commit: 20873c20812ebb870e9fdce159daa1da97cea074
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 15 13:34:07 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 15 13:34:07 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=20873c20
sci-chemistry/coot: Fix for latest HEAD
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-chemistry/coot/coot-9999.ebuild | 76 +-
sci-chemistry/coot/files/9999-pc.patch | 1047 ---------------------
sci-chemistry/coot/files/coot-9999-desktop.patch | 21 +
sci-chemistry/coot/files/coot-9999-libguile.patch | 29 +
sci-chemistry/coot/files/coot-9999-libtool.patch | 39 +
5 files changed, 126 insertions(+), 1086 deletions(-)
diff --git a/sci-chemistry/coot/coot-9999.ebuild
b/sci-chemistry/coot/coot-9999.ebuild
index 1ea16a3..d6b0be9 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
AUTOTOOLS_AUTORECONF="true"
-inherit autotools-utils python-single-r1 subversion toolchain-funcs versionator
+inherit autotools-utils git-r3 python-single-r1 toolchain-funcs versionator
MY_S2_PV=$(replace_version_separator 2 - ${PV})
MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
@@ -17,9 +17,9 @@ MY_PV=${PV}
MY_P=${PN}-${MY_PV}
DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building,
completion and validation"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/";
-SRC_URI="test? (
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/data/greg-data.tar.gz )"
-ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk";
+HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/";
+SRC_URI="test? (
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
+EGIT_REPO_URI="https://github.com/pemsley/coot.git";
SLOT="0"
LICENSE="GPL-3"
@@ -31,25 +31,26 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
AUTOTOOLS_IN_SOURCE_BUILD=1
SCIDEPS="
- >=sci-libs/ccp4-libs-6.1
+ sci-libs/libccp4
sci-libs/clipper
>=sci-libs/coot-data-2
>=sci-libs/gsl-1.3
- >=sci-libs/mmdb-1.23
- sci-libs/ssm
+ sci-libs/fftw:2.1=
+ sci-libs/mmdb:2
sci-libs/monomer-db
+ sci-libs/ssm
sci-chemistry/reduce
- sci-chemistry/refmac
sci-chemistry/probe"
XDEPS="
gnome-base/libgnomecanvas
gnome-base/librsvg:2
- media-libs/libpng
+ media-libs/libpng:0=
media-libs/freeglut
x11-libs/gtk+:2
x11-libs/goocanvas:0
- x11-libs/gtkglext"
+ x11-libs/gtkglext
+ virtual/opengl"
SCHEMEDEPS="
dev-scheme/net-http
@@ -63,18 +64,23 @@ RDEPEND="
${XDEPS}
${SCHEMEDEPS}
${PYTHON_DEPS}
+ dev-db/sqlite:3
+ dev-libs/boost:0=[python,${PYTHON_USEDEP}]
+ dev-libs/glib:2
+ >=dev-libs/gmp-4.2.2-r2:0=
+ dev-python/pygobject:2[${PYTHON_USEDEP}]
dev-python/pygtk:2[${PYTHON_USEDEP}]
- >=dev-libs/gmp-4.2.2-r2
>=net-misc/curl-7.19.6
- net-dns/libidn"
+ net-dns/libidn
+ sys-libs/readline:0=
+ "
DEPEND="${RDEPEND}
+ virtual/pkgconfig
>=sys-devel/libtool-2.4-r2
dev-lang/swig
sys-devel/bc
test? ( dev-scheme/greg )"
-S="${WORKDIR}"
-
pkg_setup() {
if use openmp; then
tc-has-openmp || die "Please use an OPENMP capable compiler"
@@ -83,53 +89,44 @@ pkg_setup() {
}
PATCHES=(
- "${FILESDIR}"/${PV}-pc.patch
+ "${FILESDIR}"/${P}-desktop.patch
"${FILESDIR}"/${P}-sandbox-icons.patch
+ "${FILESDIR}"/${P}-libtool.patch
+ "${FILESDIR}"/${P}-libguile.patch
)
src_unpack() {
- subversion_src_unpack
+ git-r3_src_unpack
if use test; then
+ cd "${S}" || die
unpack ${A}
- ln -sf . "${S}"/coot-ccp4
+ ln -sf . "${S}"/coot-ccp4 || die
fi
}
src_prepare() {
sed \
-e
"s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ;
AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
- -i configure.in || die
+ -i configure.ac || die
autotools-utils_src_prepare
-
- cat >> src/svn-revision.cc <<- EOF
- extern "C" {
- int svn_revision() {
- return ${ESVN_WC_REVISION:-0};
