From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
Date: Sun, 2 Jun 2013 16:48:57 +0000 (UTC) [thread overview]
Message-ID: <1370191344.eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1.jlec@gentoo> (raw)
commit: eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 2 16:42:24 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 2 16:42:24 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb7653c7
sci-chemistry/coot: Update pc patches
Package-Manager: portage-2.2.0_alpha177
---
sci-chemistry/coot/ChangeLog | 5 +
sci-chemistry/coot/coot-9999.ebuild | 20 +-
sci-chemistry/coot/files/9999-clipper-config.patch | 17 -
sci-chemistry/coot/files/9999-goocanvas.patch | 25 -
sci-chemistry/coot/files/9999-mmdb-config.patch | 18 -
sci-chemistry/coot/files/9999-pc.patch | 1040 ++++++++++++++++++++
sci-chemistry/coot/files/9999-ssm.patch | 56 --
7 files changed, 1054 insertions(+), 127 deletions(-)
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index c729ace..2bbf002 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 02 Jun 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+ -files/9999-clipper-config.patch, -files/9999-goocanvas.patch,
+ -files/9999-mmdb-config.patch, +files/9999-pc.patch, -files/9999-ssm.patch:
+ Update pc patches
+
02 Jun 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
Fix PYTHON() -> ${EPYTHON} for new eclasses
diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index 4a7ee55..c8831ad 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -37,9 +37,9 @@ SCIDEPS="
>=sci-libs/gsl-1.3
>=sci-libs/mmdb-1.23
sci-libs/ssm
- <sci-libs/monomer-db-1
+ sci-libs/monomer-db
sci-chemistry/reduce
- <sci-chemistry/refmac-5.6
+ sci-chemistry/refmac
sci-chemistry/probe"
XDEPS="
@@ -82,21 +82,19 @@ pkg_setup() {
python-single-r1_pkg_setup
}
-PATCHES=(
- "${FILESDIR}"/${PV}-clipper-config.patch
- "${FILESDIR}"/${PV}-goocanvas.patch
- "${FILESDIR}"/${PV}-mmdb-config.patch
- "${FILESDIR}"/${PV}-ssm.patch
- )
+PATCHES=( "${FILESDIR}"/${PV}-pc.patch )
src_unpack() {
subversion_src_unpack
- use test && unpack ${A}
+ if use test; then
+ unpack ${A}
+ ln -sf . "${S}"/coot-ccp4
+ fi
}
src_prepare() {
sed \
- -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${PYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
+ -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
-i configure.in || die
autotools-utils_src_prepare
@@ -128,7 +126,7 @@ src_configure() {
src_compile() {
autotools-utils_src_compile
- python_fix_shebang "${S}"/src/coot_gtk2.py "${S}"/python-tests/coot_unittest.py
+ python_fix_shebang "${S}"/src/coot_gtk2.py
cp "${S}"/src/coot_gtk2.py python/coot.py || die
}
diff --git a/sci-chemistry/coot/files/9999-clipper-config.patch b/sci-chemistry/coot/files/9999-clipper-config.patch
deleted file mode 100644
index 311b5e8..0000000
--- a/sci-chemistry/coot/files/9999-clipper-config.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- macros/clipper.m4 | 3 +++
- 1 files changed, 3 insertions(+), 0 deletions(-)
-
-diff --git a/macros/clipper.m4 b/macros/clipper.m4
-index 0bf087a..d0e8b6b 100644
---- a/macros/clipper.m4
-+++ b/macros/clipper.m4
-@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
- ;;
- esac
-
-+CLIPPER_CXXFLAGS=`clipper-config --cflags`
-+CLIPPER_LDOPTS=`clipper-config --libs`
-+
- AC_MSG_CHECKING([for Clipper])
-
