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-rw-r--r--sci-chemistry/coot/ChangeLog13
-rw-r--r--sci-chemistry/coot/files/0.3.1-as-needed.patch449
-rw-r--r--sci-chemistry/coot/files/0.3.1-fix-compilation-with-guile-1.8.patch32
-rw-r--r--sci-chemistry/coot/files/0.3.1-link-against-guile-gtk-properly.patch15
-rw-r--r--sci-chemistry/coot/files/0.3.3-as-needed.patch464
-rw-r--r--sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch15
-rw-r--r--sci-chemistry/coot/files/0.4_pre2-as-needed.patch490
-rw-r--r--sci-chemistry/coot/files/0.4_pre2-link-against-guile-gtk-properly.patch15
-rw-r--r--sci-chemistry/coot/files/0.4_pre2-r549-fix-namespace-error.patch52
-rw-r--r--sci-chemistry/coot/files/glib.m4196
-rw-r--r--sci-chemistry/coot/files/gtk.m4199
11 files changed, 12 insertions, 1928 deletions
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 1208728cdcab..65717a898a18 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,17 @@
# ChangeLog for sci-chemistry/coot
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.37 2011/06/28 17:01:28 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.38 2011/06/28 19:13:23 jlec Exp $
+
+ 28 Jun 2011; Justin Lecher <jlec@gentoo.org> -files/0.3.1-as-needed.patch,
+ -files/0.4_pre2-as-needed.patch,
+ -files/0.3.1-fix-compilation-with-guile-1.8.patch,
+ -files/0.3.1-link-against-guile-gtk-properly.patch,
+ -files/0.3.3-as-needed.patch,
+ -files/0.3.3-link-against-guile-gtk-properly.patch,
+ -files/0.4_pre2-link-against-guile-gtk-properly.patch,
+ -files/0.4_pre2-r549-fix-namespace-error.patch, -files/glib.m4,
+ -files/gtk.m4:
+ Cleaned unneeded patches
*coot-0.6.2 (28 Jun 2011)
diff --git a/sci-chemistry/coot/files/0.3.1-as-needed.patch b/sci-chemistry/coot/files/0.3.1-as-needed.patch
deleted file mode 100644
index cf334b77f2e7..000000000000
--- a/sci-chemistry/coot/files/0.3.1-as-needed.patch
+++ /dev/null
@@ -1,449 +0,0 @@
-diff -urN coot-0.3.1.orig/analysis/Makefile.am coot-0.3.1/analysis/Makefile.am
---- coot-0.3.1.orig/analysis/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/analysis/Makefile.am 2007-05-28 19:58:13.000000000 -0700
-@@ -9,6 +9,7 @@
- $(MMDB_CXXFLAGS)
-
- libcoot_analysis_la_SOURCES = bfkurt.cc
-+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
-
- bin_PROGRAMS = bfactan
-
-@@ -16,7 +17,6 @@
-
- bfactan_LDADD = \
- libcoot-analysis.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(CLIPPER_LIBS) \
-diff -urN coot-0.3.1.orig/coords/Makefile.am coot-0.3.1/coords/Makefile.am
---- coot-0.3.1.orig/coords/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/coords/Makefile.am 2007-05-29 00:42:28.000000000 -0700
-@@ -18,4 +18,6 @@
- libcoot_coords_la_SOURCES = Bond_lines.cc Cartesian.cc cos-sin.cc \
- mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \
- Bond_lines_ext.cc coot-close.cc
--
-+libcoot_coords_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/mini-mol/libcoot-mini-mol.la
-diff -urN coot-0.3.1.orig/coot-surface/Makefile.am coot-0.3.1/coot-surface/Makefile.am
---- coot-0.3.1.orig/coot-surface/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/coot-surface/Makefile.am 2007-05-29 00:34:34.000000000 -0700
-@@ -6,3 +6,4 @@
-
- libcoot_surface_la_SOURCES = \
- coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h
-+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la
-diff -urN coot-0.3.1.orig/coot-utils/Makefile.am coot-0.3.1/coot-utils/Makefile.am
---- coot-0.3.1.orig/coot-utils/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/coot-utils/Makefile.am 2007-05-28 20:08:39.000000000 -0700
-@@ -20,9 +20,11 @@
-
- # for pure coordinates (mmdb) things
- libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc
-+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
-
- # shelx
- libcoot_shelx_la_SOURCES = coot-shelx-ins.cc
-+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la
-
- # for non-simple coordinates things
- libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc
-@@ -32,21 +34,20 @@
-
- # for map things that need mmdb, clipper, gsl and other things
- libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc
-+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS)
-
- noinst_PROGRAMS = testshelxreader testcootutils
-
- testshelxreader_SOURCES = test-shelx-reader.cc
- testshelxreader_LDADD = \