- }
- }
- EOF
}
src_configure() {
# All the --with's are used to activate various parts.
# Yes, this is broken behavior.
local myeconfargs=(
- --includedir='${prefix}/include/coot'
--with-goocanvas-prefix="${EPREFIX}/usr"
- --with-guile
+ --with-guile="${EPREFIX}/usr"
--with-python="${EPREFIX}/usr"
--with-guile-gtk
- --with-pygtk
- $(use_enable openmp)
+ --with-pygtk="${EPREFIX}/usr"
+ --with-sqlite3
+ --with-boost="${EPREFIX}/usr"
)
autotools-utils_src_configure
}
-src_compile() {
- autotools-utils_src_compile
- cp "${S}"/src/coot_gtk2.py python/coot.py || die
-}
src_test() {
source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
mkdir "${T}"/coot_test || die
@@ -143,10 +140,11 @@ src_test() {
export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
export PYTHONHOME="${EPREFIX}"/usr/
export CCP4_SCR="${T}"/coot_test/
- export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/"
+ export CLIBD_MON="${EPREFIX}/usr/share/data/monomers/"
+ export COOT_REF_STRUCTS="${EPREFIX}/usr/share/data/monomers/"
export SYMINFO="${S}/syminfo.lib"
- export COOT_TEST_DATA_DIR="${S}"/data/greg-data/
+ export COOT_TEST_DATA_DIR="${S}"/greg-data/
cat > command-line-greg.scm <<- EOF
(use-modules (ice-9 greg))
@@ -172,6 +170,6 @@ src_test() {
einfo "CLIBD_MON ${CLIBD_MON}"
einfo "SYMINFO ${SYMINFO}"
- "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
- "${S}"/src/coot-real --no-graphics --script
python-tests/coot_unittest.py || die
+ "${S}"/src/coot-bin --no-graphics --script command-line-greg.scm || die
+ "${S}"/src/coot-bin --no-graphics --script
python-tests/coot_unittest.py || die
}
diff --git a/sci-chemistry/coot/files/9999-pc.patch
b/sci-chemistry/coot/files/9999-pc.patch
deleted file mode 100644
index 32d08e1..0000000
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ /dev/null
@@ -1,1047 +0,0 @@
-diff --git a/ChangeLog b/ChangeLog
-index 46f6362..fd3fd9a 100644
---- a/ChangeLog
-+++ b/ChangeLog
-@@ -1963,7 +1963,7 @@
- 2005-01-29 Paul Emsley <paulems...@ysbl.york.ac.uk>
-
- * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in
-- MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel
-+ MMDBSSM_CFLAGS [Oops]. Hopefully fixes problems spotted by Joel
- Bard and Joseph Toth.
-
- * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add
-@@ -2256,14 +2256,14 @@
-
- 2004-11-20 Paul Emsley <paulems...@ysbl.york.ac.uk>
-
-- * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for
-+ * coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for
- coot-close.cc usage].
-
- 2004-11-19 Paul Emsley <paulems...@ysbl.york.ac.uk>
-
-- * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS
-+ * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS
-
-- * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS
-+ * analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS
-
- 2004-11-16 Paul Emsley <emsley@localhost>
-
-@@ -2273,7 +2273,7 @@
-
- 2004-11-15 Paul Emsley <emsley@localhost>
-
-- * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks
-+ * coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks
- Joseph Toth].
-
- * surface/CXXSphereNode.h: removed the ; again!
-diff --git a/analysis/Makefile.am b/analysis/Makefile.am
-index 8a873dc..ef4a9cf 100644
---- a/analysis/Makefile.am
-+++ b/analysis/Makefile.am
-@@ -8,8 +8,8 @@ pkgincludedir = $(includedir)/coot/analysis
-
- INCLUDES = \
- -I$(top_srcdir) \
-- $(CLIPPER_CXXFLAGS) \
-- $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) \
-+ $(MMDB_CFLAGS)
-
- libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc kolmogorov.hh kolmogorov.cc
cablam.hh cablam.cc
-
-diff --git a/angles/Makefile.am b/angles/Makefile.am
-index b89276d..935ce06 100644
---- a/angles/Makefile.am
-+++ b/angles/Makefile.am
-@@ -7,7 +7,7 @@ EXTRA_DIST = \
- pkginclude_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h
- pkgincludedir = $(includedir)/coot/angles
-
--INCLUDES = $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS)
-
- libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h \
- AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc
-diff --git a/auxil/catcheck/Makefile.am b/auxil/catcheck/Makefile.am
-index 41e1766..69e6091 100644
---- a/auxil/catcheck/Makefile.am
-+++ b/auxil/catcheck/Makefile.am
-@@ -1,7 +1,7 @@
-
- EXTRA_DIST = Makefile.simple
-
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
-
- check_PROGRAMS = catcheck
-
-diff --git a/auxil/catcheck/Makefile.simple b/auxil/catcheck/Makefile.simple
-index 5157398..0e25fb2 100644
---- a/auxil/catcheck/Makefile.simple
-+++ b/auxil/catcheck/Makefile.simple
-@@ -1,17 +1,17 @@
-
--# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-
-
- BASE = /home/paule/autobuild/Linux-kalypso-pre-release
--CLIPPER_CXXFLAGS = -I$(BASE)/include
--MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
-+CLIPPER_CFLAGS = -I$(BASE)/include
-+MMDB_CFLAGS = -I$(BASE)/include/mmdb
-
- CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
- -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- -lclipper-core -lccp4c -L$(BASE)/lib \
- -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
-
- catcheck: catcheck.cc catcheck.hh
-diff --git a/auxil/rama/Makefile.am b/auxil/rama/Makefile.am
-index cdbb54e..12c6731 100644
---- a/auxil/rama/Makefile.am
-+++ b/auxil/rama/Makefile.am
-@@ -1,7 +1,7 @@
-
- EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
-
- check_PROGRAMS = rama-data rama-doughnut
-diff --git a/auxil/rama/Makefile.simple b/auxil/rama/Makefile.simple
-index 10fe22e..715a270 100644
---- a/auxil/rama/Makefile.simple
-+++ b/auxil/rama/Makefile.simple
-@@ -1,12 +1,12 @@
