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
+ 
+ AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
+ 
+Index: src/Makefile.am
+===================================================================
+--- src/Makefile.am	(revision 4651)
++++ src/Makefile.am	(working copy)
+@@ -220,11 +220,11 @@
+         $(GOOCANVAS_CFLAGS)             \
+ 	@GTK_CFLAGS@ 			\
+ 	$(GLUT_CFLAGS)			\
+-	$(MMDBSSM_CXXFLAGS) 		\
+-	$(MMDB_CXXFLAGS) 		\
++	$(MMDBSSM_CFLAGS) 		\
++	$(MMDB_CFLAGS) 		\
+ 	$(CCP4SRS_CXXFLAGS) 		\
+ 	$(GSL_CFLAGS)			\
+-	$(CLIPPER_CXXFLAGS) 		\
++	$(CLIPPER_CFLAGS) 		\
+ 	$(PYGTK_CFLAGS)                 \
+ 	$(GLOB_CFLAGS)                 \
+ 	$(CURL_CFLAGS)                 
+Index: surface/Makefile.am
+===================================================================
+--- surface/Makefile.am	(revision 4651)
++++ surface/Makefile.am	(working copy)
+@@ -1,5 +1,5 @@
+ 
+-INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
++INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS)
+ 
+ AM_CXXFLAGS = $(OPENMP_CFLAGS)
+ 

diff --git a/sci-chemistry/coot/files/9999-ssm.patch b/sci-chemistry/coot/files/9999-ssm.patch
deleted file mode 100644
index c801da7..0000000
--- a/sci-chemistry/coot/files/9999-ssm.patch
+++ /dev/null
@@ -1,56 +0,0 @@
- macros/mmdb-ssm.m4 |   42 +-----------------------------------------
- 1 files changed, 1 insertions(+), 41 deletions(-)
-
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 1937a16..6ef547c 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -22,47 +22,7 @@
- AC_DEFUN([AM_WITH_MMDBSSM],
- [AC_PROVIDE([AM_USE_MMDBSSM])
- 
--
--AC_ARG_WITH(ssmlib-prefix, 
--	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
--	[ with_ssmlib_prefix="$withval" ],
-- with_ssmlib_prefix="")
--
--AC_MSG_CHECKING([for SSMLib])
--
--if test x$with_ssmlib_prefix != x; then
--
--   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
--   MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
--
--ac_mmdb_dirs='
--.
--include
--include/ssm
--include/mmdb
--lib
--src
--lib/src
--lib/src/mmdb'
--
--   for ac_dir in $ac_mmdb_dirs; do
--      if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
--         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
--         break
--      fi
--   done
--
--  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
--  
--else 
--
--   MMDBSSM_CXXFLAGS=""
--   MMDBSSM_LIBS=""
--   with_ssmlib_prefix=no 
--
--fi
--
--AC_MSG_RESULT([$with_ssmlib_prefix])
-+PKG_CHECK_MODULES([MMDBSSM],[ssm])
- 
- AC_SUBST(MMDBSSM_CXXFLAGS)
- AC_SUBST(MMDBSSM_LIBS)


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2013-07-22 13:29 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2013-07-22 13:29 UTC (permalink / raw
  To: gentoo-commits

commit:     08254da42ea02327ab985f6ccf4d3d0b20e10e14
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 22 13:29:11 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jul 22 13:29:11 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=08254da4

sci-chemistry/coot: Don't use relative path

Package-Manager: portage-2.2.0_alpha188

---
 sci-chemistry/coot/ChangeLog           | 3 +++
 sci-chemistry/coot/files/9999-pc.patch | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 0095d45..1c966c0 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: $
 
+  22 Jul 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
+  Don't use relative path
+
   11 Jul 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
   Update pc patch
 

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 86e1584..0cf7a2e 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -463,7 +463,7 @@ index cec561d..c207a43 100644
 +CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
  
 -INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/mini-mol
  
  CXXFLAGS = -g $(INCLUDES)
  LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) 


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2013-08-27  6:58 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2013-08-27  6:58 UTC (permalink / raw
  To: gentoo-commits

commit:     e76da5ba2d87e85005bd3f41ebf9eee23bb6bba8
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 27 06:58:21 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Aug 27 06:58:21 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e76da5ba

sci-chemistry/coot: Fix pc patch

Package-Manager: portage-2.2.1

---
 sci-chemistry/coot/ChangeLog           |  3 ++
 sci-chemistry/coot/files/9999-pc.patch | 51 +++++++++++++++++++---------------
 2 files changed, 31 insertions(+), 23 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 1c966c0..54fba79 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: $
 
+  27 Aug 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
+  Fix pc patch
+
   22 Jul 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
   Don't use relative path
 

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 0cf7a2e..16e899f 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -39,7 +39,7 @@ index 46f6362..fd3fd9a 100644
  
  	* surface/CXXSphereNode.h: removed the ; again!
 diff --git a/analysis/Makefile.am b/analysis/Makefile.am
-index 8754df4..1174dfd 100644
+index 8a873dc..ef4a9cf 100644
 --- a/analysis/Makefile.am
 +++ b/analysis/Makefile.am
 @@ -8,8 +8,8 @@ pkgincludedir = $(includedir)/coot/analysis
@@ -51,7 +51,7 @@ index 8754df4..1174dfd 100644
 +	$(CLIPPER_CFLAGS)		\
 +	$(MMDB_CFLAGS)
  
- libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc kolmogorov.cc
+ libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc kolmogorov.hh kolmogorov.cc cablam.hh cablam.cc
  
 diff --git a/angles/Makefile.am b/angles/Makefile.am
 index b89276d..935ce06 100644
@@ -313,7 +313,7 @@ index 399f453..3d2ff55 100755
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/configure.in b/configure.in
-index d99d280..eca9b91 100644
+index 5928c3c..9e235b5 100644
 --- a/configure.in
 +++ b/configure.in
 @@ -108,14 +108,18 @@ esac
@@ -338,7 +338,7 @@ index d99d280..eca9b91 100644
  
  # we set default coot_guile to true
  coot_guile=true
-@@ -189,11 +193,15 @@ AM_PATH_LIBGLADE
+@@ -186,11 +190,15 @@ AM_PATH_LIBGLADE
  
  dnl =========================== GooCanvas ================================
  
@@ -443,7 +443,7 @@ index 3a85b9e..1a11cdf 100644
  pkginclude_HEADERS = db-main.hh db-strands.hh
  pkgincludedir = $(includedir)/coot/db-main
 diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..c207a43 100644
+index cec561d..31d35a0 100644
 --- a/db-main/Makefile.simple
 +++ b/db-main/Makefile.simple
 @@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
@@ -848,29 +848,34 @@ index 30fdcb9..3e4c0c6 100644
  ifelse([$1], , :, [$1])
  
 diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 1937a16..26101d3 100644
+index 25dc502..fcfde1d 100644
 --- a/macros/mmdb-ssm.m4
 +++ b/macros/mmdb-ssm.m4
-@@ -32,7 +32,7 @@ AC_MSG_CHECKING([for SSMLib])
+@@ -31,14 +31,13 @@ AC_ARG_WITH(ssmlib-prefix,
+ AC_MSG_CHECKING([for ssm library])
  
  if test x$with_ssmlib_prefix != x; then
+-
+    if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
  
--   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
+-      MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
 +   MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
-    MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
- 
- ac_mmdb_dirs='
-@@ -47,16 +47,16 @@ lib/src/mmdb'
- 
-    for ac_dir in $ac_mmdb_dirs; do
-       if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
--         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
-+         ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/$ac_dir"
-          break
-       fi
-    done
- 
--  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
+       # AFAICS, ssm does not put its libs in $acl_libdirstem
+       # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+       MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
+-      ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/include"
++      ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/include"
+ 
+       # saved_LIBS="$LIBS"
+       # saved_CPPFLAGS="$CPPFLAGS"
+@@ -49,12 +48,13 @@ if test x$with_ssmlib_prefix != x; then
+ 
+    else 
+       AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found])
+-   fi
+-   MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
++      fi
++
 +  MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
    
  else 
@@ -880,7 +885,7 @@ index 1937a16..26101d3 100644
     MMDBSSM_LIBS=""
     with_ssmlib_prefix=no 
  
-@@ -64,6 +64,6 @@ fi
+@@ -62,6 +62,6 @@ fi
  
  AC_MSG_RESULT([$with_ssmlib_prefix])
  


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2013-09-28  9:15 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2013-09-28  9:15 UTC (permalink / raw
  To: gentoo-commits

commit:     4e20152045ceb0f0a851b14fe5e867c844e97b73
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 21 09:23:14 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Sep 28 09:06:59 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4e201520

sci-chemistry/coot: Adjust pc patch for latest head

Package-Manager: portage-2.2.6

---
 sci-chemistry/coot/ChangeLog           |  3 +++
 sci-chemistry/coot/files/9999-pc.patch | 42 +++++++++++++++-------------------
 2 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 43da818..2d2b7c3 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: $
 
+  21 Sep 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
+  Adjust pc patch for latest head
+
   19 Sep 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Clean for latest HEAD
 