- ./libcoot-shelx.la \
-- ./libcoot-coord-utils.la \
-- ./libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ ./libcoot-utils.la
-
- testcootutils_SOURCES = test-utils.cc
- testcootutils_LDADD = \
- ./libcoot-shelx.la \
- ./libcoot-coord-utils.la \
- ./libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ $(MMDB_LIBS)
-
-
-diff -urN coot-0.3.1.orig/geometry/Makefile.am coot-0.3.1/geometry/Makefile.am
---- coot-0.3.1.orig/geometry/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/geometry/Makefile.am 2007-05-28 18:02:38.000000000 -0700
-@@ -15,6 +15,9 @@
- libcoot_geometry_a_sources = protein-geometry.cc protein-geometry-mmdb.cc
-
- libcoot_geometry_la_SOURCES = $(libcoot_geometry_a_sources)
-+libcoot_geometry_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- # libcoot_geometry_la_CXXFLAGS = -g -O1
-
-@@ -22,6 +25,4 @@
-
- test_geometry_SOURCES = test-geometry.cc
-
--test_geometry_LDADD = ./libcoot-geometry.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+test_geometry_LDADD = ./libcoot-geometry.la
-diff -urN coot-0.3.1.orig/high-res/Makefile.am coot-0.3.1/high-res/Makefile.am
---- coot-0.3.1.orig/high-res/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/high-res/Makefile.am 2007-05-28 19:52:12.000000000 -0700
-@@ -20,13 +20,16 @@
-
- libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
- sequence-assignment.cc
-+libcoot_high_res_la_LIBADD = \
-+ $(top_builddir)/ligand/libcoot-ligand.la \
-+ $(top_builddir)/coot-utils/libcoot-map-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- noinst_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein
-
- testatomgraph_SOURCES = test-atom-graph.cc
-
- testatomgraph_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-@@ -34,90 +37,73 @@
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
- testseqassignment_SOURCES = testseqassignment.cc
- testseqassignment_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
- # tracehighres_LDFLAGS = -static
- tracehighres_SOURCES = trace-high-res.cc
- tracehighres_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
--
-+ $(GSL_LIBS)
-
- testseqalign_SOURCES = testseqalign.cc
-
- # why do we need to link with all this (junk)?
- testseqalign_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
--
-+ $(GSL_LIBS)
-
- globularize_protein_SOURCES = globularize.cc
-
- globularize_protein_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
--
-+ $(GSL_LIBS)
-
-diff -urN coot-0.3.1.orig/ideal/Makefile.am coot-0.3.1/ideal/Makefile.am
---- coot-0.3.1.orig/ideal/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/ideal/Makefile.am 2007-05-28 19:00:33.000000000 -0700
-@@ -24,6 +24,12 @@
- AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
-
- libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc
-+libcoot_ideal_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-utils.la \
-+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-+ $(GSL_LIBS)
-
- noinst_PROGRAMS = test-indexing with-geometry with-map
- # bin_PROGRAMS =
-@@ -41,31 +47,20 @@
- with_geometry_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- with_map_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- test_indexing_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
-diff -urN coot-0.3.1.orig/ligand/Makefile.am coot-0.3.1/ligand/Makefile.am
---- coot-0.3.1.orig/ligand/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/ligand/Makefile.am 2007-05-28 19:33:52.000000000 -0700
-@@ -23,6 +23,16 @@
- libcoot_ligand_la_SOURCES = ligand.cc ligand-extras.cc residue_by_phi_psi.cc \
- wiggly-ligand.cc monomer-utils.cc dunbrack.cc chi-angles-autogen.cc \
- chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc
-+libcoot_ligand_la_LIBADD = \
-+ $(top_builddir)/ideal/libcoot-ideal.la \
-+ $(top_builddir)/coords/libcoot-coords.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-+ $(top_builddir)/coot-utils/libcoot-map-utils.la \
-+ $(top_builddir)/db-main/libcoot-db-main.la \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/geometry/libcoot-geometry.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
-
- AM_CXXFLAGS = \
- -DPKGDATADIR='"$(pkgdatadir)"' \
-@@ -40,35 +50,17 @@
- test_random_SOURCES = test-random.cc
- test_random_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- test_helix_placement_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -76,19 +68,10 @@