- LIBS="$save_LIBS $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/9999-goocanvas.patch b/sci-chemistry/coot/files/9999-goocanvas.patch
deleted file mode 100644
index ce0d4a0..0000000
--- a/sci-chemistry/coot/files/9999-goocanvas.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Index: macros/goo-canvas.m4
-===================================================================
---- macros/goo-canvas.m4 (revision 3307)
-+++ macros/goo-canvas.m4 (working copy)
-@@ -56,9 +56,9 @@
- fi
- fi
-
--AC_MSG_CHECKING([for Goocanvas])
-+PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
-
--LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
-+LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
- CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
- #
- # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
-@@ -76,7 +76,7 @@
- if test x$have_goocanvas = xyes; then
-
- GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
-- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
-+ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
-
- ifelse([$1], , :, [$1])
-
diff --git a/sci-chemistry/coot/files/9999-mmdb-config.patch b/sci-chemistry/coot/files/9999-mmdb-config.patch
deleted file mode 100644
index b3b66ab..0000000
--- a/sci-chemistry/coot/files/9999-mmdb-config.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Index: macros/mmdb.m4
-===================================================================
---- macros/mmdb.m4 (revision 3579)
-+++ macros/mmdb.m4 (working copy)
-@@ -86,8 +86,12 @@
- ac_MMDB_LDOPTS="-lmmdb -lm"
- fi
-
--AC_MSG_CHECKING([for MMDB])
-+PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
-+ac_MMDB_LDOPTS="${MMDB_LIBS}"
-+ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
-
-+AC_MSG_CHECKING([for CISPEP in MMDB])
-+
- LIBS="$save_LIBS $ac_MMDB_LDOPTS"
- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
- #
diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
new file mode 100644
index 0000000..a6bc18e
--- /dev/null
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -0,0 +1,1040 @@
+Index: ChangeLog
+===================================================================
+--- ChangeLog (revision 4651)
++++ ChangeLog (working copy)
+@@ -1959,7 +1959,7 @@
+ 2005-01-29 Paul Emsley <paulemsley@ysbl.york.ac.uk>
+
+ * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in
+- MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel
++ MMDBSSM_CFLAGS [Oops]. Hopefully fixes problems spotted by Joel
+ Bard and Joseph Toth.
+
+ * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add
+@@ -2252,14 +2252,14 @@
+
+ 2004-11-20 Paul Emsley <paulemsley@ysbl.york.ac.uk>
+
+- * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for
++ * coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for
+ coot-close.cc usage].
+
+ 2004-11-19 Paul Emsley <paulemsley@ysbl.york.ac.uk>
+
+- * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS
++ * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS
+
+- * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS
++ * analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS
+
+ 2004-11-16 Paul Emsley <emsley@localhost>
+
+@@ -2269,7 +2269,7 @@
+
+ 2004-11-15 Paul Emsley <emsley@localhost>
+
+- * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks
++ * coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks
+ Joseph Toth].
+
+ * surface/CXXSphereNode.h: removed the ; again!