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 16e899f..2f97194 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -313,7 +313,7 @@ index 399f453..3d2ff55 100755
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/configure.in b/configure.in
-index 5928c3c..9e235b5 100644
+index cc549a5..d56f856 100644
 --- a/configure.in
 +++ b/configure.in
 @@ -108,14 +108,18 @@ esac
@@ -357,15 +357,15 @@ index 5928c3c..9e235b5 100644
 +		fi
 +	])
  
- AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ],
-  coot_enterprise_additions="true",
+ AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with optional complicated/experimental ligand-related dependencies ],
+  coot_enhanced_ligand_additions="true",
 diff --git a/coords/Makefile.am b/coords/Makefile.am
-index 009841e..7687d56 100644
+index 05fdf70..1e1c5d2 100644
 --- a/coords/Makefile.am
 +++ b/coords/Makefile.am
 @@ -29,7 +29,7 @@ INCLUDES = \
  	-I$(top_srcdir) \
- 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
  	$(RDKIT_CXXFLAGS) 		\
 -	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
 +	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
@@ -443,7 +443,7 @@ index 3a85b9e..1a11cdf 100644
  pkginclude_HEADERS = db-main.hh db-strands.hh
  pkgincludedir = $(includedir)/coot/db-main
 diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..31d35a0 100644
+index cec561d..c207a43 100644
 --- a/db-main/Makefile.simple
 +++ b/db-main/Makefile.simple
 @@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
@@ -463,7 +463,7 @@ index cec561d..31d35a0 100644
 +CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
  
 -INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/mini-mol
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
  
  CXXFLAGS = -g $(INCLUDES)
  LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) 
@@ -584,7 +584,7 @@ index 3c32c3c..0abd514 100644
  	-I$(top_srcdir)/geometry
  
 diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index 12d4ca6..5367e39 100644
+index df74b90..7f54567 100644
 --- a/lbg/Makefile.am
 +++ b/lbg/Makefile.am
 @@ -6,7 +6,7 @@ INCLUDES = \
@@ -594,7 +594,7 @@ index 12d4ca6..5367e39 100644
 -	$(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
 +	$(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
  	$(COOT_WINDOWS_CFLAGS) \
- 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
  	$(RDKIT_CXXFLAGS) \
 diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple
 index 48d091b..5b148b4 100644
@@ -624,7 +624,7 @@ index 48d091b..5b148b4 100644
  
  lbg:  lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
 diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 2fcb96b..201ceb0 100644
+index 72b28ca..2a184b4 100644
 --- a/lidia-core/Makefile.am
 +++ b/lidia-core/Makefile.am
 @@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core
@@ -636,7 +636,7 @@ index 2fcb96b..201ceb0 100644
  #
  INCLUDES = \
  	 -I$(top_srcdir) \
- 	$(ENTERPRISE_TOOLS_CFLAGS)      \
+ 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
  	$(RDKIT_CXXFLAGS) 		\
 -        $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
 +        $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
@@ -848,18 +848,15 @@ index 30fdcb9..3e4c0c6 100644
  ifelse([$1], , :, [$1])
  
 diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 25dc502..fcfde1d 100644
+index 25dc502..21646a5 100644
 --- a/macros/mmdb-ssm.m4
 +++ b/macros/mmdb-ssm.m4
-@@ -31,14 +31,13 @@ AC_ARG_WITH(ssmlib-prefix,
- AC_MSG_CHECKING([for ssm library])
+@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then
  
- if test x$with_ssmlib_prefix != x; then
--
     if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
  
 -      MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-+   MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
++      MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
        # AFAICS, ssm does not put its libs in $acl_libdirstem
        # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
        MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
@@ -868,15 +865,12 @@ index 25dc502..fcfde1d 100644
  
        # saved_LIBS="$LIBS"
        # saved_CPPFLAGS="$CPPFLAGS"
-@@ -49,12 +48,13 @@ if test x$with_ssmlib_prefix != x; then
- 
+@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then
     else 
        AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found])
--   fi
+    fi
 -   MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
-+      fi
-+
-+  MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
++   MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
    
  else 
  
@@ -1015,7 +1009,7 @@ index 54872fe..bef7d0e 100644
  AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
  
 diff --git a/src/Makefile.am b/src/Makefile.am
-index fe9656f..384991b 100644
+index af5276b..d0ab482 100644
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
 @@ -195,11 +195,11 @@ INCLUDES = \


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2013-10-02  6:49 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2013-10-02  6:49 UTC (permalink / raw
  To: gentoo-commits

commit:     1639fbdaa00e3a3f8bd4c4f0e9386bf0d73a6cde
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Oct  2 06:49:15 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Oct  2 06:49:15 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1639fbda

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 2d2b7c3..d1c9584 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 2f97194..7f85532 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 @@


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2013-11-25 18:48 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2013-11-25 18:48 UTC (permalink / raw
  To: gentoo-commits

commit:     8bc5d1aa056cdb7ad01e708ff37fc956b98374fa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 25 18:47:36 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 25 18:47:36 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8bc5d1aa

sci-chemistry/coot: Update patch for current HEAD

Package-Manager: portage-2.2.7

---
 sci-chemistry/coot/ChangeLog           |  3 +++
 sci-chemistry/coot/files/9999-pc.patch | 43 ++++++++++++++++++++--------------
 2 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index d1c9584..9baf726 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: $
 
+  25 Nov 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
+  Update patch for current HEAD
+
   02 Oct 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
   Update patch for HEAD
 

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 7f85532..32d08e1 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -262,9 +262,7 @@ 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
-old mode 100755
-new mode 100644
-index d0651db..d4e0bf8
+index d0651db..d4e0bf8 100755
 --- a/ccp4mg-utils/mmut/Makefile.am
 +++ b/ccp4mg-utils/mmut/Makefile.am
 @@ -70,9 +70,9 @@ INCLUDES = \
@@ -281,9 +279,7 @@ index d0651db..d4e0bf8
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am
-old mode 100755
-new mode 100644
-index a7e68b5..e26a6c8
+index a7e68b5..e26a6c8 100755
 --- a/ccp4mg-utils/pygl/Makefile.am
 +++ b/ccp4mg-utils/pygl/Makefile.am
 @@ -108,9 +108,9 @@ INCLUDES = \
@@ -300,9 +296,7 @@ index a7e68b5..e26a6c8
  #	$(WITH_SCRIPT_CFLAGS) 
  
 diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am
-old mode 100755
-new mode 100644
-index 399f453..3d2ff55
+index 399f453..3d2ff55 100755
 --- a/ccp4mg-utils/util/Makefile.am
 +++ b/ccp4mg-utils/util/Makefile.am
 @@ -73,9 +73,9 @@ INCLUDES = \
@@ -546,10 +540,10 @@ index cf81182..3a2af5c 100644
  libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
  	sequence-assignment.cc
 diff --git a/ideal/Makefile.am b/ideal/Makefile.am
-index be4dc3e..f4cc8eb 100644
+index e52c271..c5c8e6a 100644
 --- a/ideal/Makefile.am
 +++ b/ideal/Makefile.am
-@@ -32,11 +32,11 @@ pkgincludedir = $(includedir)/coot/ideal
+@@ -33,11 +33,11 @@ pkgincludedir = $(includedir)/coot/ideal
  
  INCLUDES = \
  	-I$(top_srcdir) \
@@ -805,19 +799,20 @@ index de8ab65..4c1b418 100644
  
  ])
 diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4
-index e2494a5..cf96688 100644
+index e2494a5..89c908e 100644
 --- a/macros/goo-canvas.m4
 +++ b/macros/goo-canvas.m4
-@@ -35,7 +35,7 @@ if test x$goocanvas_prefix != x; then
+@@ -35,8 +35,7 @@ if test x$goocanvas_prefix != x; then
    # SGI compiler CC (CXX=CC) needs -lm to link maths library, but 
    # GCC c++ does not.
    #
 -  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)
-@@ -54,15 +54,15 @@ else
+ 
+@@ -54,18 +53,16 @@ else
      break;;
    esac
    if test -z "${PKG_CONFIG}"; then
@@ -834,9 +829,23 @@ index e2494a5..cf96688 100644
 -LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
 +LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
  CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
+-
+-
+ dnl # 20130929: why do I do this?  I don't remember.  Using libtool 
+ dnl # in this way is not a good idea (configure makes libtool).
+ dnl #
+@@ -85,18 +82,15 @@ dnl     # note that we use ./libtool (running in the build dir) because $LIBTOOL
+ dnl     CXX="libtool --mode=link $CXX"
+ dnl     break;;
+ dnl esac
+-
+-
+ AC_LANG_PUSH(C++)
+ AC_TRY_LINK([#include "goocanvas.h"] ,[ GooCanvas *a;  ], have_goocanvas=yes, have_goocanvas=no)
+ AC_LANG_POP
+-
+ AC_MSG_RESULT($have_goocanvas)
  
- 
-@@ -96,7 +96,7 @@ AC_MSG_RESULT($have_goocanvas)
  if test x$have_goocanvas = xyes; then
  
   GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2014-06-30 19:02 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2014-06-30 19:02 UTC (permalink / raw
  To: gentoo-commits

commit:     6a07207adec9b6152a0ab28c72f724c3972f1e8e
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 30 19:02:25 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 30 19:02:25 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6a07207a

sci-chemistry/coot: Fix sandbox violation

Package-Manager: portage-2.2.10

---
 sci-chemistry/coot/ChangeLog                           |  8 ++++++++
 sci-chemistry/coot/coot-9999.ebuild                    |  5 ++++-
 sci-chemistry/coot/files/coot-9999-sandbox-icons.patch | 16 ++++++++++++++++
 3 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index cee77b1..cd498bb 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Jun 2014; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+  +files/coot-9999-sandbox-icons.patch:
+  Fix sandbox violation
+
+  30 Jun 2014; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+  +files/coot-9999-sandbox-icons.patch:
+  Fix sandbox violation
+
   08 Jun 2014; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
   Fix problem with shebang correction
 

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index f0fd7dc..79aed91 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -82,7 +82,10 @@ pkg_setup() {
 	python-single-r1_pkg_setup
 }
 
-PATCHES=( "${FILESDIR}"/${PV}-pc.patch	)
+PATCHES=(
+	"${FILESDIR}"/${PV}-pc.patch
+	"${FILESDIR}"/${P}-sandbox-icons.patch
+)
 
 src_unpack() {
 	subversion_src_unpack

diff --git a/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch b/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch
new file mode 100644
index 0000000..2a9ff2d
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch
@@ -0,0 +1,16 @@
+ pixmaps/icons/Makefile.am | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am
+index 0c183ae..dddc11a 100644
+--- a/pixmaps/icons/Makefile.am
++++ b/pixmaps/icons/Makefile.am
+@@ -11,6 +11,6 @@ install-data-local:
+ 		CONTEXT=` echo $$icon | cut -d_ -f2`; \
+ 		SIZE=`    echo $$icon | cut -d_ -f3`; \
+ 		ICONFILE=`echo $$icon | cut -d_ -f4`; \
+-		mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
+-		$(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
++		mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
++		$(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
+ 	done;


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2015-09-15 13:34 Justin Lecher
  0 siblings, 0 replies; 24+ messages in thread
From: Justin Lecher @ 2015-09-15 13:34 UTC (permalink / raw
  To: gentoo-commits

commit:     20873c20812ebb870e9fdce159daa1da97cea074
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 15 13:34:07 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 15 13:34:07 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=20873c20

sci-chemistry/coot: Fix for latest HEAD

Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-chemistry/coot/coot-9999.ebuild               |   76 +-
 sci-chemistry/coot/files/9999-pc.patch            | 1047 ---------------------
 sci-chemistry/coot/files/coot-9999-desktop.patch  |   21 +
 sci-chemistry/coot/files/coot-9999-libguile.patch |   29 +
 sci-chemistry/coot/files/coot-9999-libtool.patch  |   39 +
 5 files changed, 126 insertions(+), 1086 deletions(-)

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 1ea16a3..d6b0be9 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 
 AUTOTOOLS_AUTORECONF="true"
 
-inherit autotools-utils python-single-r1 subversion toolchain-funcs versionator
+inherit autotools-utils git-r3 python-single-r1 toolchain-funcs versionator
 
 MY_S2_PV=$(replace_version_separator 2 - ${PV})
 MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
@@ -17,9 +17,9 @@ MY_PV=${PV}
 MY_P=${PN}-${MY_PV}
 
 DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
-SRC_URI="test? ( http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/data/greg-data.tar.gz )"
-ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk"
+HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/"
+SRC_URI="test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
+EGIT_REPO_URI="https://github.com/pemsley/coot.git"
 
 SLOT="0"
 LICENSE="GPL-3"
@@ -31,25 +31,26 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 AUTOTOOLS_IN_SOURCE_BUILD=1
 
 SCIDEPS="
-	>=sci-libs/ccp4-libs-6.1
+	sci-libs/libccp4
 	sci-libs/clipper
 	>=sci-libs/coot-data-2
 	>=sci-libs/gsl-1.3
-	>=sci-libs/mmdb-1.23
-	sci-libs/ssm
+	sci-libs/fftw:2.1=
+	sci-libs/mmdb:2
 	sci-libs/monomer-db
+	sci-libs/ssm
 	sci-chemistry/reduce
-	sci-chemistry/refmac
 	sci-chemistry/probe"
 
 XDEPS="
 	gnome-base/libgnomecanvas
 	gnome-base/librsvg:2
-	media-libs/libpng
+	media-libs/libpng:0=
 	media-libs/freeglut
 	x11-libs/gtk+:2
 	x11-libs/goocanvas:0
-	x11-libs/gtkglext"
+	x11-libs/gtkglext
+	virtual/opengl"
 
 SCHEMEDEPS="
 	dev-scheme/net-http
@@ -63,18 +64,23 @@ RDEPEND="
 	${XDEPS}
 	${SCHEMEDEPS}
 	${PYTHON_DEPS}
+	dev-db/sqlite:3
+	dev-libs/boost:0=[python,${PYTHON_USEDEP}]
+	dev-libs/glib:2
+	>=dev-libs/gmp-4.2.2-r2:0=
+	dev-python/pygobject:2[${PYTHON_USEDEP}]
 	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=dev-libs/gmp-4.2.2-r2
 	>=net-misc/curl-7.19.6
-	net-dns/libidn"
+	net-dns/libidn
+	sys-libs/readline:0=
+	"
 DEPEND="${RDEPEND}
+	virtual/pkgconfig
 	>=sys-devel/libtool-2.4-r2
 	dev-lang/swig
 	sys-devel/bc
 	test? ( dev-scheme/greg )"
 
-S="${WORKDIR}"
-
 pkg_setup() {
 	if use openmp; then
 		tc-has-openmp || die "Please use an OPENMP capable compiler"
@@ -83,53 +89,44 @@ pkg_setup() {
 }
 
 PATCHES=(
-	"${FILESDIR}"/${PV}-pc.patch
+	"${FILESDIR}"/${P}-desktop.patch
 	"${FILESDIR}"/${P}-sandbox-icons.patch
+	"${FILESDIR}"/${P}-libtool.patch
+	"${FILESDIR}"/${P}-libguile.patch
 )
 
 src_unpack() {
-	subversion_src_unpack
+	git-r3_src_unpack
 	if use test; then
+		cd "${S}" || die
 		unpack ${A}
-		ln -sf . "${S}"/coot-ccp4
+		ln -sf . "${S}"/coot-ccp4 || die
 	fi
 }
 
 src_prepare() {
 	sed \
 		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.in || die
+		-i configure.ac || die
 
 	autotools-utils_src_prepare
-
-	cat >> src/svn-revision.cc <<- EOF
-	extern "C" {
-	int svn_revision() {
-		return  ${ESVN_WC_REVISION:-0};
-	}
-	}
-	EOF
 }
 
 src_configure() {
 	# All the --with's are used to activate various parts.
 	# Yes, this is broken behavior.
 	local myeconfargs=(
-		--includedir='${prefix}/include/coot'
 		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile
+		--with-guile="${EPREFIX}/usr"
 		--with-python="${EPREFIX}/usr"
 		--with-guile-gtk
-		--with-pygtk
-		$(use_enable openmp)
+		--with-pygtk="${EPREFIX}/usr"
+		--with-sqlite3
+		--with-boost="${EPREFIX}/usr"
 		)
 	autotools-utils_src_configure
 }
 
-src_compile() {
-	autotools-utils_src_compile
-	cp "${S}"/src/coot_gtk2.py python/coot.py || die
-}
 src_test() {
 	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
 	mkdir "${T}"/coot_test || die
@@ -143,10 +140,11 @@ src_test() {
 	export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
 	export PYTHONHOME="${EPREFIX}"/usr/
 	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
+	export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/"
+	export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/"
 	export SYMINFO="${S}/syminfo.lib"
 
-	export COOT_TEST_DATA_DIR="${S}"/data/greg-data/
+	export COOT_TEST_DATA_DIR="${S}"/greg-data/
 
 	cat > command-line-greg.scm <<- EOF
 	(use-modules (ice-9 greg))
@@ -172,6 +170,6 @@ src_test() {
 	einfo "CLIBD_MON ${CLIBD_MON}"
 	einfo "SYMINFO ${SYMINFO}"
 