-
- test_fffear_in_coot_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-map-heavy.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -100,33 +83,15 @@
-
- findligand_real_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- findwaters_real_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -147,17 +112,8 @@
- testdunbrack_SOURCES = testdunbrack.cc
-
- testdunbrack_LDADD = ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- # lib coot-coords depends on mmdb, even though Cartesian doesn't
-diff -urN coot-0.3.1.orig/Makefile.am coot-0.3.1/Makefile.am
---- coot-0.3.1.orig/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/Makefile.am 2007-05-29 00:46:45.000000000 -0700
-@@ -5,8 +5,8 @@
-
- # see configure.in for po intl
- SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \
-- skeleton ccp4mg-utils density-contour coords angles \
-- mini-mol db-main geometry \
-+ skeleton ccp4mg-utils density-contour mini-mol coords angles \
-+ db-main geometry \
- ideal ligand high-res build \
- analysis sequence-view tw atom-utils src doc
-
-diff -urN coot-0.3.1.orig/mini-mol/Makefile.am coot-0.3.1/mini-mol/Makefile.am
---- coot-0.3.1.orig/mini-mol/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/mini-mol/Makefile.am 2007-05-28 17:52:14.000000000 -0700
-@@ -13,8 +13,9 @@
- testminimol_SOURCES = testminimol.cc
-
- libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc
-+libcoot_mini_mol_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(CLIPPER_LIBS)
-
- testminimol_LDADD = libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ $(MMDB_LIBS)
-diff -urN coot-0.3.1.orig/tw/Makefile.am coot-0.3.1/tw/Makefile.am
---- coot-0.3.1.orig/tw/Makefile.am 2007-05-28 17:08:04.000000000 -0700
-+++ coot-0.3.1/tw/Makefile.am 2007-05-28 20:17:13.000000000 -0700
-@@ -20,15 +20,15 @@
- include_HEADERS = coot-tw.hh
-
- libcoot_tw_la_SOURCES = tw.cc
-+libcoot_tw_la_LIBADD = \
-+ $(GTKCANVAS_LIBS) \
-+ @GTK_LIBS@
-
- noinst_PROGRAMS = coot-tiddly
-
- coot_tiddly_SOURCES = tiddly.cc
-
--coot_tiddly_LDADD = libcoot-tw.la \
-- $(GTKCANVAS_LIBS) \
-- @GTK_LIBS@
--
-+coot_tiddly_LDADD = libcoot-tw.la
-
- # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao
-
diff --git a/sci-chemistry/coot/files/0.3.1-fix-compilation-with-guile-1.8.patch b/sci-chemistry/coot/files/0.3.1-fix-compilation-with-guile-1.8.patch
deleted file mode 100644
index 211376121c5b..000000000000
--- a/sci-chemistry/coot/files/0.3.1-fix-compilation-with-guile-1.8.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Index: src/c-interface.h
-===================================================================
---- src/c-interface.h (revision 219)
-+++ src/c-interface.h (revision 220)
-@@ -57,6 +57,14 @@
-
- */
-
-+/* Francois says move this up here so that things don't get wrapped
-+ twice in C-declarations inside gmp library. Hmm! */
-+#ifdef __cplusplus
-+#ifdef USE_GUILE
-+#include <libguile.h> /* for SCM type (returned by safe_scheme_command) */
-+#endif // USE_GUILE
-+#endif
-+
- #ifndef BEGIN_C_DECLS
-
- #ifdef __cplusplus
-@@ -83,12 +91,6 @@
-
- #define COOT_SCHEME_DIR "COOT_SCHEME_DIR"
-
--#ifdef __cplusplus
--#ifdef USE_GUILE
--#include <libguile.h> /* for SCM type (returned by safe_scheme_command) */
--#endif // USE_GUILE
--#endif
--
- /* ------------------------------------------------------------------------ */
- /* File system Functions: */
- /* ------------------------------------------------------------------------ */
diff --git a/sci-chemistry/coot/files/0.3.1-link-against-guile-gtk-properly.patch b/sci-chemistry/coot/files/0.3.1-link-against-guile-gtk-properly.patch
deleted file mode 100644
index 18af14a2966e..000000000000
--- a/sci-chemistry/coot/files/0.3.1-link-against-guile-gtk-properly.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff -urN coot-0.3.1.orig/macros/guile-gtk.m4 coot-0.3.1/macros/guile-gtk.m4
---- coot-0.3.1.orig/macros/guile-gtk.m4 2007-06-21 22:48:39.000000000 -0700
-+++ coot-0.3.1/macros/guile-gtk.m4 2007-06-21 22:55:17.000000000 -0700
-@@ -47,9 +47,9 @@
- # we have the variable coot_gtk2 in configure.in, which is either TRUE or FALSE
- # Let's use that here. Perhaps there is a better (set by gtk macro?) variable?