+Index: analysis/Makefile.am
+===================================================================
+--- analysis/Makefile.am (revision 4651)
++++ analysis/Makefile.am (working copy)
+@@ -11,8 +11,8 @@
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/mini-mol \
+ -I$(top_srcdir)/utils \
+- $(CLIPPER_CXXFLAGS) \
+- $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) \
++ $(MMDB_CFLAGS)
+
+ libcoot_analysis_la_SOURCES = bfkurt.cc mogul.cc
+
+Index: angles/Makefile.am
+===================================================================
+--- angles/Makefile.am (revision 4651)
++++ angles/Makefile.am (working copy)
+@@ -6,7 +6,7 @@
+
+ include_HEADERS = AngleInfo.h ncube.h wrapped-ncube.h
+
+-INCLUDES = $(CLIPPER_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS)
+
+ libcoot_AngleInfo_a_sources = AngleInfo.cc AngleInfo.h \
+ AngleInfo-angle-torsions-autogen.cc AngleInfo-theta_2-autogen.cc
+Index: auxil/catcheck/Makefile.am
+===================================================================
+--- auxil/catcheck/Makefile.am (revision 4651)
++++ auxil/catcheck/Makefile.am (working copy)
+@@ -1,7 +1,7 @@
+
+ EXTRA_DIST = Makefile.simple
+
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+
+ check_PROGRAMS = catcheck
+
+Index: auxil/catcheck/Makefile.simple
+===================================================================
+--- auxil/catcheck/Makefile.simple (revision 4651)
++++ auxil/catcheck/Makefile.simple (working copy)
+@@ -1,17 +1,17 @@
+
+-# CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
++# CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
+
+
+ BASE = /home/paule/autobuild/Linux-kalypso-pre-release
+-CLIPPER_CXXFLAGS = -I$(BASE)/include
+-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
++CLIPPER_CFLAGS = -I$(BASE)/include
++MMDB_CFLAGS = -I$(BASE)/include/mmdb
+
+ CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ -lclipper-core -lccp4c -L$(BASE)/lib \
+ -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+
+ catcheck: catcheck.cc catcheck.hh
+Index: auxil/rama/Makefile.am
+===================================================================
+--- auxil/rama/Makefile.am (revision 4651)
++++ auxil/rama/Makefile.am (working copy)
+@@ -1,7 +1,7 @@
+
+ EXTRA_DIST = Makefile.simple fit-rama.scm run.scm test-arr.scm
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+
+ check_PROGRAMS = rama-data rama-doughnut
+Index: auxil/rama/Makefile.simple
+===================================================================
+--- auxil/rama/Makefile.simple (revision 4651)
++++ auxil/rama/Makefile.simple (working copy)
+@@ -1,12 +1,12 @@
+
+-CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
++CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
+
+ CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
+ -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
+
+-INCLUDES = $(CLIPPER_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+
+ rama-data: rama-data.cc
+Index: auxil/sec-str/Makefile.am
+===================================================================
+--- auxil/sec-str/Makefile.am (revision 4651)
++++ auxil/sec-str/Makefile.am (working copy)
+@@ -1,6 +1,6 @@
+
+ EXTRA_DIST = Makefile.simple sec-str-dist-check.cc sec-str-dist-check.hh
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+
+ #check_PROGRAMS = sec-str-dist-check
+
+Index: auxil/sec-str/Makefile.simple
+===================================================================
+--- auxil/sec-str/Makefile.simple (revision 4651)
++++ auxil/sec-str/Makefile.simple (working copy)
+@@ -1,27 +1,27 @@
+
+-#CLIPPER_CXXFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
++#CLIPPER_CFLAGS = -I/Users/paulemsley/ccp4/ysbl-distro-based/include
+
+ #CLIPPER_LIBS = -L/Users/paulemsley/ccp4/ysbl-distro-based/lib -lclipper-ccp4 \