-
--CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-
- CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
- -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
- -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw
-lz -lm
-
--INCLUDES = $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
-
- rama-data: rama-data.cc
-diff --git a/auxil/sec-str/Makefile.am b/auxil/sec-str/Makefile.am
-index 81f79e8..bfef73a 100644
---- a/auxil/sec-str/Makefile.am
-+++ b/auxil/sec-str/Makefile.am
-@@ -1,6 +1,6 @@
-
- EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
-
- #check_PROGRAMS = sec-str-dist-check
-
-diff --git a/auxil/sec-str/Makefile.simple b/auxil/sec-str/Makefile.simple
-index eb6db20..8b22930 100644
---- a/auxil/sec-str/Makefile.simple
-+++ b/auxil/sec-str/Makefile.simple
-@@ -1,27 +1,27 @@
-
--#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-+#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
-
- #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4
\
- # -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- # -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
- # -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw
-lz -lm
-
--#INCLUDES = $(CLIPPER_CXXFLAGS)
-+#INCLUDES = $(CLIPPER_CFLAGS)
- #LDLIBS = $(CLIPPER_LIBS)
-
-
- #
-
- BASE = /home/paule/autobuild/Linux-kalypso-pre-release
--CLIPPER_CXXFLAGS = -I$(BASE)/include
--MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
-+CLIPPER_CFLAGS = -I$(BASE)/include
-+MMDB_CFLAGS = -I$(BASE)/include/mmdb
-
- CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
- -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- -lclipper-core -lccp4c -L$(BASE)/lib \
- -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
-
- sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh
-diff --git a/auxil/strand-analysis/Makefile.am
b/auxil/strand-analysis/Makefile.am
-index 11686ba..9c24b3b 100644
---- a/auxil/strand-analysis/Makefile.am
-+++ b/auxil/strand-analysis/Makefile.am
-@@ -3,8 +3,8 @@ EXTRA_DIST = Makefile.simple strand-analysis.cc
-
-
- INCLUDES = -I$(top_srcdir)/auxil/sec-str \
-- $(MMDB_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS)
-+ $(MMDB_CFLAGS) \
-+ $(CLIPPER_CFLAGS)
-
-
- check_PROGRAMS =
-diff --git a/auxil/strand-analysis/Makefile.simple
b/auxil/strand-analysis/Makefile.simple
-index d5c21a4..2f58b8d 100644
---- a/auxil/strand-analysis/Makefile.simple
-+++ b/auxil/strand-analysis/Makefile.simple
-@@ -2,13 +2,13 @@
-
- CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based
-
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include
-
- CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \
- -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
- -lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm
-
--INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS)
-+INCLUDES = -I../sec-str $(CLIPPER_CFLAGS)
- LDLIBS = $(CLIPPER_LIBS)
-
- .cc:
-diff --git a/auxil/vectors/Makefile.am b/auxil/vectors/Makefile.am
-index 8826587..4a8d72e 100644
---- a/auxil/vectors/Makefile.am
-+++ b/auxil/vectors/Makefile.am
-@@ -1,6 +1,6 @@
-
- EXTRA_DIST = Makefile.simple diff-vec.cc
--INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
- check_PROGRAMS =
-
- #diff_vec_SOURCES = diff-vec.cc
-diff --git a/build/Makefile.am b/build/Makefile.am
-index 6afe5a3..748341b 100644
---- a/build/Makefile.am
-+++ b/build/Makefile.am
-@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/build
-
- INCLUDES = \
- -I$(top_srcdir) \
-- $(CLIPPER_CXXFLAGS) \
-- $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) \
-+ $(MMDB_CFLAGS)
-
- noinst_PROGRAMS = testcabuild
-
-diff --git a/ccp4mg-utils/Makefile.am b/ccp4mg-utils/Makefile.am
-index 7734f09..c58fe1d 100644
---- a/ccp4mg-utils/Makefile.am
-+++ b/ccp4mg-utils/Makefile.am
-@@ -26,7 +26,7 @@ pkgincludedir = $(includedir)/coot/ccp4mg-utils
- EXTRA_DIST = convert.sh get-new-utils.sh
-
- INCLUDES = \
-- $(MMDB_CXXFLAGS) \
-+ $(MMDB_CFLAGS) \
- $(LIBPNG_CFLAGS)
-
- libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \
-diff --git a/ccp4mg-utils/mmut/Makefile.am b/ccp4mg-utils/mmut/Makefile.am
-index d0651db..d4e0bf8 100755
---- a/ccp4mg-utils/mmut/Makefile.am
-+++ b/ccp4mg-utils/mmut/Makefile.am
-@@ -70,9 +70,9 @@ INCLUDES = \
- $(LIBGLADE_CFLAGS) \
- @GTK_CFLAGS@ \
- $(GLUT_CFLAGS) \
-- $(MMDBSSM_CXXFLAGS) \
-- $(MMDB_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS)
-+ $(MMDBSSM_CFLAGS) \
-+ $(MMDB_CFLAGS) \
-+ $(CLIPPER_CFLAGS)
-
- # $(WITH_SCRIPT_CFLAGS)
-
-diff --git a/ccp4mg-utils/pygl/Makefile.am b/ccp4mg-utils/pygl/Makefile.am
-index a7e68b5..e26a6c8 100755
---- a/ccp4mg-utils/pygl/Makefile.am
-+++ b/ccp4mg-utils/pygl/Makefile.am
-@@ -108,9 +108,9 @@ INCLUDES = \
- $(LIBGLADE_CFLAGS) \
- @GTK_CFLAGS@ \
- $(GLUT_CFLAGS) \
-- $(MMDBSSM_CXXFLAGS) \
-- $(MMDB_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS)
-+ $(MMDBSSM_CFLAGS) \
-+ $(MMDB_CFLAGS) \
-+ $(CLIPPER_CFLAGS)
-
- # $(WITH_SCRIPT_CFLAGS)
-
-diff --git a/ccp4mg-utils/util/Makefile.am b/ccp4mg-utils/util/Makefile.am
-index 399f453..3d2ff55 100755
---- a/ccp4mg-utils/util/Makefile.am
-+++ b/ccp4mg-utils/util/Makefile.am
-@@ -73,9 +73,9 @@ INCLUDES = \
- $(LIBGLADE_CFLAGS) \
- @GTK_CFLAGS@ \
- $(GLUT_CFLAGS) \
-- $(MMDBSSM_CXXFLAGS) \
-- $(MMDB_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS)
-+ $(MMDBSSM_CFLAGS) \
-+ $(MMDB_CFLAGS) \
-+ $(CLIPPER_CFLAGS)
-
- # $(WITH_SCRIPT_CFLAGS)
-
-diff --git a/configure.in b/configure.in
-index cc549a5..d56f856 100644
---- a/configure.in
-+++ b/configure.in
-@@ -108,14 +108,18 @@ esac
-
-
- dnl Check for MMDB.
--AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating
necessary mmdb; exit 1],,)])
-
--AM_WITH_MMDBSSM
-+PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM])
- AM_WITH_CCP4SRS
-
- dnl Check for Clipper. we exit if clipper is not found.
- #
--AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of
Clipper \(2.1-090520-ac or later\) is required now; exit
1],AC_MSG_ERROR([Cannot find Clipper]))
-+PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [
-+ CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS])
-+ ], [
-+ AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of
Clipper \(2.1-090520-ac or later\) is required now; exit
1],AC_MSG_ERROR([Cannot find Clipper]))
-+ ])
-
- # we set default coot_guile to true
- coot_guile=true
-@@ -186,11 +190,15 @@ AM_PATH_LIBGLADE
-
- dnl =========================== GooCanvas ================================
-
--AM_PATH_GOOCANVAS
--# give something for the preprocessor to chew on...
--if test "$GOOCANVAS_CFLAGS" != "" ; then
-- GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
--fi
-+PKG_CHECK_MODULES([GOOCANVAS], [goocanvas],
-+ [GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS";
AC_SUBST(GOOCANVAS_CFLAGS)],
-+ [
-+ AM_PATH_GOOCANVAS
-+ # give something for the preprocessor to chew on...
-+ if test "$GOOCANVAS_CFLAGS" != "" ; then
-+ GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
-+ fi
-+ ])
-
- AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with
optional complicated/experimental ligand-related dependencies ],
- coot_enhanced_ligand_additions="true",
-diff --git a/coords/Makefile.am b/coords/Makefile.am
-index 05fdf70..1e1c5d2 100644
---- a/coords/Makefile.am
-+++ b/coords/Makefile.am
-@@ -29,7 +29,7 @@ INCLUDES = \
- -I$(top_srcdir) \
- $(ENHANCED_LIGAND_TOOLS_CFLAGS) \
- $(RDKIT_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
- AM_CXXFLAGS = \
- -DPKGDATADIR='"$(pkgdatadir)"' \
-diff --git a/coot-surface/Makefile.am b/coot-surface/Makefile.am
-index d2243d6..2434219 100644
---- a/coot-surface/Makefile.am
-+++ b/coot-surface/Makefile.am
-@@ -19,7 +19,7 @@
- # 02110-1301, USA
-
- INCLUDES = -I$(top_srcdir) \
-- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
-+ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
-
- lib_LTLIBRARIES = libcoot-surface.la
-
-diff --git a/coot-utils/Makefile.am b/coot-utils/Makefile.am
-index 87810dc..c5b05b4 100644
---- a/coot-utils/Makefile.am
-+++ b/coot-utils/Makefile.am
-@@ -34,11 +34,10 @@ pkginclude_HEADERS = peak-search.hh coot-trim.hh \
- read-sm-cif.hh bonded-pairs.hh tree.hh helix-analysis.hh elastic.hh
- pkgincludedir = $(includedir)/coot/coot-utils
-
--
- INCLUDES = \
- -I$(top_srcdir) \
-- $(CLIPPER_CXXFLAGS) \
-- $(MMDB_CXXFLAGS) \
-+ $(CLIPPER_CFLAGS) \
-+ $(MMDB_CFLAGS) \
- $(GSL_CFLAGS) \
- $(WITH_GUILE_CFLAGS) \
- $(WITH_PYTHON_CFLAGS)
-diff --git a/cootaneer/Makefile.am b/cootaneer/Makefile.am
-index 3a1d720..cfca0fd 100644
---- a/cootaneer/Makefile.am
-+++ b/cootaneer/Makefile.am
-@@ -20,7 +20,7 @@
- EXTRA_DIST = \
- cootaneer-llk-2.40.dat
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
- cootaneer_demo_SOURCES = cootaneer-demo.cpp
-
-diff --git a/cootilus/Makefile.am b/cootilus/Makefile.am
-index 7e4169d..4492014 100644
---- a/cootilus/Makefile.am
-+++ b/cootilus/Makefile.am
-@@ -20,7 +20,7 @@
- EXTRA_DIST = \
- nautilus_lib.pdb
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
- cootilus_demo_SOURCES = cootilus-demo.cpp
-
-diff --git a/db-main/Makefile.am b/db-main/Makefile.am
-index 3a85b9e..1a11cdf 100644
---- a/db-main/Makefile.am
-+++ b/db-main/Makefile.am
-@@ -6,7 +6,7 @@ AM_CXXFLAGS = \
- -DDATADIR='"$(datadir)"'
-
- INCLUDES = -I$(top_srcdir) \
-- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
-
- pkginclude_HEADERS = db-main.hh db-strands.hh
- pkgincludedir = $(includedir)/coot/db-main
-diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..c207a43 100644
---- a/db-main/Makefile.simple
-+++ b/db-main/Makefile.simple
-@@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
- MCCP4 = $(HOME)/crystal
-
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include
-+MMDB_CFLAGS = -I$(MMDB)/include
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
-
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb
-@@ -28,9 +28,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
-
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
-
- CXXFLAGS = -g $(INCLUDES)
- LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS)
-@@ -44,4 +44,4 @@ libcoot-db-main.a: db-main.o
- db-main.o: db-main.cc db-main.hh
-
- testmmdbbits: testmmdbbits.cc
-- $(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@
-+ $(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@
-diff --git a/density-contour/Makefile.am b/density-contour/Makefile.am
-index 7f705e8..f5dcc00 100644
---- a/density-contour/Makefile.am
-+++ b/density-contour/Makefile.am
-@@ -20,7 +20,7 @@
-
- COORD_INCLUDES = -I$(top_srcdir)
-
--INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS)
-+INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS)
-
- lib_LTLIBRARIES = libcoot-isosurface.la
-
-diff --git a/geometry/Makefile.am b/geometry/Makefile.am
-index 6dd665f..57aaa04 100644
---- a/geometry/Makefile.am
-+++ b/geometry/Makefile.am
-@@ -26,7 +26,7 @@ pkginclude_HEADERS = protein-geometry.hh read-sbase.hh
lbg-graph.hh srs-interfa
- pkgincludedir = $(includedir)/coot/geometry
-
- INCLUDES = -I$(top_srcdir) \
-- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS)
-
- AM_CXXFLAGS = \
- -DDATADIR='"$(datadir)"' \
-diff --git a/geometry/Makefile.simple b/geometry/Makefile.simple
-index 370b2fa..c3b0106 100644
---- a/geometry/Makefile.simple
-+++ b/geometry/Makefile.simple
-@@ -46,7 +46,7 @@ MCCP4 = $(HOME)/mapview
-
-
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include
-+MMDB_CFLAGS = -I$(MMDB)/include
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
-
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb
-@@ -55,9 +55,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
-
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords
-
- top_srcdir = ..