- if test $coot_gtk2 = TRUE ; then
-- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-2.0.la
-+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-2.0"
- else
-- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-1.2.la
-+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-1.2"
- fi
- # do we need to set this in fact?
- GUILE_GTK_CFLAGS="-I$guile_gtk_prefix/include"
diff --git a/sci-chemistry/coot/files/0.3.3-as-needed.patch b/sci-chemistry/coot/files/0.3.3-as-needed.patch
deleted file mode 100644
index 6dec443dd231..000000000000
--- a/sci-chemistry/coot/files/0.3.3-as-needed.patch
+++ /dev/null
@@ -1,464 +0,0 @@
-diff -urN coot-0.3.3.orig/analysis/Makefile.am coot-0.3.3/analysis/Makefile.am
---- coot-0.3.3.orig/analysis/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/analysis/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -9,6 +9,7 @@
- $(MMDB_CXXFLAGS)
-
- libcoot_analysis_la_SOURCES = bfkurt.cc
-+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
-
- bin_PROGRAMS = bfactan
-
-@@ -16,7 +17,6 @@
-
- bfactan_LDADD = \
- libcoot-analysis.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(CLIPPER_LIBS) \
-diff -urN coot-0.3.3.orig/coords/Makefile.am coot-0.3.3/coords/Makefile.am
---- coot-0.3.3.orig/coords/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/coords/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -37,4 +37,6 @@
- libcoot_coords_la_SOURCES = Bond_lines.cc Cartesian.cc cos-sin.cc \
- mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \
- Bond_lines_ext.cc coot-close.cc
--
-+libcoot_coords_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/mini-mol/libcoot-mini-mol.la
-diff -urN coot-0.3.3.orig/coot-surface/Makefile.am coot-0.3.3/coot-surface/Makefile.am
---- coot-0.3.3.orig/coot-surface/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/coot-surface/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -25,3 +25,4 @@
-
- libcoot_surface_la_SOURCES = \
- coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h
-+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la
-diff -urN coot-0.3.3.orig/coot-utils/Makefile.am coot-0.3.3/coot-utils/Makefile.am
---- coot-0.3.3.orig/coot-utils/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/coot-utils/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -39,9 +39,11 @@
-
- # for pure coordinates (mmdb) things
- libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc
-+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
-
- # shelx
- libcoot_shelx_la_SOURCES = coot-shelx-ins.cc
-+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la
-
- # for non-simple coordinates things
- libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc
-@@ -51,21 +53,20 @@
-
- # for map things that need mmdb, clipper, gsl and other things
- libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc
-+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS)
-
- noinst_PROGRAMS = testshelxreader testcootutils
-
- testshelxreader_SOURCES = test-shelx-reader.cc
- testshelxreader_LDADD = \
- ./libcoot-shelx.la \
-- ./libcoot-coord-utils.la \
-- ./libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ ./libcoot-utils.la
-
- testcootutils_SOURCES = test-utils.cc
- testcootutils_LDADD = \
- ./libcoot-shelx.la \
- ./libcoot-coord-utils.la \
- ./libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ $(MMDB_LIBS)
-
-
-diff -urN coot-0.3.3.orig/geometry/Makefile.am coot-0.3.3/geometry/Makefile.am
---- coot-0.3.3.orig/geometry/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/geometry/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -34,6 +34,9 @@
- libcoot_geometry_a_sources = protein-geometry.cc protein-geometry-mmdb.cc
-
- libcoot_geometry_la_SOURCES = $(libcoot_geometry_a_sources)
-+libcoot_geometry_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- # libcoot_geometry_la_CXXFLAGS = -g -O1
-
-@@ -41,6 +44,4 @@
-
- test_geometry_SOURCES = test-geometry.cc
-
--test_geometry_LDADD = ./libcoot-geometry.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+test_geometry_LDADD = ./libcoot-geometry.la
-diff -urN coot-0.3.3.orig/high-res/Makefile.am coot-0.3.3/high-res/Makefile.am
---- coot-0.3.3.orig/high-res/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/high-res/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -39,13 +39,16 @@
-
- libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
- sequence-assignment.cc
-+libcoot_high_res_la_LIBADD = \
-+ $(top_builddir)/ligand/libcoot-ligand.la \
-+ $(top_builddir)/coot-utils/libcoot-map-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- noinst_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein
-
- testatomgraph_SOURCES = test-atom-graph.cc
-
- testatomgraph_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-@@ -53,90 +56,73 @@
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
- testseqassignment_SOURCES = testseqassignment.cc
- testseqassignment_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
- # tracehighres_LDFLAGS = -static
- tracehighres_SOURCES = trace-high-res.cc
- tracehighres_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
--
-+ $(GSL_LIBS)
-
- testseqalign_SOURCES = testseqalign.cc
-
- # why do we need to link with all this (junk)?
