Bump to 0.4 prerelease, unkeyworded. Use a package.keywords entry with '**' for the keyword to install.

Package-Manager: portage-2.1.4_rc9

7 files changed, 724 insertions, 5 deletions

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 77b6dba82e9c..534b9871b2bb 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.14 2007/08/16 06:05:12 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.15 2007/12/19 18:46:31 dberkholz Exp $
+
+*coot-0.4_pre2-r549 (19 Dec 2007)
+
+  19 Dec 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/0.4_pre2-as-needed.patch,
+  +files/0.4_pre2-link-against-guile-gtk-properly.patch,
+  +files/0.4_pre2-r549-fix-namespace-error.patch,
+  +coot-0.4_pre2-r549.ebuild:
+  Bump to 0.4 prerelease, unkeyworded. Use a package.keywords entry with '**'
+  for the keyword to install.
 
 *coot-0.3.3 (16 Aug 2007)
 
diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index fe571b45450f..b548a71bbb28 100644
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -1,3 +1,6 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 0.3.1-as-needed.patch 18766 RMD160 00b020d46457f9e335b92c2f48088cdc950fce3a SHA1 bd2835ba0a974c8e01d6fa30f670827e6e72fc70 SHA256 cb395ba53839e16aa9e3248b2cfb16794c137730e02a41ca80927538717c4d83
 MD5 5c1b5db01f341e29a1c366002e3cc789 files/0.3.1-as-needed.patch 18766
 RMD160 00b020d46457f9e335b92c2f48088cdc950fce3a files/0.3.1-as-needed.patch 18766
@@ -18,9 +21,22 @@ AUX 0.3.3-link-against-guile-gtk-properly.patch 785 RMD160 7c98e6510b484baa6a47c
 MD5 b7801512f56bd0fe6f40a34c8488a493 files/0.3.3-link-against-guile-gtk-properly.patch 785
 RMD160 7c98e6510b484baa6a47cd12e219d6c45ce3344a files/0.3.3-link-against-guile-gtk-properly.patch 785
 SHA256 b92ca0f392b9ad7d6afe89fd69be91506e494651492544e9e8eb92cd3878ba81 files/0.3.3-link-against-guile-gtk-properly.patch 785
+AUX 0.4_pre2-as-needed.patch 19258 RMD160 a9ad8cbc84f9c2a35edb9ea7ec8926c3c4eb9491 SHA1 b49cee7d3cb03e1c4ac4c7c65e71cde99b9fa19d SHA256 a3c3bc4ac1ba9c2f7c6bed75b99f777f568989fc39253f352000f012949e87ab
+MD5 e9e4d4ec6f63e1e44e65e45ca3203fbe files/0.4_pre2-as-needed.patch 19258
+RMD160 a9ad8cbc84f9c2a35edb9ea7ec8926c3c4eb9491 files/0.4_pre2-as-needed.patch 19258
+SHA256 a3c3bc4ac1ba9c2f7c6bed75b99f777f568989fc39253f352000f012949e87ab files/0.4_pre2-as-needed.patch 19258
+AUX 0.4_pre2-link-against-guile-gtk-properly.patch 800 RMD160 e4a9931de152385d552542e11d9a74a548810964 SHA1 74264270682a9135af92bf40a030c008876252e4 SHA256 c7271c82bb6e9e1ba89096ef0a7416609a81b455a1633637b84952db686d5080
+MD5 3017de95bc2f50ea6f2d43b2026b4ad6 files/0.4_pre2-link-against-guile-gtk-properly.patch 800
+RMD160 e4a9931de152385d552542e11d9a74a548810964 files/0.4_pre2-link-against-guile-gtk-properly.patch 800
+SHA256 c7271c82bb6e9e1ba89096ef0a7416609a81b455a1633637b84952db686d5080 files/0.4_pre2-link-against-guile-gtk-properly.patch 800