-
-diff --git a/high-res/Makefile.am b/high-res/Makefile.am
-index cf81182..3a2af5c 100644
---- a/high-res/Makefile.am
-+++ b/high-res/Makefile.am
-@@ -29,8 +29,8 @@ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS)
-
- INCLUDES = \
- -I$(top_srcdir) \
-- $(MMDB_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS)
-+ $(MMDB_CFLAGS) \
-+ $(CLIPPER_CFLAGS)
-
- libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc
residue-distortions.cc \
- sequence-assignment.cc
-diff --git a/ideal/Makefile.am b/ideal/Makefile.am
-index e52c271..c5c8e6a 100644
---- a/ideal/Makefile.am
-+++ b/ideal/Makefile.am
-@@ -33,11 +33,11 @@ pkgincludedir = $(includedir)/coot/ideal
-
- INCLUDES = \
- -I$(top_srcdir) \
-- $(CLIPPER_CXXFLAGS) \
-- $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) \
-+ $(MMDB_CFLAGS)
-
- AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \
-- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS)
-+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS)
- AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS)
-
-
-diff --git a/ideal/Makefile.simple b/ideal/Makefile.simple
-index 3c32c3c..0abd514 100644
---- a/ideal/Makefile.simple
-+++ b/ideal/Makefile.simple
-@@ -44,7 +44,7 @@ MMDB = $(HOME)/mapview
-
-
- CXX = g++
--MMDB_CXXFLAGS = -I$(MMDB)/include
-+MMDB_CFLAGS = -I$(MMDB)/include
- FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
-
- MMDB_LIBS = -L$(MMDB)/lib -lmmdb
-@@ -53,9 +53,9 @@ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-contrib \
- -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
-
- MCCP4_CFLAGS = -I$(MCCP4)/include
--CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-
--INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \
-+INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \
- -I$(top_srcdir)/coords \
- -I$(top_srcdir)/geometry
-
-diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index df74b90..7f54567 100644
---- a/lbg/Makefile.am
-+++ b/lbg/Makefile.am
-@@ -6,7 +6,7 @@ INCLUDES = \
- $(GSL_CFLAGS) \
- $(GOOCANVAS_CFLAGS) \
- $(GTK_CFLAGS) \
-- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
-+ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
- $(COOT_WINDOWS_CFLAGS) \
- $(ENHANCED_LIGAND_TOOLS_CFLAGS) \
- $(RDKIT_CXXFLAGS) \
-diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple
-index 48d091b..5b148b4 100644
---- a/lbg/Makefile.simple
-+++ b/lbg/Makefile.simple
-@@ -24,11 +24,11 @@ GSL_LDFLAGS=$(CRYST)/lib/libgsl.la
$(CRYST)/lib/libgslcblas.la -lm
- MMDB=$(CRYST)
- # MMDB=$(HOME)/test/mmdb
-
--MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb
-+MMDB_CFLAGS=-I$(MMDB)/include/mmdb
- MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la
-
- CLIPPER=$(CRYST)
--CLIPPER_CXXFLAGS=-I$(CLIPPER)/include
-+CLIPPER_CFLAGS=-I$(CLIPPER)/include
- CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \
- $(CLIPPER)/lib/librfftw.la \
- $(CLIPPER)/lib/libfftw.la
-@@ -40,7 +40,7 @@ LIDIA_CORE_CXXFLAGS = -I ../lidia-core
- LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la
-
-
--CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
$(LIDIA_CORE_CXXFLAGS) \
-+CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
$(LIDIA_CORE_CXXFLAGS) \
- -I$(top_srcdir)/compat
-
- lbg: lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o
residue-circles.o
-diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 72b28ca..2a184b4 100644
---- a/lidia-core/Makefile.am
-+++ b/lidia-core/Makefile.am
-@@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core
-
- # 20110408 I add a CResidue,dictionary_residue_restraints_t constructor to
molfile_molecule_t
- # simple
--#INCLUDES = $(CLIPPER_CXXFLAGS)
-+#INCLUDES = $(CLIPPER_CFLAGS)
- #
- INCLUDES = \
- -I$(top_srcdir) \
- $(ENHANCED_LIGAND_TOOLS_CFLAGS) \
- $(RDKIT_CXXFLAGS) \
-- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
- libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc
rdkit-interface.cc \
- cod-types.cc
-diff --git a/ligand/Makefile.am b/ligand/Makefile.am
-index 202979e..5173204 100644
---- a/ligand/Makefile.am
-+++ b/ligand/Makefile.am
-@@ -27,7 +27,7 @@ INCLUDES = \
- -I$(top_srcdir) \
- $(COOT_GSL_FLAGS) \
- $(GSL_CFLAGS) \
-- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
- pkginclude_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh
monomer-utils.hh \
- chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh \
-diff --git a/macros/clipper.m4 b/macros/clipper.m4
-index da11e74..ad2af81 100644
---- a/macros/clipper.m4
-+++ b/macros/clipper.m4
-@@ -56,7 +56,7 @@ if test x$clipper_prefix != x; then
- #
- # should use clipper-config --cflags
- #
-- CLIPPER_CXXFLAGS="-I$clipper_prefix/include"
-+ CLIPPER_CFLAGS="-I$clipper_prefix/include"
- # -I$clipper_prefix/cctbx
-
- # yes, libmmtz.a is in -L$clipper_prefix/umtz!