- testseqalign_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
--
-+ $(GSL_LIBS)
-
- globularize_protein_SOURCES = globularize.cc
-
- globularize_protein_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
--
-+ $(GSL_LIBS)
-
-diff -urN coot-0.3.3.orig/ideal/Makefile.am coot-0.3.3/ideal/Makefile.am
---- coot-0.3.3.orig/ideal/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/ideal/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -43,6 +43,12 @@
- AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
-
- libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc
-+libcoot_ideal_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-utils.la \
-+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-+ $(GSL_LIBS)
-
- noinst_PROGRAMS = test-indexing with-geometry with-map
- # bin_PROGRAMS =
-@@ -60,31 +66,20 @@
- with_geometry_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- with_map_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- test_indexing_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
-diff -urN coot-0.3.3.orig/ligand/Makefile.am coot-0.3.3/ligand/Makefile.am
---- coot-0.3.3.orig/ligand/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/ligand/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -42,6 +42,16 @@
- libcoot_ligand_la_SOURCES = ligand.cc ligand-extras.cc residue_by_phi_psi.cc \
- wiggly-ligand.cc monomer-utils.cc dunbrack.cc chi-angles-autogen.cc \
- chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc
-+libcoot_ligand_la_LIBADD = \
-+ $(top_builddir)/ideal/libcoot-ideal.la \
-+ $(top_builddir)/coords/libcoot-coords.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-+ $(top_builddir)/coot-utils/libcoot-map-utils.la \
-+ $(top_builddir)/db-main/libcoot-db-main.la \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/geometry/libcoot-geometry.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
-
- AM_CXXFLAGS = \
- -DPKGDATADIR='"$(pkgdatadir)"' \
-@@ -59,35 +69,17 @@
- test_random_SOURCES = test-random.cc
- test_random_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- test_helix_placement_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -95,19 +87,10 @@
-
- test_fffear_in_coot_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-map-heavy.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -119,33 +102,15 @@
-
- findligand_real_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- findwaters_real_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -166,17 +131,8 @@
- testdunbrack_SOURCES = testdunbrack.cc
-
- testdunbrack_LDADD = ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- # lib coot-coords depends on mmdb, even though Cartesian doesn't
-diff -urN coot-0.3.3.orig/Makefile.am coot-0.3.3/Makefile.am
---- coot-0.3.3.orig/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/Makefile.am 2007-08-15 21:09:11.000000000 -0700
-@@ -25,10 +25,10 @@
-
- # see configure.in for po intl
- SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \
-- skeleton ccp4mg-utils density-contour coords angles \
-- mini-mol db-main geometry \
-+ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \
-+ db-main geometry \
- ideal ligand high-res build \
-- analysis sequence-view tw atom-utils src doc
-+ analysis sequence-view tw src doc
-
- # po, no po today.
-
-diff -urN coot-0.3.3.orig/mini-mol/Makefile.am coot-0.3.3/mini-mol/Makefile.am
---- coot-0.3.3.orig/mini-mol/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/mini-mol/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -32,8 +32,9 @@
- testminimol_SOURCES = testminimol.cc
-
- libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc
-+libcoot_mini_mol_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(CLIPPER_LIBS)
-
- testminimol_LDADD = libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ $(MMDB_LIBS)
-diff -urN coot-0.3.3.orig/skeleton/Makefile.am coot-0.3.3/skeleton/Makefile.am
---- coot-0.3.3.orig/skeleton/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/skeleton/Makefile.am 2007-08-15 17:20:44.000000000 -0700
-@@ -36,7 +36,7 @@
-
-
- libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources)
--
-+libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la
-
- # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2
-
-diff -urN coot-0.3.3.orig/tw/Makefile.am coot-0.3.3/tw/Makefile.am
---- coot-0.3.3.orig/tw/Makefile.am 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/tw/Makefile.am 2007-08-15 12:21:22.000000000 -0700
-@@ -39,15 +39,15 @@
- include_HEADERS = coot-tw.hh
-
- libcoot_tw_la_SOURCES = tw.cc
-+libcoot_tw_la_LIBADD = \
-+ $(GTKCANVAS_LIBS) \
-+ @GTK_LIBS@
-
- noinst_PROGRAMS = coot-tiddly
-
- coot_tiddly_SOURCES = tiddly.cc
-
--coot_tiddly_LDADD = libcoot-tw.la \
-- $(GTKCANVAS_LIBS) \
-- @GTK_LIBS@
--
-+coot_tiddly_LDADD = libcoot-tw.la
-
- # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao
-
diff --git a/sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch b/sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch
deleted file mode 100644
index d0f57b287426..000000000000
--- a/sci-chemistry/coot/files/0.3.3-link-against-guile-gtk-properly.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff -urN coot-0.3.3.orig/macros/guile-gtk.m4 coot-0.3.3/macros/guile-gtk.m4
---- coot-0.3.3.orig/macros/guile-gtk.m4 2007-08-15 12:20:04.000000000 -0700
-+++ coot-0.3.3/macros/guile-gtk.m4 2007-08-15 12:20:32.000000000 -0700
-@@ -66,9 +66,9 @@
- # we have the variable coot_gtk2 in configure.in, which is either TRUE or FALSE
- # Let's use that here. Perhaps there is a better (set by gtk macro?) variable?