+AUX 0.4_pre2-r549-fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
+MD5 8f25b9b99631f20b7e8106ca190cdb29 files/0.4_pre2-r549-fix-namespace-error.patch 1081
+RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 files/0.4_pre2-r549-fix-namespace-error.patch 1081
+SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb files/0.4_pre2-r549-fix-namespace-error.patch 1081
 DIST coot-0.1.2.tar.gz 2704638 RMD160 bb0ff46297fc7135b1bf31159bf41b18462b916c SHA1 66f4b13f37cab6537b454a0ad23050044eb4a95f SHA256 fcd2e5862ef57baffc19aa30b1bb48b5271baf0667cc72bf5ecd8a02911fe22a
 DIST coot-0.3.1.tar.gz 3708033 RMD160 8fefe5498171563d0ee660c87175b9af419f07ca SHA1 d612fde00e538682f64c4d204b27556fa742de5e SHA256 f13142b478a1bc9c94a242dd0bf18ac074707f7bd80bf72c8f0f906675099a34
 DIST coot-0.3.3.tar.gz 3870046 RMD160 b23ca227894a469456c5af0284d0bb8530c855b5 SHA1 63755615b05572b43e8f0768a5c0315191f698bf SHA256 f3a7d6f789846b1f7670d4dc3e61a430cbab811f2f22349b84f49e10aaa4a41c
+DIST coot-0.4-pre-2-revision-549.tar.gz 5732300 RMD160 20020fc02dc6e44fc12ac392a7dc35d9f9885bec SHA1 8ae8302b7d32c31860e30c625f2899dd2436cafc SHA256 01cc5ad8d5331cbcb902d40abf4219795c482c42a0ef99347f4fe97a6d7f71c4
 EBUILD coot-0.1.2.ebuild 2308 RMD160 b59de80ec0ab129eb3d739710d9f07388e6582e0 SHA1 d534ac54efd5b2a8be66b5e23e6992d49419d625 SHA256 6ce0825594abf6d21ac17cdc715cb2c9d522b809f798a7f1d70cc6cd8c392717
 MD5 d61e130fcb36e9fbc37937d6fce495c7 coot-0.1.2.ebuild 2308
 RMD160 b59de80ec0ab129eb3d739710d9f07388e6582e0 coot-0.1.2.ebuild 2308
@@ -33,10 +49,14 @@ EBUILD coot-0.3.3.ebuild 3156 RMD160 8e0eafaee723edcac57a246e96e8bdfb473ff8d6 SH
 MD5 b6d771a431db0f7f1ea348891697aab4 coot-0.3.3.ebuild 3156
 RMD160 8e0eafaee723edcac57a246e96e8bdfb473ff8d6 coot-0.3.3.ebuild 3156
 SHA256 f7b72e46e5294c70601a1de7cd4b5f6fca44608e21df4bb0ecc61c7981b0712b coot-0.3.3.ebuild 3156
-MISC ChangeLog 2615 RMD160 33a67e92960400c04d0a94d231c98411d50e90b6 SHA1 6e48a8d2559843c5e389a51413e0e935e50210ad SHA256 7ca40221006727ac6893b49d6173f08cdeb58df5314943eef032e26502171d2a
-MD5 34447bee5df5f87d055742c5a5b96df6 ChangeLog 2615
-RMD160 33a67e92960400c04d0a94d231c98411d50e90b6 ChangeLog 2615
-SHA256 7ca40221006727ac6893b49d6173f08cdeb58df5314943eef032e26502171d2a ChangeLog 2615
+EBUILD coot-0.4_pre2-r549.ebuild 3223 RMD160 3d2722459c85ef138d7a4727eac949196520ab6e SHA1 0961456dda5f305776a03e942a4ffd4d687b9c64 SHA256 d28b84bcbaad0163212bca3d1d40698dfcefa24c0f9ff2137be08a2ba506cdce
+MD5 4031c4bb10b7e955d7ac9589eb082de3 coot-0.4_pre2-r549.ebuild 3223
+RMD160 3d2722459c85ef138d7a4727eac949196520ab6e coot-0.4_pre2-r549.ebuild 3223
+SHA256 d28b84bcbaad0163212bca3d1d40698dfcefa24c0f9ff2137be08a2ba506cdce coot-0.4_pre2-r549.ebuild 3223
+MISC ChangeLog 2986 RMD160 55c48ee737e5d7e53e4fd2d7727138f341fcbb2b SHA1 51784830d7c34edbc6842e04ffe44ac6be4e4e6c SHA256 5c3d41cebdea213d876641161a2ea0e2191aa313631f0fd0b12af9b35feb015b