-@@ -75,7 +75,7 @@ if test x$clipper_prefix != x; then
- #
- ccp4c=ccp4c
-
-- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif
-lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb
-lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif
-lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb
-lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
- # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib
-lsgtbx -luctbx
-
-
-@@ -102,8 +102,8 @@ else
- # this needs to be 'configured' - typically either s or blank.
- fftw_pre=
-
-- CLIPPER_CXXFLAGS="$CCP4_CFLAGS"
-- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib
-lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS
$MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
-+ CLIPPER_CFLAGS="$CCP4_CFLAGS"
-+ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib
-lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS
$MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
- fi
-
- # BL: workaround needed for new MinGW
-@@ -113,17 +113,17 @@ ac_cv_build_alias=${ac_cv_build_alias:=$build_alias}
- case $ac_cv_build_alias in
- # BL says:: same as for cygwin in mingw
- MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*)
-- CLIPPER_LDOPTS=$CLIPPER_LDOPTS
-+ CLIPPER_LIBS=$CLIPPER_LIBS
- ;;
- *)
-- CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread"
-+ CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread"
- ;;
- esac
-
- AC_MSG_CHECKING([for Clipper])
-
-- LIBS="$save_LIBS $CLIPPER_LDOPTS"
-- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
-+ LIBS="$save_LIBS $CLIPPER_LIBS"
-+ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
- # AC_TRY_LINK uses the c compiler, so we will temporarily
- # reassign $CC to the c++ compiler.
- #
-@@ -140,7 +140,7 @@ if test x$have_clipper = xyes; then
-
- LIBS="$saved_LIBS"
- CFLAGS="$saved_CFLAGS"
-- CLIPPER_LIBS="$CLIPPER_LDOPTS"
-+ CLIPPER_LIBS="$CLIPPER_LIBS"
- ifelse([$1], , :, [$1])
-
- else
-@@ -148,12 +148,12 @@ else
- LIBS="$saved_LIBS"
- CFLAGS="$saved_CFLAGS"
- CLIPPER_LIBS=""
-- CLIPPER_CXXFLAGS=""
-+ CLIPPER_CFLAGS=""
- ifelse([$2], , :, [$2])
-
- fi
-
--AC_SUBST(CLIPPER_CXXFLAGS)
-+AC_SUBST(CLIPPER_CFLAGS)
- AC_SUBST(CLIPPER_LIBS)
-
- ])
-diff --git a/macros/clipper.m4.old b/macros/clipper.m4.old
-index de8ab65..4c1b418 100644
---- a/macros/clipper.m4.old
-+++ b/macros/clipper.m4.old
-@@ -34,7 +34,7 @@ if test x$clipper_prefix != x; then
- # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
- # when clipper and dependencies get installed.
- #
-- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include
-I$clipper_prefix/boost -I$clipper_prefix/include"
-+ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include
-I$clipper_prefix/boost -I$clipper_prefix/include"
- # -I$clipper_prefix/cctbx
-
- # yes, libmmtz.a is in -L$clipper_prefix/umtz!
-@@ -45,20 +45,20 @@ if test x$clipper_prefix != x; then
- # HACK! FIXME
- # added lz, we should have proper autoconf check for this.
- #
-- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif
-lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper
-L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw
-lfftw -lz -lm"
-+ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif
-lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper
-L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw
-lfftw -lz -lm"
- # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib
-lsgtbx -luctbx
- else
- # the compiler looks in the "standard" places for clipper. In real life,
- # it would be quite unlikely that clipper would be installed in
/usr/include,
- # /usr/lib etc. so this code will not usually find the right dependencies.
-- CLIPPER_CXXFLAGS=""
-- CLIPPER_LDOPTS=""
-+ CLIPPER_CFLAGS=""
-+ CLIPPER_LIBS=""
- fi
-
- AC_MSG_CHECKING([for Clipper])
-
-- LIBS="$save_LIBS $CLIPPER_LDOPTS"
-- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
-+ LIBS="$save_LIBS $CLIPPER_LIBS"
-+ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
- # AC_TRY_LINK uses the c compiler, so we will temporarily
- # reassign $CC to the c++ compiler.
- #
-@@ -72,7 +72,7 @@ if test x$have_clipper = xyes; then
-
- LIBS="$saved_LIBS"
- CFLAGS="$saved_CFLAGS"
-- CLIPPER_LIBS="$CLIPPER_LDOPTS"
-+ CLIPPER_LIBS="$CLIPPER_LIBS"
- ifelse([$1], , :, [$1])
-
- else
-@@ -80,12 +80,12 @@ else
- LIBS="$saved_LIBS"
- CFLAGS="$saved_CFLAGS"
- CLIPPER_LIBS=""
-- CLIPPER_CXXFLAGS=""
-+ CLIPPER_CFLAGS=""
- ifelse([$2], , :, [$2])
-
- fi
-
--AC_SUBST(CLIPPER_CXXFLAGS)
-+AC_SUBST(CLIPPER_CFLAGS)
- AC_SUBST(CLIPPER_LIBS)
-
- ])
-diff --git a/macros/goo-canvas.m4 b/macros/goo-canvas.m4
-index e2494a5..89c908e 100644
---- a/macros/goo-canvas.m4
-+++ b/macros/goo-canvas.m4
-@@ -35,8 +35,7 @@ if test x$goocanvas_prefix != x; then
- # SGI compiler CC (CXX=CC) needs -lm to link maths library, but
- # GCC c++ does not.