- if test $coot_gtk2 = TRUE ; then
-- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-2.0.la
-+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-2.0"
- else
-- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-1.2.la
-+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-1.2"
- fi
- # do we need to set this in fact?
- GUILE_GTK_CFLAGS="-I$guile_gtk_prefix/include"
diff --git a/sci-chemistry/coot/files/0.4_pre2-as-needed.patch b/sci-chemistry/coot/files/0.4_pre2-as-needed.patch
deleted file mode 100644
index ed533252ab38..000000000000
--- a/sci-chemistry/coot/files/0.4_pre2-as-needed.patch
+++ /dev/null
@@ -1,490 +0,0 @@
-Index: mini-mol/Makefile.am
-===================================================================
---- mini-mol/Makefile.am (revision 555)
-+++ mini-mol/Makefile.am (working copy)
-@@ -32,8 +32,9 @@
- testminimol_SOURCES = testminimol.cc
-
- libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc
-+libcoot_mini_mol_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(CLIPPER_LIBS)
-
- testminimol_LDADD = libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ $(MMDB_LIBS)
-Index: coords/Makefile.am
-===================================================================
---- coords/Makefile.am (revision 555)
-+++ coords/Makefile.am (working copy)
-@@ -37,4 +37,6 @@
- libcoot_coords_la_SOURCES = Bond_lines.cc Cartesian.cc cos-sin.cc \
- mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \
- Bond_lines_ext.cc coot-close.cc
--
-+libcoot_coords_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/mini-mol/libcoot-mini-mol.la
-Index: ligand/Makefile.am
-===================================================================
---- ligand/Makefile.am (revision 555)
-+++ ligand/Makefile.am (working copy)
-@@ -44,6 +44,16 @@
- wiggly-ligand.cc monomer-utils.cc dunbrack.cc chi-angles-autogen.cc \
- chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc \
- richardson-rotamers.cc richardson-rotamer.cc rotamer.cc
-+libcoot_ligand_la_LIBADD = \
-+ $(top_builddir)/ideal/libcoot-ideal.la \
-+ $(top_builddir)/coords/libcoot-coords.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-+ $(top_builddir)/coot-utils/libcoot-map-utils.la \
-+ $(top_builddir)/db-main/libcoot-db-main.la \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/geometry/libcoot-geometry.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la
-
- AM_CXXFLAGS = \
- -DPKGDATADIR='"$(pkgdatadir)"' \
-@@ -61,35 +71,17 @@
- test_random_SOURCES = test-random.cc
- test_random_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- test_helix_placement_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -97,19 +89,10 @@
-
- test_fffear_in_coot_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-map-heavy.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -121,33 +104,15 @@
-
- findligand_real_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- findwaters_real_LDADD = \
- ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
-@@ -168,17 +133,8 @@
- testdunbrack_SOURCES = testdunbrack.cc
-
- testdunbrack_LDADD = ./libcoot-ligand.la \
-- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
-- $(top_builddir)/db-main/libcoot-db-main.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-
- # lib coot-coords depends on mmdb, even though Cartesian doesn't
-Index: analysis/Makefile.am
-===================================================================
---- analysis/Makefile.am (revision 555)
-+++ analysis/Makefile.am (working copy)
-@@ -9,6 +9,7 @@
- $(MMDB_CXXFLAGS)
-
- libcoot_analysis_la_SOURCES = bfkurt.cc
-+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la
-
- bin_PROGRAMS = bfactan
-
-@@ -16,7 +17,6 @@
-
- bfactan_LDADD = \
- libcoot-analysis.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(CLIPPER_LIBS) \
-Index: skeleton/Makefile.am
-===================================================================
---- skeleton/Makefile.am (revision 555)
-+++ skeleton/Makefile.am (working copy)
-@@ -36,8 +36,8 @@
-
-
- libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources)
-+libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la
-
--
- # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2
-
- # ncssearch_SOURCES = ncs-search.cc ncs-search.h
-Index: coot-surface/Makefile.am
-===================================================================
---- coot-surface/Makefile.am (revision 555)