-	"${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die
+	"${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die
+	"${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die
 }

diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
deleted file mode 100644
index 32d08e1..0000000
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ /dev/null
@@ -1,1047 +0,0 @@
-diff --git a/ChangeLog b/ChangeLog
-index 46f6362..fd3fd9a 100644
---- a/ChangeLog
-+++ b/ChangeLog
-@@ -1963,7 +1963,7 @@
- 2005-01-29  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
- 
- 	* macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in
--	MMDBSSM_CXXFLAGS [Oops].  Hopefully fixes problems spotted by Joel
-+	MMDBSSM_CFLAGS [Oops].  Hopefully fixes problems spotted by Joel
- 	Bard and Joseph Toth.
- 
- 	* src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add
-@@ -2256,14 +2256,14 @@
- 
- 2004-11-20  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
- 
--	* coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for
-+	* coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for
- 	coot-close.cc usage].
- 
- 2004-11-19  Paul Emsley  <paulemsley@ysbl.york.ac.uk>
- 
--	* sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS
-+	* sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS
- 
--	* analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS
-+	* analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS
- 
- 2004-11-16  Paul Emsley  <emsley@localhost>
- 
-@@ -2273,7 +2273,7 @@
-  
- 2004-11-15  Paul Emsley  <emsley@localhost>
- 
--	* coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks 
-+	* coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks 
-           Joseph Toth].
- 
- 	* surface/CXXSphereNode.h: removed the ; again!
-diff --git a/analysis/Makefile.am b/analysis/Makefile.am
-index 8a873dc..ef4a9cf 100644
---- a/analysis/Makefile.am
-+++ b/analysis/Makefile.am
-@@ -8,8 +8,8 @@ pkgincludedir = $(includedir)/coot/analysis
- 
- INCLUDES = \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS)		\
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS)		\
-+	$(MMDB_CFLAGS)
- 
- libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc kolmogorov.hh kolmogorov.cc cablam.hh cablam.cc
- 
-diff --git a/angles/Makefile.am b/angles/Makefile.am
-index b89276d..935ce06 100644
---- a/angles/Makefile.am
-+++ b/angles/Makefile.am
-@@ -7,7 +7,7 @@ EXTRA_DIST = \
- pkginclude_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h
- pkgincludedir = $(includedir)/coot/angles
- 
--INCLUDES = $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS)
- 
- libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h  \
- 	AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc
-diff --git a/auxil/catcheck/Makefile.am b/auxil/catcheck/Makefile.am
-index 41e1766..69e6091 100644
---- a/auxil/catcheck/Makefile.am
-+++ b/auxil/catcheck/Makefile.am
-@@ -1,7 +1,7 @@
- 
- EXTRA_DIST = Makefile.simple
- 
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
- 
- check_PROGRAMS = catcheck
- 
-diff --git a/auxil/catcheck/Makefile.simple b/auxil/catcheck/Makefile.simple
-index 5157398..0e25fb2 100644
---- a/auxil/catcheck/Makefile.simple
-+++ b/auxil/catcheck/Makefile.simple
-@@ -1,17 +1,17 @@
- 
--# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
- 
- 
- BASE = /home/paule/autobuild/Linux-kalypso-pre-release
--CLIPPER_CXXFLAGS = -I$(BASE)/include
--MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
-+CLIPPER_CFLAGS = -I$(BASE)/include
-+MMDB_CFLAGS = -I$(BASE)/include/mmdb
- 
- CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -L$(BASE)/lib \
- 	-L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- catcheck: catcheck.cc catcheck.hh
-diff --git a/auxil/rama/Makefile.am b/auxil/rama/Makefile.am
-index cdbb54e..12c6731 100644
---- a/auxil/rama/Makefile.am
-+++ b/auxil/rama/Makefile.am
-@@ -1,7 +1,7 @@
- 
- EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm
- 
--INCLUDES =  $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES =  $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- 
- 
- check_PROGRAMS = rama-data rama-doughnut 
-diff --git a/auxil/rama/Makefile.simple b/auxil/rama/Makefile.simple
-index 10fe22e..715a270 100644
---- a/auxil/rama/Makefile.simple
-+++ b/auxil/rama/Makefile.simple
-@@ -1,12 +1,12 @@
- 
--CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
- 
- CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
- 	-L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- rama-data: rama-data.cc
-diff --git a/auxil/sec-str/Makefile.am b/auxil/sec-str/Makefile.am
-index 81f79e8..bfef73a 100644
---- a/auxil/sec-str/Makefile.am
-+++ b/auxil/sec-str/Makefile.am
-@@ -1,6 +1,6 @@
- 
- EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
- 
- #check_PROGRAMS = sec-str-dist-check
- 
-diff --git a/auxil/sec-str/Makefile.simple b/auxil/sec-str/Makefile.simple
-index eb6db20..8b22930 100644
---- a/auxil/sec-str/Makefile.simple
-+++ b/auxil/sec-str/Makefile.simple
-@@ -1,27 +1,27 @@
- 
--#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
- 
- #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
- #	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- #	-lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
- #	-L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--#INCLUDES = $(CLIPPER_CXXFLAGS)
-+#INCLUDES = $(CLIPPER_CFLAGS)
- #LDLIBS = $(CLIPPER_LIBS)
- 
- 
- # 
- 
- BASE = /home/paule/autobuild/Linux-kalypso-pre-release
--CLIPPER_CXXFLAGS = -I$(BASE)/include
--MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
-+CLIPPER_CFLAGS = -I$(BASE)/include
-+MMDB_CFLAGS = -I$(BASE)/include/mmdb
- 
- CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -L$(BASE)/lib \
- 	-L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh
-diff --git a/auxil/strand-analysis/Makefile.am b/auxil/strand-analysis/Makefile.am
-index 11686ba..9c24b3b 100644
---- a/auxil/strand-analysis/Makefile.am
-+++ b/auxil/strand-analysis/Makefile.am
-@@ -3,8 +3,8 @@ EXTRA_DIST = Makefile.simple strand-analysis.cc
- 
- 
- INCLUDES = -I$(top_srcdir)/auxil/sec-str \
--	$(MMDB_CXXFLAGS) 	         \
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDB_CFLAGS) 	         \
-+	$(CLIPPER_CFLAGS) 		
- 
- 
- check_PROGRAMS = 
-diff --git a/auxil/strand-analysis/Makefile.simple b/auxil/strand-analysis/Makefile.simple
-index d5c21a4..2f58b8d 100644
---- a/auxil/strand-analysis/Makefile.simple
-+++ b/auxil/strand-analysis/Makefile.simple
-@@ -2,13 +2,13 @@
- 
- CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based
- 
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include
- 
- CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \
- 	-lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- 	-lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm
- 
--INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS)
-+INCLUDES = -I../sec-str $(CLIPPER_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
- 
- .cc:
-diff --git a/auxil/vectors/Makefile.am b/auxil/vectors/Makefile.am
-index 8826587..4a8d72e 100644
---- a/auxil/vectors/Makefile.am
-+++ b/auxil/vectors/Makefile.am
-@@ -1,6 +1,6 @@
- 
- EXTRA_DIST = Makefile.simple diff-vec.cc
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
- check_PROGRAMS = 
- 
- #diff_vec_SOURCES = diff-vec.cc
-diff --git a/build/Makefile.am b/build/Makefile.am
-index 6afe5a3..748341b 100644
---- a/build/Makefile.am
-+++ b/build/Makefile.am
-@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/build
- 
- INCLUDES =  \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS) \
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS) \
-+	$(MMDB_CFLAGS)
- 
- noinst_PROGRAMS = testcabuild
- 
-diff --git a/ccp4mg-utils/Makefile.am b/ccp4mg-utils/Makefile.am
-index 7734f09..c58fe1d 100644
---- a/ccp4mg-utils/Makefile.am
-+++ b/ccp4mg-utils/Makefile.am
-@@ -26,7 +26,7 @@ pkgincludedir = $(includedir)/coot/ccp4mg-utils
- EXTRA_DIST = convert.sh get-new-utils.sh
- 
- INCLUDES =  \
--	$(MMDB_CXXFLAGS) \
-+	$(MMDB_CFLAGS) \
- 	$(LIBPNG_CFLAGS)
- 
- 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
---- a/ccp4mg-utils/mmut/Makefile.am
-+++ b/ccp4mg-utils/mmut/Makefile.am
-@@ -70,9 +70,9 @@ INCLUDES = \
- 	$(LIBGLADE_CFLAGS)		\
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		
- 
- #	$(WITH_SCRIPT_CFLAGS) 
- 
-diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am
-index a7e68b5..e26a6c8 100755
---- a/ccp4mg-utils/pygl/Makefile.am
-+++ b/ccp4mg-utils/pygl/Makefile.am
-@@ -108,9 +108,9 @@ INCLUDES = \
- 	$(LIBGLADE_CFLAGS)		\
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		
- 
- #	$(WITH_SCRIPT_CFLAGS) 
- 
-diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am
-index 399f453..3d2ff55 100755
---- a/ccp4mg-utils/util/Makefile.am
-+++ b/ccp4mg-utils/util/Makefile.am
-@@ -73,9 +73,9 @@ INCLUDES = \
- 	$(LIBGLADE_CFLAGS)		\
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) 		
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		
- 
- #	$(WITH_SCRIPT_CFLAGS) 
- 
-diff --git a/configure.in b/configure.in
-index cc549a5..d56f856 100644
---- a/configure.in
-+++ b/configure.in
-@@ -108,14 +108,18 @@ esac
- 
- 
- dnl Check for MMDB.
--AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)])
- 
--AM_WITH_MMDBSSM
-+PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM])
- AM_WITH_CCP4SRS
- 
- dnl Check for Clipper.  we exit if clipper is not found.
- #
--AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
-+PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [
-+  CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS])
-+  ], [
-+  AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
-+  ])
- 
- # we set default coot_guile to true
- coot_guile=true
-@@ -186,11 +190,15 @@ AM_PATH_LIBGLADE
- 
- dnl =========================== GooCanvas ================================
- 
--AM_PATH_GOOCANVAS
--# give something for the preprocessor to chew on...
--if test "$GOOCANVAS_CFLAGS" != "" ; then
--   GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
--fi
-+PKG_CHECK_MODULES([GOOCANVAS], [goocanvas],
-+	[GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)],
-+	[
-+		AM_PATH_GOOCANVAS
-+		# give something for the preprocessor to chew on...
-+		if test "$GOOCANVAS_CFLAGS" != "" ; then
-+   		GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
-+		fi
-+	])
- 
- AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with optional complicated/experimental ligand-related dependencies ],