- #
-- GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas"
--
-+ GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas"
- else
- # the compiler looks in the "standard" places for GOOCANVAS. (or uses
pkgconfig)
-
-@@ -54,18 +53,16 @@ else
- break;;
- esac
- if test -z "${PKG_CONFIG}"; then
-- GOOCANVAS_LDOPTS="-lgoocanvas"
-+ GOOCANVAS_LIBS="-lgoocanvas"
- else
-- GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
-+ GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
- fi
- fi
-
- AC_MSG_CHECKING([for Goocanvas])
-
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
--
--
- dnl # 20130929: why do I do this? I don't remember. Using libtool
- dnl # in this way is not a good idea (configure makes libtool).
- dnl #
-@@ -85,18 +82,15 @@ dnl # note that we use ./libtool (running in the build
dir) because $LIBTOOL
- dnl CXX="libtool --mode=link $CXX"
- dnl break;;
- dnl esac
--
--
- AC_LANG_PUSH(C++)
- AC_TRY_LINK([#include "goocanvas.h"] ,[ GooCanvas *a; ], have_goocanvas=yes,
have_goocanvas=no)
- AC_LANG_POP
--
- AC_MSG_RESULT($have_goocanvas)
-
- if test x$have_goocanvas = xyes; then
-
- GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
-
- ifelse([$1], , :, [$1])
-
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 25dc502..21646a5 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then
-
- if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
-
-- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-+ MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
- # AFAICS, ssm does not put its libs in $acl_libdirstem
- # MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
- MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
-- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/include"
-+ ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/include"
-
- # saved_LIBS="$LIBS"
- # saved_CPPFLAGS="$CPPFLAGS"
-@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then
- else
- AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not
found])
- fi
-- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
-+ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
-
- else
-
-- MMDBSSM_CXXFLAGS=""
-+ MMDBSSM_CFLAGS=""
- MMDBSSM_LIBS=""
- with_ssmlib_prefix=no
-
-@@ -62,6 +62,6 @@ fi
-
- AC_MSG_RESULT([$with_ssmlib_prefix])
-
--AC_SUBST(MMDBSSM_CXXFLAGS)
-+AC_SUBST(MMDBSSM_CFLAGS)
- AC_SUBST(MMDBSSM_LIBS)
- ])
-diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
-index 7c1cbcf..72613f3 100644
---- a/macros/mmdb.m4
-+++ b/macros/mmdb.m4
-@@ -55,7 +55,7 @@ if test x$mmdb_prefix != x; then
- # --with-mmdb=/some/thing
- #
-
-- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like
-+ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like
- # when MMDB and dependencies get installed - we infact, include both
- # directories.
- #
-@@ -69,7 +69,7 @@ lib/src
- lib/src/mmdb'
- for ac_dir in $ac_mmdb_dirs; do
- if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then
-- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir"
-+ ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir"
- break
- fi
- done
-@@ -82,14 +82,14 @@ else
- # the compiler looks in the "standard" places for MMDB. In real life,
- # it would be quite unlikely that MMDB would be installed in /usr/include,
- # /usr/lib etc. so this code will not usually find the right dependencies.
-- ac_MMDB_CXXFLAGS=""
-+ ac_MMDB_CFLAGS=""
- ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
-
- AC_MSG_CHECKING([for MMDB])
-
- LIBS="$save_LIBS $ac_MMDB_LDOPTS"
-- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
-+ CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS"
- #
- # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
- # temporarily reassign $CC to the c++ compiler.
-@@ -118,7 +118,7 @@ if test x$have_mmdb = xyes; then
- CLINKR_FLAG=-DMMDB_WITHOUT_LINKR
- fi
- CXXFLAGS="$saved_CXXFLAGS"
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
-+ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
- MMDB_LIBS="$ac_MMDB_LDOPTS"
- ifelse([$1], , :, [$1])
-
-@@ -134,12 +134,12 @@ else
- LIBS="$saved_LIBS"
- CXXFLAGS="$saved_CXXFLAGS"
- MMDB_LIBS=""
-- MMDB_CXXFLAGS=""
-+ MMDB_CFLAGS=""
- ifelse([$2], , :, [$2])
-
- fi
-
--AC_SUBST(MMDB_CXXFLAGS)
-+AC_SUBST(MMDB_CFLAGS)
- AC_SUBST(MMDB_LIBS)
-
- ])
-diff --git a/mini-mol/Makefile.am b/mini-mol/Makefile.am
-index 2f6e3a3..4865b0b 100644
---- a/mini-mol/Makefile.am
-+++ b/mini-mol/Makefile.am
-@@ -25,8 +25,8 @@ pkgincludedir = $(includedir)/coot/mini-mol
-
- INCLUDES = \
- -I$(top_srcdir) \
-- $(CLIPPER_CXXFLAGS) \
-- $(MMDB_CXXFLAGS)
-+ $(CLIPPER_CFLAGS) \
-+ $(MMDB_CFLAGS)
-
- AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
-
-diff --git a/protein_db/Makefile.am b/protein_db/Makefile.am
-index 268fcf6..cdd5c9e 100644
---- a/protein_db/Makefile.am
-+++ b/protein_db/Makefile.am
-@@ -19,7 +19,7 @@
-
- lib_LTLIBRARIES=libcoot-protein-db.la
-
--INCLUDES= $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
-+INCLUDES= $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
-
- pkginclude_HEADERS=protein_db.h protein_db_utils.h rna_db.h