-+++ coot-surface/Makefile.am (working copy)
-@@ -25,3 +25,4 @@
-
- libcoot_surface_la_SOURCES = \
- coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h
-+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la
-Index: high-res/Makefile.am
-===================================================================
---- high-res/Makefile.am (revision 555)
-+++ high-res/Makefile.am (working copy)
-@@ -39,13 +39,16 @@
-
- libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
- sequence-assignment.cc
-+libcoot_high_res_la_LIBADD = \
-+ $(top_builddir)/ligand/libcoot-ligand.la \
-+ $(top_builddir)/coot-utils/libcoot-map-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- noinst_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein
-
- testatomgraph_SOURCES = test-atom-graph.cc
-
- testatomgraph_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-@@ -53,90 +56,73 @@
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
- testseqassignment_SOURCES = testseqassignment.cc
- testseqassignment_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
- # tracehighres_LDFLAGS = -static
- tracehighres_SOURCES = trace-high-res.cc
- tracehighres_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
--
- testseqalign_SOURCES = testseqalign.cc
-
- # why do we need to link with all this (junk)?
- testseqalign_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
--
- globularize_protein_SOURCES = globularize.cc
-
- globularize_protein_LDADD = libcoot-high-res.la \
-- $(top_builddir)/ligand/libcoot-ligand.la \
- $(top_builddir)/db-main/libcoot-db-main.la \
- $(top_builddir)/ideal/libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
- $(top_builddir)/coords/libcoot-coords.la \
- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-map-utils.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
- $(top_builddir)/coot-utils/libcoot-shelx.la \
- $(top_builddir)/coot-utils/libcoot-utils.la \
- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \
- $(top_builddir)/compat/libcoot-compat.la \
-- $(GSL_LIBS) \
-- $(CLIPPER_LIBS)
-+ $(GSL_LIBS)
-
--
-Index: cootaneer/Makefile.am
-===================================================================
---- cootaneer/Makefile.am (revision 555)
-+++ cootaneer/Makefile.am (working copy)
-@@ -34,6 +34,7 @@
- buccaneer-sequence.cpp cootaneer-sequence.cpp \
- buccaneer-lib.h buccaneer-prot.h \
- buccaneer-sequence.h cootaneer-sequence.h
-+libcootaneer_la_LIBADD = $(CLIPPER_LIBS)
-
- subpkgdatadir = $(pkgdatadir)
- subpkgdata_DATA = cootaneer-llk-2.40.dat
-Index: geometry/Makefile.am
-===================================================================
---- geometry/Makefile.am (revision 555)
-+++ geometry/Makefile.am (working copy)
-@@ -34,6 +34,9 @@
- libcoot_geometry_a_sources = protein-geometry.cc protein-geometry-mmdb.cc
-
- libcoot_geometry_la_SOURCES = $(libcoot_geometry_a_sources)
-+libcoot_geometry_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- # libcoot_geometry_la_CXXFLAGS = -g -O1
-
-@@ -41,6 +44,4 @@
-
- test_geometry_SOURCES = test-geometry.cc
-
--test_geometry_LDADD = ./libcoot-geometry.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+test_geometry_LDADD = ./libcoot-geometry.la
-Index: ideal/Makefile.am
-===================================================================
---- ideal/Makefile.am (revision 555)
-+++ ideal/Makefile.am (working copy)
-@@ -44,6 +44,12 @@
- AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
-
- libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc
-+libcoot_ideal_la_LIBADD = \
-+ $(top_builddir)/coot-utils/libcoot-utils.la \
-+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-+ $(top_builddir)/coot-utils/libcoot-shelx.la \
-+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-+ $(GSL_LIBS)
-
- noinst_PROGRAMS = test-indexing with-geometry with-map
- # bin_PROGRAMS =
-@@ -61,32 +67,20 @@
- with_geometry_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- with_map_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
- $(top_builddir)/coords/libcoot-coords.la \
-- $(top_builddir)/coot-utils/libcoot-shelx.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
-- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(top_builddir)/compat/libcoot-compat.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
- test_indexing_LDADD = \
- ./libcoot-ideal.la \