-  coot_enhanced_ligand_additions="true",
-diff --git a/coords/Makefile.am b/coords/Makefile.am
-index 05fdf70..1e1c5d2 100644
---- a/coords/Makefile.am
-+++ b/coords/Makefile.am
-@@ -29,7 +29,7 @@ INCLUDES = \
- 	-I$(top_srcdir) \
- 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
- 	$(RDKIT_CXXFLAGS) 		\
--	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = \
- 	-DPKGDATADIR='"$(pkgdatadir)"' \
-diff --git a/coot-surface/Makefile.am b/coot-surface/Makefile.am
-index d2243d6..2434219 100644
---- a/coot-surface/Makefile.am
-+++ b/coot-surface/Makefile.am
-@@ -19,7 +19,7 @@
- # 02110-1301, USA
- 
- INCLUDES = -I$(top_srcdir) \
--	$(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
-+	$(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
- 
- lib_LTLIBRARIES = libcoot-surface.la
- 
-diff --git a/coot-utils/Makefile.am b/coot-utils/Makefile.am
-index 87810dc..c5b05b4 100644
---- a/coot-utils/Makefile.am
-+++ b/coot-utils/Makefile.am
-@@ -34,11 +34,10 @@ pkginclude_HEADERS = peak-search.hh coot-trim.hh \
- 	read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh 
- pkgincludedir = $(includedir)/coot/coot-utils
- 
--
- INCLUDES = \
- 	-I$(top_srcdir)	\
--	$(CLIPPER_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
- 	$(GSL_CFLAGS)			\
- 	$(WITH_GUILE_CFLAGS)		\
- 	$(WITH_PYTHON_CFLAGS)
-diff --git a/cootaneer/Makefile.am b/cootaneer/Makefile.am
-index 3a1d720..cfca0fd 100644
---- a/cootaneer/Makefile.am
-+++ b/cootaneer/Makefile.am
-@@ -20,7 +20,7 @@
- EXTRA_DIST = 		\
- 	cootaneer-llk-2.40.dat
- 
--INCLUDES = 	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
-+INCLUDES = 	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
- 
- cootaneer_demo_SOURCES = cootaneer-demo.cpp
- 
-diff --git a/cootilus/Makefile.am b/cootilus/Makefile.am
-index 7e4169d..4492014 100644
---- a/cootilus/Makefile.am
-+++ b/cootilus/Makefile.am
-@@ -20,7 +20,7 @@
- EXTRA_DIST = 		\
- 	nautilus_lib.pdb
- 
--INCLUDES = 	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
-+INCLUDES = 	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
- 
- cootilus_demo_SOURCES = cootilus-demo.cpp
- 
-diff --git a/db-main/Makefile.am b/db-main/Makefile.am
-index 3a85b9e..1a11cdf 100644
---- a/db-main/Makefile.am
-+++ b/db-main/Makefile.am
-@@ -6,7 +6,7 @@ AM_CXXFLAGS = \
- 	-DDATADIR='"$(datadir)"'
- 
- INCLUDES = -I$(top_srcdir) \
--   $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+   $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
- 
- pkginclude_HEADERS = db-main.hh db-strands.hh
- pkgincludedir = $(includedir)/coot/db-main
-diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..c207a43 100644
---- a/db-main/Makefile.simple
-+++ b/db-main/Makefile.simple
-@@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
- MCCP4   = $(HOME)/crystal
- 
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include 
-+MMDB_CFLAGS = -I$(MMDB)/include 
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
- 
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
-@@ -28,9 +28,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
- 
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
- 
- CXXFLAGS = -g $(INCLUDES)
- LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS) 
-@@ -44,4 +44,4 @@ libcoot-db-main.a: db-main.o
- db-main.o: db-main.cc db-main.hh
- 
- testmmdbbits: testmmdbbits.cc
--	$(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@
-+	$(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@
-diff --git a/density-contour/Makefile.am b/density-contour/Makefile.am
-index 7f705e8..f5dcc00 100644
---- a/density-contour/Makefile.am
-+++ b/density-contour/Makefile.am
-@@ -20,7 +20,7 @@
- 
- COORD_INCLUDES = -I$(top_srcdir)
- 
--INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS) 
-+INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS) 
- 
- lib_LTLIBRARIES = libcoot-isosurface.la
- 
-diff --git a/geometry/Makefile.am b/geometry/Makefile.am
-index 6dd665f..57aaa04 100644
---- a/geometry/Makefile.am
-+++ b/geometry/Makefile.am
-@@ -26,7 +26,7 @@ pkginclude_HEADERS =  protein-geometry.hh read-sbase.hh lbg-graph.hh srs-interfa
- pkgincludedir = $(includedir)/coot/geometry
- 
- INCLUDES = -I$(top_srcdir) \
--	 $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS)
-+	 $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = \
- 	-DDATADIR='"$(datadir)"'       \
-diff --git a/geometry/Makefile.simple b/geometry/Makefile.simple
-index 370b2fa..c3b0106 100644
---- a/geometry/Makefile.simple
-+++ b/geometry/Makefile.simple
-@@ -46,7 +46,7 @@ MCCP4   = $(HOME)/mapview
- 
- 
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include 
-+MMDB_CFLAGS = -I$(MMDB)/include 
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
- 
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
-@@ -55,9 +55,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
- 
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords 
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords 
- 
- top_srcdir = ..
- 
-diff --git a/high-res/Makefile.am b/high-res/Makefile.am
-index cf81182..3a2af5c 100644
---- a/high-res/Makefile.am
-+++ b/high-res/Makefile.am
-@@ -29,8 +29,8 @@ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
- 
- INCLUDES = \
- 	-I$(top_srcdir)   \
--	$(MMDB_CXXFLAGS)  \
--	$(CLIPPER_CXXFLAGS)
-+	$(MMDB_CFLAGS)  \
-+	$(CLIPPER_CFLAGS)
- 
- libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
- 	sequence-assignment.cc
-diff --git a/ideal/Makefile.am b/ideal/Makefile.am
-index e52c271..c5c8e6a 100644
---- a/ideal/Makefile.am
-+++ b/ideal/Makefile.am
-@@ -33,11 +33,11 @@ pkgincludedir = $(includedir)/coot/ideal
- 
- INCLUDES = \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS)        \
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS)        \
-+	$(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \
--     $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS) 
-+     $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS) 
- AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS)
- 
- 
-diff --git a/ideal/Makefile.simple b/ideal/Makefile.simple
-index 3c32c3c..0abd514 100644
---- a/ideal/Makefile.simple
-+++ b/ideal/Makefile.simple
-@@ -44,7 +44,7 @@ MMDB    = $(HOME)/mapview
- 
- 
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include 
-+MMDB_CFLAGS = -I$(MMDB)/include 
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
- 
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb 
-@@ -53,9 +53,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- 	-L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
- 
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include 
- 
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \
- 	-I$(top_srcdir)/coords  \
- 	-I$(top_srcdir)/geometry
- 
-diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index df74b90..7f54567 100644
---- a/lbg/Makefile.am
-+++ b/lbg/Makefile.am
-@@ -6,7 +6,7 @@ INCLUDES = \
-         $(GSL_CFLAGS) \
-         $(GOOCANVAS_CFLAGS) \
-         $(GTK_CFLAGS) \
--	$(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
-+	$(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
- 	$(COOT_WINDOWS_CFLAGS) \
- 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
- 	$(RDKIT_CXXFLAGS) \
-diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple
-index 48d091b..5b148b4 100644
---- a/lbg/Makefile.simple
-+++ b/lbg/Makefile.simple
-@@ -24,11 +24,11 @@ GSL_LDFLAGS=$(CRYST)/lib/libgsl.la  $(CRYST)/lib/libgslcblas.la -lm
- MMDB=$(CRYST)
- # MMDB=$(HOME)/test/mmdb
- 
--MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb
-+MMDB_CFLAGS=-I$(MMDB)/include/mmdb
- MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la
- 
- CLIPPER=$(CRYST)
--CLIPPER_CXXFLAGS=-I$(CLIPPER)/include
-+CLIPPER_CFLAGS=-I$(CLIPPER)/include
- CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \
-         $(CLIPPER)/lib/librfftw.la \
-         $(CLIPPER)/lib/libfftw.la
-@@ -40,7 +40,7 @@ LIDIA_CORE_CXXFLAGS = -I ../lidia-core
- LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la
- 
- 
--CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \
-+CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \
-     -I$(top_srcdir)/compat
- 
- lbg:  lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
-diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 72b28ca..2a184b4 100644
---- a/lidia-core/Makefile.am
-+++ b/lidia-core/Makefile.am
-@@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core
- 
- #  20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t
- # simple
--#INCLUDES = $(CLIPPER_CXXFLAGS)
-+#INCLUDES = $(CLIPPER_CFLAGS)
- #
- INCLUDES = \
- 	 -I$(top_srcdir) \
- 	$(ENHANCED_LIGAND_TOOLS_CFLAGS)      \
- 	$(RDKIT_CXXFLAGS) 		\
--        $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+        $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- 
- libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \
- 	cod-types.cc
-diff --git a/ligand/Makefile.am b/ligand/Makefile.am
-index 202979e..5173204 100644
---- a/ligand/Makefile.am
-+++ b/ligand/Makefile.am
-@@ -27,7 +27,7 @@ INCLUDES = \
- 	-I$(top_srcdir) \
- 	$(COOT_GSL_FLAGS)		\
- 	$(GSL_CFLAGS)			\
--	$(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) 
-+	$(CLIPPER_CFLAGS) $(MMDB_CFLAGS) 
- 
- pkginclude_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \
- 	chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh        \
-diff --git a/macros/clipper.m4 b/macros/clipper.m4
-index da11e74..ad2af81 100644
---- a/macros/clipper.m4
-+++ b/macros/clipper.m4
-@@ -56,7 +56,7 @@ if test x$clipper_prefix != x; then
-  #
-  # should use clipper-config --cflags
-  #
-- CLIPPER_CXXFLAGS="-I$clipper_prefix/include"
-+ CLIPPER_CFLAGS="-I$clipper_prefix/include"
-  # -I$clipper_prefix/cctbx
-  
-  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
-@@ -75,7 +75,7 @@ if test x$clipper_prefix != x; then
-  #
-  ccp4c=ccp4c
- 
-- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-  # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
- 
- 
-@@ -102,8 +102,8 @@ else
-  # this needs to be 'configured' - typically either s or blank.
-  fftw_pre=
- 
-- CLIPPER_CXXFLAGS="$CCP4_CFLAGS"
-- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-+ CLIPPER_CFLAGS="$CCP4_CFLAGS"
-+ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
- fi
- 
- # BL: workaround needed for new MinGW
-@@ -113,17 +113,17 @@ ac_cv_build_alias=${ac_cv_build_alias:=$build_alias}
- case $ac_cv_build_alias in