- pkgincludedir = $(includedir)/coot/protein_db
-diff --git a/sequence-view/Makefile.am b/sequence-view/Makefile.am
-index 7af6384..742e6d7 100644
---- a/sequence-view/Makefile.am
-+++ b/sequence-view/Makefile.am
-@@ -55,9 +55,9 @@ INCLUDES = \
- -I$(top_srcdir)/analysis \
- -I$(top_srcdir)/cootaneer \
- -I$(top_srcdir)/src \
-- $(CLIPPER_CXXFLAGS) \
-- $(MMDB_CXXFLAGS) \
-- $(MMDBSSM_CXXFLAGS) \
-+ $(CLIPPER_CFLAGS) \
-+ $(MMDB_CFLAGS) \
-+ $(MMDBSSM_CFLAGS) \
- $(GLUT_CFLAGS) \
- $(CANVAS_CFLAGS) \
- $(GTKGL_CONTEXT_CFLAGS) \
-diff --git a/skeleton/Makefile.am b/skeleton/Makefile.am
-index 54872fe..bef7d0e 100644
---- a/skeleton/Makefile.am
-+++ b/skeleton/Makefile.am
-@@ -23,7 +23,7 @@ lib_LTLIBRARIES=libcoot-skeleton.la
-
- INCLUDES = \
- -I$(top_srcdir) \
-- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
-+ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
-
- AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index af5276b..d0ab482 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -195,11 +195,11 @@ INCLUDES = \
- $(GOOCANVAS_CFLAGS) \
- @GTK_CFLAGS@ \
- $(GLUT_CFLAGS) \
-- $(MMDBSSM_CXXFLAGS) \
-- $(MMDB_CXXFLAGS) \
-+ $(MMDBSSM_CFLAGS) \
-+ $(MMDB_CFLAGS) \
- $(CCP4SRS_CXXFLAGS) \
- $(GSL_CFLAGS) \
-- $(CLIPPER_CXXFLAGS) \
-+ $(CLIPPER_CFLAGS) \
- $(PYGTK_CFLAGS) \
- $(GLOB_CFLAGS) \
- $(CURL_CFLAGS)
-diff --git a/surface/Makefile.am b/surface/Makefile.am
-index 3de5953..2461f58 100644
---- a/surface/Makefile.am
-+++ b/surface/Makefile.am
-@@ -1,5 +1,5 @@
-
--INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
$(FFTW_CXXFLAGS)
-+INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
$(FFTW_CXXFLAGS)
-
- AM_CXXFLAGS = $(OPENMP_CFLAGS)
-
diff --git a/sci-chemistry/coot/files/coot-9999-desktop.patch
b/sci-chemistry/coot/files/coot-9999-desktop.patch
new file mode 100644
index 0000000..c264dd5
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-desktop.patch
@@ -0,0 +1,21 @@
+ coot.desktop | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/coot.desktop b/coot.desktop
+index 74aecf3..8668018 100644
+--- a/coot.desktop
++++ b/coot.desktop
+@@ -1,10 +1,9 @@
+ [Desktop Entry]
+ Type=Application
+-Encoding=UTF-8
+ Name=Coot
+ Comment=Macromolecular model builder
+ Exec=coot
+-Icon=coot.png
++Icon=coot
+ Terminal=true
+-Categories=Science;Graphics
+-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
++Categories=Science;Graphics;
++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;
diff --git a/sci-chemistry/coot/files/coot-9999-libguile.patch
b/sci-chemistry/coot/files/coot-9999-libguile.patch
new file mode 100644
index 0000000..cbaccef
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-libguile.patch
@@ -0,0 +1,29 @@
+ src/graphics-info-modelling.cc | 1 +
+ src/graphics-info.cc | 2 ++
+ 2 files changed, 3 insertions(+)
+
+diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
+index 05a63ad..4b7d129 100644
+--- a/src/graphics-info-modelling.cc
++++ b/src/graphics-info-modelling.cc
+@@ -102,6 +102,7 @@
+
+ #include "utils/coot-utils.hh"
+
++#include <libguile.h>
+
+ // Idealize the geometry without considering the map.
+ //
+diff --git a/src/graphics-info.cc b/src/graphics-info.cc
+index e2f9d52..76b6769 100644
+--- a/src/graphics-info.cc
++++ b/src/graphics-info.cc
+@@ -92,6 +92,8 @@
+ #include "cc-interface-scripting.hh"
+ #endif
+
++#include <libguile.h>
++
+ // A few non-class members - should be somewhere else, I guess.
+ //
+ void initialize_graphics_molecules() {
diff --git a/sci-chemistry/coot/files/coot-9999-libtool.patch
b/sci-chemistry/coot/files/coot-9999-libtool.patch
new file mode 100644
index 0000000..10c43ad
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-libtool.patch
@@ -0,0 +1,39 @@
+ configure.ac | 2 +-
+ lbg/Makefile.am | 11 -----------
+ 2 files changed, 1 insertion(+), 12 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 73d6ed7..b04dcd6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
+
+ AC_SUBST(COOT_STDTYPES)
+
+-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
+ AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
+
+
+diff --git a/lbg/Makefile.am b/lbg/Makefile.am
+index 1277afe..a79ebe0 100644
+--- a/lbg/Makefile.am
++++ b/lbg/Makefile.am
+@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh
flev-annotations.hh graphics-c-interfa
+ lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
+ pkgincludedir = $(includedir)/coot/lbg
+
+-# 20140521
+-# lidia_LDFLAGS = -Wl,--export-dynamic
+-#
+-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to
${wl}--export-dynamic
+-# (but not for MacOSX, where it Does The Right Thing (hopefully)).
+-# We manually set the value of wl here, but maybe the Right Thing To Do for
that is
+-# run (eval) $($LIBTOOL --config | grep ^wl). How do I do that here though?
+-# I don't understand. Maybe the setting of wl should be done in configure?
But then
+-# I have to force the output of libtool. Bleugh. Hmm...
+-# Anyway, thankyou Gary Vaughan.
+-wl=-Wl,
+ lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
+
+ # res spec output operator means we include libcoot-coord-utils