- $(top_builddir)/geometry/libcoot-geometry.la \
-- $(top_builddir)/mini-mol/libcoot-mini-mol.la \
-- $(top_builddir)/coot-utils/libcoot-coord-extras.la \
- $(top_builddir)/coot-utils/libcoot-coord-utils.la \
-- $(top_builddir)/coot-utils/libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS)
-+ $(CLIPPER_LIBS) $(MMDB_LIBS)
-
-Index: tw/Makefile.am
-===================================================================
---- tw/Makefile.am (revision 555)
-+++ tw/Makefile.am (working copy)
-@@ -39,15 +39,15 @@
- include_HEADERS = coot-tw.hh
-
- libcoot_tw_la_SOURCES = tw.cc
-+libcoot_tw_la_LIBADD = \
-+ $(GTKCANVAS_LIBS) \
-+ @GTK_LIBS@
-
- noinst_PROGRAMS = coot-tiddly
-
- coot_tiddly_SOURCES = tiddly.cc
-
--coot_tiddly_LDADD = libcoot-tw.la \
-- $(GTKCANVAS_LIBS) \
-- @GTK_LIBS@
-+coot_tiddly_LDADD = libcoot-tw.la
-
--
- # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao
-
-Index: coot-utils/Makefile.am
-===================================================================
---- coot-utils/Makefile.am (revision 555)
-+++ coot-utils/Makefile.am (working copy)
-@@ -49,9 +49,11 @@
-
- # for pure coordinates (mmdb) things
- libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc
-+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la
-
- # shelx
- libcoot_shelx_la_SOURCES = coot-shelx-ins.cc
-+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la
-
- # for non-simple coordinates things
- libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc
-@@ -61,21 +63,20 @@
-
- # for map things that need mmdb, clipper, gsl and other things
- libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc
-+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS)
-
- noinst_PROGRAMS = testshelxreader testcootutils
-
- testshelxreader_SOURCES = test-shelx-reader.cc
- testshelxreader_LDADD = \
- ./libcoot-shelx.la \
-- ./libcoot-coord-utils.la \
-- ./libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ ./libcoot-utils.la
-
- testcootutils_SOURCES = test-utils.cc
- testcootutils_LDADD = \
- ./libcoot-shelx.la \
- ./libcoot-coord-utils.la \
- ./libcoot-utils.la \
-- $(CLIPPER_LIBS) $(MMDB_LIBS)
-+ $(MMDB_LIBS)
-
-
-Index: Makefile.am
-===================================================================
---- Makefile.am (revision 555)
-+++ Makefile.am (working copy)
-@@ -25,10 +25,10 @@
-
- # see configure.in for po intl
- SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \
-- skeleton ccp4mg-utils density-contour coords angles \
-- mini-mol db-main geometry \
-+ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \
-+ db-main geometry \
- ideal ligand high-res build greg-tests \
-- analysis sequence-view tw atom-utils cootaneer src doc
-+ analysis sequence-view tw cootaneer src doc
-
- # po, no po today.
-
diff --git a/sci-chemistry/coot/files/0.4_pre2-link-against-guile-gtk-properly.patch b/sci-chemistry/coot/files/0.4_pre2-link-against-guile-gtk-properly.patch
deleted file mode 100644
index cb777cefafa0..000000000000
--- a/sci-chemistry/coot/files/0.4_pre2-link-against-guile-gtk-properly.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff -ur coot-0.4-pre-1.orig/macros/guile-gtk.m4 coot-0.4-pre-1/macros/guile-gtk.m4
---- coot-0.4-pre-1.orig/macros/guile-gtk.m4 2007-11-07 18:25:15.000000000 -0800
-+++ coot-0.4-pre-1/macros/guile-gtk.m4 2007-11-07 18:25:20.000000000 -0800
-@@ -66,9 +66,9 @@
- # we have the variable coot_gtk2 in configure.in, which is either TRUE or FALSE
- # Let's use that here. Perhaps there is a better (set by gtk macro?) variable?
- if test $coot_gtk2 = TRUE ; then
-- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-2.0.la
-+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-2.0"
- else
-- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-1.2.la
-+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-1.2"
- fi
- # do we need to set this in fact?
- GUILE_GTK_CFLAGS="-I$guile_gtk_prefix/include"
diff --git a/sci-chemistry/coot/files/0.4_pre2-r549-fix-namespace-error.patch b/sci-chemistry/coot/files/0.4_pre2-r549-fix-namespace-error.patch
deleted file mode 100644
index 5bf8a2d4be88..000000000000
--- a/sci-chemistry/coot/files/0.4_pre2-r549-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 b3c632b0e19e..000000000000
--- 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 beb1859e36bc..000000000000
--- 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
-])