-         # BL says:: same as for cygwin in mingw
-         MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*)
--                CLIPPER_LDOPTS=$CLIPPER_LDOPTS
-+                CLIPPER_LIBS=$CLIPPER_LIBS
- 	;; 
- 	*)
--		CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread"
-+		CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread"
-         ;;
- esac
- 
- AC_MSG_CHECKING([for Clipper])
- 
--	LIBS="$save_LIBS $CLIPPER_LDOPTS"
--	CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
-+	LIBS="$save_LIBS $CLIPPER_LIBS"
-+	CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
- 	# AC_TRY_LINK uses the c compiler, so we will temporarily 
- 	# reassign $CC to the c++ compiler.
-  	#
-@@ -140,7 +140,7 @@ if test x$have_clipper = xyes; then
- 
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-- CLIPPER_LIBS="$CLIPPER_LDOPTS"
-+ CLIPPER_LIBS="$CLIPPER_LIBS"
-  ifelse([$1], , :, [$1])
- 
- else
-@@ -148,12 +148,12 @@ else
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-  CLIPPER_LIBS=""
-- CLIPPER_CXXFLAGS=""
-+ CLIPPER_CFLAGS=""
-  ifelse([$2], , :, [$2])
- 
- fi
- 
--AC_SUBST(CLIPPER_CXXFLAGS)
-+AC_SUBST(CLIPPER_CFLAGS)
- AC_SUBST(CLIPPER_LIBS)
- 
- ])
-diff --git a/macros/clipper.m4.old b/macros/clipper.m4.old
-index de8ab65..4c1b418 100644
---- a/macros/clipper.m4.old
-+++ b/macros/clipper.m4.old
-@@ -34,7 +34,7 @@ if test x$clipper_prefix != x; then
-  # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
-  # when clipper and dependencies get installed.
-  #  
-- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
-+ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
- # -I$clipper_prefix/cctbx
-  
-  # yes, libmmtz.a is in -L$clipper_prefix/umtz!
-@@ -45,20 +45,20 @@ if test x$clipper_prefix != x; then
-  # HACK! FIXME
-  # added lz, we should have proper autoconf check for this.
-  #
-- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
-+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
- # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx 
- else
-  # the compiler looks in the "standard" places for clipper.  In real life,
-  # it would be quite unlikely that clipper would be installed in /usr/include, 
-  # /usr/lib etc. so this code will not usually find the right dependencies.
-- CLIPPER_CXXFLAGS=""
-- CLIPPER_LDOPTS=""
-+ CLIPPER_CFLAGS=""
-+ CLIPPER_LIBS=""
- fi
- 
- AC_MSG_CHECKING([for Clipper])
- 
--	LIBS="$save_LIBS $CLIPPER_LDOPTS"
--	CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
-+	LIBS="$save_LIBS $CLIPPER_LIBS"
-+	CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
- 	# AC_TRY_LINK uses the c compiler, so we will temporarily 
- 	# reassign $CC to the c++ compiler.
-  	#
-@@ -72,7 +72,7 @@ if test x$have_clipper = xyes; then
- 
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-- CLIPPER_LIBS="$CLIPPER_LDOPTS"
-+ CLIPPER_LIBS="$CLIPPER_LIBS"
-  ifelse([$1], , :, [$1])
- 
- else
-@@ -80,12 +80,12 @@ else
-  LIBS="$saved_LIBS"
-  CFLAGS="$saved_CFLAGS"
-  CLIPPER_LIBS=""
-- CLIPPER_CXXFLAGS=""
-+ CLIPPER_CFLAGS=""
-  ifelse([$2], , :, [$2])
- 
- fi
- 
--AC_SUBST(CLIPPER_CXXFLAGS)
-+AC_SUBST(CLIPPER_CFLAGS)
- AC_SUBST(CLIPPER_LIBS)
- 
- ])
-diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4
-index e2494a5..89c908e 100644
---- a/macros/goo-canvas.m4
-+++ b/macros/goo-canvas.m4
-@@ -35,8 +35,7 @@ if test x$goocanvas_prefix != x; then
-   # SGI compiler CC (CXX=CC) needs -lm to link maths library, but 
-   # GCC c++ does not.
-   #
--  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)
- 
-@@ -54,18 +53,16 @@ else
-     break;;
-   esac
-   if test -z "${PKG_CONFIG}"; then
--     GOOCANVAS_LDOPTS="-lgoocanvas"
-+     GOOCANVAS_LIBS="-lgoocanvas"
-   else
--     GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
-+     GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
-   fi
- fi
- 
- AC_MSG_CHECKING([for Goocanvas])
- 
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
--
--
- dnl # 20130929: why do I do this?  I don't remember.  Using libtool 
- dnl # in this way is not a good idea (configure makes libtool).
- dnl #
-@@ -85,18 +82,15 @@ dnl     # note that we use ./libtool (running in the build dir) because $LIBTOOL
- dnl     CXX="libtool --mode=link $CXX"
- dnl     break;;
- dnl esac
--
--
- AC_LANG_PUSH(C++)
- AC_TRY_LINK([#include "goocanvas.h"] ,[ GooCanvas *a;  ], have_goocanvas=yes, have_goocanvas=no)
- AC_LANG_POP
--
- AC_MSG_RESULT($have_goocanvas)
- 
- if test x$have_goocanvas = xyes; then
- 
-  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
- 
- ifelse([$1], , :, [$1])
- 
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 25dc502..21646a5 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then
- 
-    if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
- 
--      MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-+      MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
-       # AFAICS, ssm does not put its libs in $acl_libdirstem
-       # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
-       MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
--      ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/include"
-+      ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/include"
- 
-       # saved_LIBS="$LIBS"
-       # saved_CPPFLAGS="$CPPFLAGS"
-@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then
-    else 
-       AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found])
-    fi
--   MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
-+   MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
-   
- else 
- 
--   MMDBSSM_CXXFLAGS=""
-+   MMDBSSM_CFLAGS=""
-    MMDBSSM_LIBS=""
-    with_ssmlib_prefix=no 
- 
-@@ -62,6 +62,6 @@ fi
- 
- AC_MSG_RESULT([$with_ssmlib_prefix])
- 
--AC_SUBST(MMDBSSM_CXXFLAGS)
-+AC_SUBST(MMDBSSM_CFLAGS)
- AC_SUBST(MMDBSSM_LIBS)
- ])
-diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
-index 7c1cbcf..72613f3 100644
---- a/macros/mmdb.m4
-+++ b/macros/mmdb.m4
-@@ -55,7 +55,7 @@ if test x$mmdb_prefix != x; then
- 	# --with-mmdb=/some/thing
- 	#
- 
-- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like
-+ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like
-  # when MMDB and dependencies get installed - we infact, include both
-  # directories.
-  #  
-@@ -69,7 +69,7 @@ lib/src
- lib/src/mmdb'
- for ac_dir in $ac_mmdb_dirs; do
-    if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then
--      ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir"
-+      ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir"
-       break
-    fi
- done
-@@ -82,14 +82,14 @@ else
-  # the compiler looks in the "standard" places for MMDB.  In real life,
-  # it would be quite unlikely that MMDB would be installed in /usr/include, 
-  # /usr/lib etc. so this code will not usually find the right dependencies.
-- ac_MMDB_CXXFLAGS=""
-+ ac_MMDB_CFLAGS=""
-  ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
- 
- AC_MSG_CHECKING([for MMDB])
- 
- 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
--	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
-+	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS"
- 	#
- 	# AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
- 	# temporarily reassign $CC to the c++ compiler.
-@@ -118,7 +118,7 @@ if test x$have_mmdb = xyes; then
-     CLINKR_FLAG=-DMMDB_WITHOUT_LINKR
-  fi
-  CXXFLAGS="$saved_CXXFLAGS"
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
-+ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
-  MMDB_LIBS="$ac_MMDB_LDOPTS"
- ifelse([$1], , :, [$1])
- 
-@@ -134,12 +134,12 @@ else
-  LIBS="$saved_LIBS"
-  CXXFLAGS="$saved_CXXFLAGS"
-  MMDB_LIBS=""
-- MMDB_CXXFLAGS=""
-+ MMDB_CFLAGS=""
-  ifelse([$2], , :, [$2])
- 
- fi
- 
--AC_SUBST(MMDB_CXXFLAGS)
-+AC_SUBST(MMDB_CFLAGS)
- AC_SUBST(MMDB_LIBS)
- 
- ])
-diff --git a/mini-mol/Makefile.am b/mini-mol/Makefile.am
-index 2f6e3a3..4865b0b 100644
---- a/mini-mol/Makefile.am
-+++ b/mini-mol/Makefile.am
-@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/mini-mol
- 
- INCLUDES =  \
- 	-I$(top_srcdir) \
--	$(CLIPPER_CXXFLAGS)    \
--	$(MMDB_CXXFLAGS)
-+	$(CLIPPER_CFLAGS)    \
-+	$(MMDB_CFLAGS)
- 
- AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
- 
-diff --git a/protein_db/Makefile.am b/protein_db/Makefile.am
-index 268fcf6..cdd5c9e 100644
---- a/protein_db/Makefile.am
-+++ b/protein_db/Makefile.am
-@@ -19,7 +19,7 @@
- 
- lib_LTLIBRARIES=libcoot-protein-db.la
- 
--INCLUDES= $(CLIPPER_CXXFLAGS)  $(MMDB_CXXFLAGS)
-+INCLUDES= $(CLIPPER_CFLAGS)  $(MMDB_CFLAGS)
- 
- pkginclude_HEADERS=protein_db.h  protein_db_utils.h rna_db.h
- pkgincludedir = $(includedir)/coot/protein_db
-diff --git a/sequence-view/Makefile.am b/sequence-view/Makefile.am
-index 7af6384..742e6d7 100644
---- a/sequence-view/Makefile.am
-+++ b/sequence-view/Makefile.am
-@@ -55,9 +55,9 @@ INCLUDES = \
- 	-I$(top_srcdir)/analysis	\
- 	-I$(top_srcdir)/cootaneer	\
- 	-I$(top_srcdir)/src     	\
--	$(CLIPPER_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
--	$(MMDBSSM_CXXFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
-+	$(MMDBSSM_CFLAGS) 		\
- 	$(GLUT_CFLAGS)			\
- 	$(CANVAS_CFLAGS) 		\
- 	$(GTKGL_CONTEXT_CFLAGS)		\
-diff --git a/skeleton/Makefile.am b/skeleton/Makefile.am
-index 54872fe..bef7d0e 100644
---- a/skeleton/Makefile.am
-+++ b/skeleton/Makefile.am
-@@ -23,7 +23,7 @@ lib_LTLIBRARIES=libcoot-skeleton.la
- 
- INCLUDES = \
- 	  -I$(top_srcdir) \
--	 $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) 
-+	 $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) 
- 
- AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index af5276b..d0ab482 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -195,11 +195,11 @@ INCLUDES = \
-         $(GOOCANVAS_CFLAGS)             \
- 	@GTK_CFLAGS@ 			\
- 	$(GLUT_CFLAGS)			\
--	$(MMDBSSM_CXXFLAGS) 		\
--	$(MMDB_CXXFLAGS) 		\
-+	$(MMDBSSM_CFLAGS) 		\
-+	$(MMDB_CFLAGS) 		\
- 	$(CCP4SRS_CXXFLAGS) 		\
- 	$(GSL_CFLAGS)			\
--	$(CLIPPER_CXXFLAGS) 		\
-+	$(CLIPPER_CFLAGS) 		\
- 	$(PYGTK_CFLAGS)                 \
- 	$(GLOB_CFLAGS)                 \
- 	$(CURL_CFLAGS)                 
-diff --git a/surface/Makefile.am b/surface/Makefile.am
-index 3de5953..2461f58 100644
---- a/surface/Makefile.am
-+++ b/surface/Makefile.am
-@@ -1,5 +1,5 @@
- 
--INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
-+INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS)
- 
- AM_CXXFLAGS = $(OPENMP_CFLAGS)
- 