+MD5 0de20aac527aea5f5af8ae542a094013 ChangeLog 2986
+RMD160 55c48ee737e5d7e53e4fd2d7727138f341fcbb2b ChangeLog 2986
+SHA256 5c3d41cebdea213d876641161a2ea0e2191aa313631f0fd0b12af9b35feb015b ChangeLog 2986
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -50,3 +70,13 @@ SHA256 2a6628adb6460117d951325f2e7bfc3ecaf3123ad537352b1f3d8f55df3fc1ce files/di
 MD5 c9c3622fb7c8a17578cfa47243a1a425 files/digest-coot-0.3.3 235
 RMD160 5ddddb6896b9284ecdf848e1cb423c25d9f6b2ad files/digest-coot-0.3.3 235
 SHA256 b2f9df048652f39fd7e4e147cc12ce41ce468a25677b5426990d772ceb7588c6 files/digest-coot-0.3.3 235
+MD5 df50204cd276e527c0df472e37442688 files/digest-coot-0.4_pre2-r549 286
+RMD160 ea513a058998da42468a47c8f00a7b4f590227b3 files/digest-coot-0.4_pre2-r549 286
+SHA256 f1402a02f61d1cc4e526895914a694d2a5dc1a5b036bc68ce774e3fd1fa1bb2b files/digest-coot-0.4_pre2-r549 286
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.7 (GNU/Linux)
+
+iD8DBQFHaWcPXVaO67S1rtsRArxtAJ0Rg8B9WcfWsfIN68Brfy3h8LW+XgCgk7GH
+HIl093uG7g0aCXY7Ltlpw3w=
+=uls/
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/coot/coot-0.4_pre2-r549.ebuild b/sci-chemistry/coot/coot-0.4_pre2-r549.ebuild
new file mode 100644
index 000000000000..dc1fce8b52fc
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.4_pre2-r549.ebuild
@@ -0,0 +1,119 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.4_pre2-r549.ebuild,v 1.1 2007/12/19 18:46:31 dberkholz Exp $
+
+inherit autotools eutils
+
+MY_S_PV=${PV/_pre/-pre-}-${PR/r/revision-}
+MY_S_P=${PN}-${MY_S_PV}
+MY_PV=${PV/_pre/-pre-}
+MY_P=${PN}-${MY_PV}
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~emsley/coot/"
+if [[ ${MY_PV} = *pre* ]]; then
+	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/pre-release/${MY_S_P}.tar.gz"
+else
+	SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${MY_P}.tar.gz"
+fi
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+RDEPEND=">=sci-libs/gsl-1.3
+	>=x11-libs/gtk+-2.2
+	gnome-base/libgnomecanvas
+	=x11-libs/guile-gtk-2*
+	x11-libs/gtkglext
+	virtual/glut
+	virtual/opengl
+	sci-chemistry/ccp4
+	dev-lang/python
+	dev-scheme/guile-gui
+	dev-scheme/net-http
+	dev-scheme/goosh
+	dev-scheme/guile-www
+	sci-libs/coot-data
+	sci-chemistry/reduce
+	sci-chemistry/probe
+	>=sci-libs/clipper-20070907
+	<sci-libs/mmdb-1.0.10"
+# These are still required to run autoreconf
+RDEPEND="${RDEPEND}
+	=dev-libs/glib-1.2*
+	=x11-libs/gtkglarea-1.2*"
+DEPEND="${RDEPEND}
+	dev-lang/swig"
+S="${WORKDIR}/${MY_P}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${PV}-as-needed.patch
+	epatch "${FILESDIR}"/${PV}-link-against-guile-gtk-properly.patch
+	epatch "${FILESDIR}"/${PVR}-fix-namespace-error.patch
+
+	# Link against single-precision fftw
+	sed -i \
+		-e "s:lfttw:lsfttw:g" \
+		-e "s:lrfttw:lsrfttw:g" \
+		"${S}"/macros/clipper.m4
+
+	# Fix where it looks for some binaries