diff --git a/sci-chemistry/coot/files/coot-9999-desktop.patch b/sci-chemistry/coot/files/coot-9999-desktop.patch
new file mode 100644
index 0000000..c264dd5
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-desktop.patch
@@ -0,0 +1,21 @@
+ coot.desktop | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/coot.desktop b/coot.desktop
+index 74aecf3..8668018 100644
+--- a/coot.desktop
++++ b/coot.desktop
+@@ -1,10 +1,9 @@
+ [Desktop Entry]
+ Type=Application
+-Encoding=UTF-8
+ Name=Coot
+ Comment=Macromolecular model builder
+ Exec=coot
+-Icon=coot.png
++Icon=coot
+ Terminal=true
+-Categories=Science;Graphics
+-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
++Categories=Science;Graphics;
++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;

diff --git a/sci-chemistry/coot/files/coot-9999-libguile.patch b/sci-chemistry/coot/files/coot-9999-libguile.patch
new file mode 100644
index 0000000..cbaccef
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-libguile.patch
@@ -0,0 +1,29 @@
+ src/graphics-info-modelling.cc | 1 +
+ src/graphics-info.cc           | 2 ++
+ 2 files changed, 3 insertions(+)
+
+diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
+index 05a63ad..4b7d129 100644
+--- a/src/graphics-info-modelling.cc
++++ b/src/graphics-info-modelling.cc
+@@ -102,6 +102,7 @@
+ 
+ #include "utils/coot-utils.hh"
+ 
++#include <libguile.h>
+ 
+ // Idealize the geometry without considering the map.
+ //
+diff --git a/src/graphics-info.cc b/src/graphics-info.cc
+index e2f9d52..76b6769 100644
+--- a/src/graphics-info.cc
++++ b/src/graphics-info.cc
+@@ -92,6 +92,8 @@
+ #include "cc-interface-scripting.hh"
+ #endif
+ 
++#include <libguile.h>
++
+ // A few non-class members - should be somewhere else, I guess.
+ // 
+ void initialize_graphics_molecules() { 

diff --git a/sci-chemistry/coot/files/coot-9999-libtool.patch b/sci-chemistry/coot/files/coot-9999-libtool.patch
new file mode 100644
index 0000000..10c43ad
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-libtool.patch
@@ -0,0 +1,39 @@
+ configure.ac    |  2 +-
+ lbg/Makefile.am | 11 -----------
+ 2 files changed, 1 insertion(+), 12 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 73d6ed7..b04dcd6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
+ 
+ AC_SUBST(COOT_STDTYPES)
+ 
+-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
+ AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ 
+diff --git a/lbg/Makefile.am b/lbg/Makefile.am
+index 1277afe..a79ebe0 100644
+--- a/lbg/Makefile.am
++++ b/lbg/Makefile.am
+@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh  flev-annotations.hh graphics-c-interfa
+ 	lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
+ pkgincludedir = $(includedir)/coot/lbg
+ 
+-# 20140521
+-# lidia_LDFLAGS = -Wl,--export-dynamic
+-# 
+-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic
+-# (but not for MacOSX, where it Does The Right Thing (hopefully)).
+-# We manually set the value of wl here, but maybe the Right Thing To Do for that is 
+-# run (eval) $($LIBTOOL --config | grep ^wl).  How do I do that here though?  
+-# I don't understand.  Maybe the setting of wl should be done in configure?  But then
+-# I have to force the output of libtool.  Bleugh.  Hmm...
+-# Anyway, thankyou Gary Vaughan.
+-wl=-Wl,
+ lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ # res spec output operator means we include libcoot-coord-utils


^ permalink raw reply related	[flat|nested] 24+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
@ 2020-09-22 13:40 Aisha Tammy
  0 siblings, 0 replies; 24+ messages in thread
From: Aisha Tammy @ 2020-09-22 13:40 UTC (permalink / raw
  To: gentoo-commits

commit:     ac002458a28fad508b966a6e7ce571603fb6b603
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 13:35:27 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 13:35:27 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac002458

sci-chemistry/coot: drop package

maintainer AWOL

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 sci-chemistry/coot/coot-9999.ebuild                | 177 ---------------------
 sci-chemistry/coot/files/coot-9999-desktop.patch   |  21 ---
 sci-chemistry/coot/files/coot-9999-libguile.patch  |  29 ----
 sci-chemistry/coot/files/coot-9999-libtool.patch   |  39 -----
 .../coot/files/coot-9999-sandbox-icons.patch       |  16 --
 sci-chemistry/coot/metadata.xml                    |  12 --
 6 files changed, 294 deletions(-)

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
deleted file mode 100644
index f13e9b681..000000000
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ /dev/null
@@ -1,177 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools git-r3 python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/"
-SRC_URI="test? ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
-EGIT_REPO_URI="https://github.com/pemsley/coot.git"
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS=""
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
-	sci-libs/libccp4
-	sci-libs/clipper
-	>=sci-libs/coot-data-2
-	>=sci-libs/gsl-1.3
-	sci-libs/fftw:2.1=
-	sci-libs/mmdb:2
-	sci-libs/monomer-db
-	sci-libs/ssm
-	sci-chemistry/reduce
-	sci-chemistry/probe"
-
-XDEPS="
-	gnome-base/libgnomecanvas
-	gnome-base/librsvg:2
-	media-libs/libpng:0=
-	media-libs/freeglut
-	x11-libs/gtk+:2
-	x11-libs/goocanvas:0
-	x11-libs/gtkglext
-	virtual/opengl"
-
-SCHEMEDEPS="
-	dev-scheme/net-http
-	dev-scheme/guile-gui
-	>=dev-scheme/guile-lib-0.1.6
-	dev-scheme/guile-www
-	>=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
-	${SCIDEPS}
-	${XDEPS}
-	${SCHEMEDEPS}
-	${PYTHON_DEPS}
-	dev-db/sqlite:3
-	dev-libs/boost:0=[python,${PYTHON_USEDEP}]
-	dev-libs/glib:2
-	>=dev-libs/gmp-4.2.2-r2:0=
-	dev-python/pygobject:2[${PYTHON_USEDEP}]
-	dev-python/pygtk:2[${PYTHON_USEDEP}]
-	>=net-misc/curl-7.19.6
-	net-dns/libidn:0
-	sys-libs/readline:0=
-	"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig
-	>=sys-devel/libtool-2.4-r2
-	dev-lang/swig
-	sys-devel/bc
-	test? ( dev-scheme/greg )"
-
-pkg_setup() {
-	if use openmp; then
-		tc-has-openmp || die "Please use an OPENMP capable compiler"
-	fi
-	python-single-r1_pkg_setup
-}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-desktop.patch
-	"${FILESDIR}"/${P}-sandbox-icons.patch
-	"${FILESDIR}"/${P}-libtool.patch
-	"${FILESDIR}"/${P}-libguile.patch
-)
-
-src_unpack() {
-	git-r3_src_unpack
-	if use test; then
-		cd "${S}" || die
-		unpack ${A}
-		ln -sf . "${S}"/coot-ccp4 || die
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e '/export LD_LIBRARY/s:^:#:g' \
-		-i src/coot.in || die
-
-	sed \
-		-e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-		-i configure.ac || die
-
-	default
-	eautoreconf
-}
-
-src_configure() {
-	# All the --with's are used to activate various parts.
-	# Yes, this is broken behavior.
-	local myeconfargs=(
-		--with-goocanvas-prefix="${EPREFIX}/usr"
-		--with-guile="${EPREFIX}/usr"
-		--with-python="${EPREFIX}/usr"
-		--with-guile-gtk
-		--with-pygtk="${EPREFIX}/usr"
-		--with-sqlite3
-		--with-boost="${EPREFIX}/usr"
-		)
-	econf ${myeconfargs[@]}
-}
-
-src_test() {
-	source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
-	mkdir "${T}"/coot_test || die
-
-	export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
-	export COOT_SCHEME_DIR="${S}/scheme/"
-	export COOT_RESOURCES_FILE="${S}/cootrc"
-	export COOT_PIXMAPS_DIR="${S}/pixmaps/"
-	export COOT_DATA_DIR="${S}/"
-	export COOT_PYTHON_DIR="${S}/python/"
-	export PYTHONPATH="${COOT_PYTHON_DIR}:${S}/src:${PYTHONPATH}"
-	export PYTHONHOME="${EPREFIX}"/usr/
-	export CCP4_SCR="${T}"/coot_test/
-	export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/"
-	export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/"
-	export SYMINFO="${S}/syminfo.lib"
-
-	export COOT_TEST_DATA_DIR="${S}"/greg-data/
-
-	cat > command-line-greg.scm <<- EOF
-	(use-modules (ice-9 greg))
-		(set! greg-tools (list "greg-tests"))
-			(set! greg-debug #t)
-			(set! greg-verbose 5)
-			(let ((r (greg-test-run)))
-				(if r
-				(coot-real-exit 0)
-				(coot-real-exit 1)))
-	EOF
-
-	einfo "Running test with following paths ..."
-	einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
-	einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
-	einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
-	einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
-	einfo "COOT_DATA_DIR $COOT_DATA_DIR"
-	einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
-	einfo "PYTHONPATH $PYTHONPATH"
-	einfo "PYTHONHOME $PYTHONHOME"
-	einfo "CCP4_SCR ${CCP4_SCR}"
-	einfo "CLIBD_MON ${CLIBD_MON}"
-	einfo "SYMINFO ${SYMINFO}"
-
-	"${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die
-	"${S}"/src/coot-bin --no-graphics --script python-tests/coot_unittest.py || die
-}

diff --git a/sci-chemistry/coot/files/coot-9999-desktop.patch b/sci-chemistry/coot/files/coot-9999-desktop.patch
deleted file mode 100644
index c264dd5a7..000000000
--- a/sci-chemistry/coot/files/coot-9999-desktop.patch
+++ /dev/null
@@ -1,21 +0,0 @@
- coot.desktop | 7 +++----
- 1 file changed, 3 insertions(+), 4 deletions(-)
-
-diff --git a/coot.desktop b/coot.desktop
-index 74aecf3..8668018 100644
---- a/coot.desktop
-+++ b/coot.desktop
-@@ -1,10 +1,9 @@
- [Desktop Entry]
- Type=Application
--Encoding=UTF-8
- Name=Coot
- Comment=Macromolecular model builder
- Exec=coot
--Icon=coot.png
-+Icon=coot
- Terminal=true
--Categories=Science;Graphics
--MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
-+Categories=Science;Graphics;
-+MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;

diff --git a/sci-chemistry/coot/files/coot-9999-libguile.patch b/sci-chemistry/coot/files/coot-9999-libguile.patch
deleted file mode 100644
index cbaccefb2..000000000
--- a/sci-chemistry/coot/files/coot-9999-libguile.patch
+++ /dev/null
@@ -1,29 +0,0 @@
- src/graphics-info-modelling.cc | 1 +
- src/graphics-info.cc           | 2 ++
- 2 files changed, 3 insertions(+)
-
-diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
-index 05a63ad..4b7d129 100644
---- a/src/graphics-info-modelling.cc
-+++ b/src/graphics-info-modelling.cc
-@@ -102,6 +102,7 @@
- 
- #include "utils/coot-utils.hh"
- 
-+#include <libguile.h>
- 
- // Idealize the geometry without considering the map.
- //
-diff --git a/src/graphics-info.cc b/src/graphics-info.cc
-index e2f9d52..76b6769 100644
---- a/src/graphics-info.cc
-+++ b/src/graphics-info.cc
-@@ -92,6 +92,8 @@
- #include "cc-interface-scripting.hh"
- #endif
- 
-+#include <libguile.h>
-+
- // A few non-class members - should be somewhere else, I guess.
- // 
- void initialize_graphics_molecules() { 

diff --git a/sci-chemistry/coot/files/coot-9999-libtool.patch b/sci-chemistry/coot/files/coot-9999-libtool.patch
deleted file mode 100644
index 10c43ad55..000000000
--- a/sci-chemistry/coot/files/coot-9999-libtool.patch
+++ /dev/null
@@ -1,39 +0,0 @@
- configure.ac    |  2 +-
- lbg/Makefile.am | 11 -----------
- 2 files changed, 1 insertion(+), 12 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 73d6ed7..b04dcd6 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
- 
- AC_SUBST(COOT_STDTYPES)
- 
--EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
-+eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
- AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
- 
- 
-diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index 1277afe..a79ebe0 100644
---- a/lbg/Makefile.am
-+++ b/lbg/Makefile.am
-@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh  flev-annotations.hh graphics-c-interfa
- 	lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
- pkgincludedir = $(includedir)/coot/lbg
- 
--# 20140521
--# lidia_LDFLAGS = -Wl,--export-dynamic
--# 
--# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic
--# (but not for MacOSX, where it Does The Right Thing (hopefully)).
--# We manually set the value of wl here, but maybe the Right Thing To Do for that is 
--# run (eval) $($LIBTOOL --config | grep ^wl).  How do I do that here though?  
--# I don't understand.  Maybe the setting of wl should be done in configure?  But then
--# I have to force the output of libtool.  Bleugh.  Hmm...
--# Anyway, thankyou Gary Vaughan.
--wl=-Wl,
- lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
- 
- # res spec output operator means we include libcoot-coord-utils

diff --git a/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch b/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch
deleted file mode 100644
index 2a9ff2d71..000000000
--- a/sci-chemistry/coot/files/coot-9999-sandbox-icons.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- pixmaps/icons/Makefile.am | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am
-index 0c183ae..dddc11a 100644
---- a/pixmaps/icons/Makefile.am
-+++ b/pixmaps/icons/Makefile.am
-@@ -11,6 +11,6 @@ install-data-local:
- 		CONTEXT=` echo $$icon | cut -d_ -f2`; \
- 		SIZE=`    echo $$icon | cut -d_ -f3`; \
- 		ICONFILE=`echo $$icon | cut -d_ -f4`; \
--		mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
--		$(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
-+		mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
-+		$(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
- 	done;

diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml
deleted file mode 100644
index 79d42af98..000000000
--- a/sci-chemistry/coot/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>jlec@gentoo.org</email>
-		<name>Justin Lecher</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>


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