+	sed -i \
+		-e "s:/y/people/emsley/coot/Linux/bin/probe.2.11.050121.linux.RH9:/usr/bin/probe:g" \
+		-e "s:/y/people/emsley/coot/Linux/bin/reduce.2.21.030604:/usr/bin/reduce:g" \
+		"${S}"/scheme/group-settings.scm
+
+	# Look for clipper slotted with '-2' suffix
+	sed -i \
+		-e "s~\(-lclipper[[:alnum:]-]*\)~\1-2~g" \
+		"${S}"/macros/clipper.m4 \
+		|| die "sed to find -2 slotted libraries failed"
+	grep 'include.*clipper' -rl . \
+		| xargs sed -i \
+			-e "s~\(include.*clipper\)/~\1-2/~g" \
+			|| die "sed to find -2 slotted headers failed"
+
+	cd "${S}"
+	AT_M4DIR="macros" eautoreconf
+}
+
+src_compile() {
+	# All the --with's are used to activate various parts.
+	# Yes, this is broken behavior.
+	econf \
+		--includedir='${prefix}/include/coot' \
+		--with-gtkcanvas-prefix=/usr \
+		--with-clipper-prefix=/usr \
+		--with-mmdb-prefix=/usr \
+		--with-ssmlib-prefix=/usr \
+		--with-guile=/usr \
+		--with-python=/usr \
+		--with-guile-gtk \
+		--with-gtk2 \
+		|| die "econf failed"
+
+	# Regenerate wrappers, otherwise at least gtk-2 build fails
+	pushd src
+	rm -f coot_wrap_python.cc coot_wrap_python_pre.cc \
+		&& emake coot_wrap_python.cc \
+		|| die "failed to regenerate python wrapper"
+
+	rm -f coot_wrap_guile.cc coot_wrap_guile_pre.cc \
+		&& emake coot_wrap_guile.cc \
+		||die "failed to regenerate guile wrapper"
+	popd
+
+	# Parallel build's broken
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	emake -j1 DESTDIR="${D}" install || die "install failed"
+
+	# Install misses this
+	insinto /usr/share/coot/python
+	doins "${S}"/src/coot.py
+}
diff --git a/sci-chemistry/coot/files/0.4_pre2-as-needed.patch b/sci-chemistry/coot/files/0.4_pre2-as-needed.patch
new file mode 100644
index 000000000000..ed533252ab38
--- /dev/null
+++ b/sci-chemistry/coot/files/0.4_pre2-as-needed.patch
@@ -0,0 +1,490 @@
+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
new file mode 100644
index 000000000000..cb777cefafa0
--- /dev/null
+++ b/sci-chemistry/coot/files/0.4_pre2-link-against-guile-gtk-properly.patch
@@ -0,0 +1,15 @@
+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
new file mode 100644
index 000000000000..5bf8a2d4be88
--- /dev/null
+++ b/sci-chemistry/coot/files/0.4_pre2-r549-fix-namespace-error.patch
@@ -0,0 +1,52 @@
+--- 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/digest-coot-0.4_pre2-r549 b/sci-chemistry/coot/files/digest-coot-0.4_pre2-r549
new file mode 100644
index 000000000000..a9b85c5d267a
--- /dev/null
+++ b/sci-chemistry/coot/files/digest-coot-0.4_pre2-r549
@@ -0,0 +1,3 @@
+MD5 3ef70fd7723aef5080f4bcecfe363e6b coot-0.4-pre-2-revision-549.tar.gz 5732300
+RMD160 20020fc02dc6e44fc12ac392a7dc35d9f9885bec coot-0.4-pre-2-revision-549.tar.gz 5732300
+SHA256 01cc5ad8d5331cbcb902d40abf4219795c482c42a0ef99347f4fe97a6d7f71c4 coot-0.4-pre-2-revision-549.tar.gz 5732300