+ # -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ # -lclipper-core -lccp4c -L/Users/paulemsley/ccp4/ysbl-distro-based/lib \
+ # -L/Users/paulemsley/ccp4/ysbl-distro-based -lmmdb -lm -lrfftw -lfftw -lz -lm
+
+-#INCLUDES = $(CLIPPER_CXXFLAGS)
++#INCLUDES = $(CLIPPER_CFLAGS)
+ #LDLIBS = $(CLIPPER_LIBS)
+
+
+ #
+
+ BASE = /home/paule/autobuild/Linux-kalypso-pre-release
+-CLIPPER_CXXFLAGS = -I$(BASE)/include
+-MMDB_CXXFLAGS = -I$(BASE)/include/mmdb
++CLIPPER_CFLAGS = -I$(BASE)/include
++MMDB_CFLAGS = -I$(BASE)/include/mmdb
+
+ CLIPPER_LIBS = -L$(BASE)/lib -lclipper-ccp4 \
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ -lclipper-core -lccp4c -L$(BASE)/lib \
+ -L$(BASE) -lmmdb -lm -lrfftw -lfftw -lz -lm
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+
+ sec-str-dist-check: sec-str-dist-check.cc sec-str-dist-check.hh
+Index: auxil/strand-analysis/Makefile.am
+===================================================================
+--- auxil/strand-analysis/Makefile.am (revision 4651)
++++ auxil/strand-analysis/Makefile.am (working copy)
+@@ -3,8 +3,8 @@
+
+
+ INCLUDES = -I$(top_srcdir)/auxil/sec-str \
+- $(MMDB_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS)
++ $(MMDB_CFLAGS) \
++ $(CLIPPER_CFLAGS)
+
+
+ check_PROGRAMS =
+Index: auxil/strand-analysis/Makefile.simple
+===================================================================
+--- auxil/strand-analysis/Makefile.simple (revision 4651)
++++ auxil/strand-analysis/Makefile.simple (working copy)
+@@ -2,13 +2,13 @@
+
+ CLIPPER = /Users/paulemsley/ccp4/ysbl-distro-based
+
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include
++CLIPPER_CFLAGS = -I$(CLIPPER)/include
+
+ CLIPPER_LIBS = -L$(CLIPPER)/lib -lclipper-ccp4 \
+ -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb \
+ -lclipper-core -lccp4c -lmmdb -lm -lrfftw -lfftw -lz -lm
+
+-INCLUDES = -I../sec-str $(CLIPPER_CXXFLAGS)
++INCLUDES = -I../sec-str $(CLIPPER_CFLAGS)
+ LDLIBS = $(CLIPPER_LIBS)
+
+ .cc:
+Index: auxil/vectors/Makefile.am
+===================================================================
+--- auxil/vectors/Makefile.am (revision 4651)
++++ auxil/vectors/Makefile.am (working copy)
+@@ -1,6 +1,6 @@
+
+ EXTRA_DIST = Makefile.simple diff-vec.cc
+-INCLUDES = $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++INCLUDES = $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+ check_PROGRAMS =
+
+ #diff_vec_SOURCES = diff-vec.cc
+Index: build/Makefile.am
+===================================================================
+--- build/Makefile.am (revision 4651)
++++ build/Makefile.am (working copy)
+@@ -24,8 +24,8 @@
+
+ INCLUDES = \
+ -I$(top_srcdir)/angles \
+- $(CLIPPER_CXXFLAGS) \
+- $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) \
++ $(MMDB_CFLAGS)
+
+ noinst_PROGRAMS = testcabuild
+
+Index: ccp4mg-utils/Makefile.am
+===================================================================
+--- ccp4mg-utils/Makefile.am (revision 4651)
++++ ccp4mg-utils/Makefile.am (working copy)
+@@ -25,7 +25,7 @@
+ EXTRA_DIST = convert.sh get-new-utils.sh
+
+ INCLUDES = \
+- $(MMDB_CXXFLAGS) \
++ $(MMDB_CFLAGS) \
+ $(LIBPNG_CFLAGS)
+
+ libccp4mg_utils_la_SOURCES = geomutil.cc mgtree.cc cartesian.cc \
+Index: ccp4mg-utils/mmut/Makefile.am
+===================================================================
+--- ccp4mg-utils/mmut/Makefile.am (revision 4651)
++++ ccp4mg-utils/mmut/Makefile.am (working copy)
+@@ -70,9 +70,9 @@
+ $(LIBGLADE_CFLAGS) \
+ @GTK_CFLAGS@ \
+ $(GLUT_CFLAGS) \
+- $(MMDBSSM_CXXFLAGS) \
+- $(MMDB_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS)
++ $(MMDBSSM_CFLAGS) \
++ $(MMDB_CFLAGS) \
++ $(CLIPPER_CFLAGS)
+
+ # $(WITH_SCRIPT_CFLAGS)
+
+Index: ccp4mg-utils/pygl/Makefile.am
+===================================================================
+--- ccp4mg-utils/pygl/Makefile.am (revision 4651)
++++ ccp4mg-utils/pygl/Makefile.am (working copy)
+@@ -108,9 +108,9 @@
+ $(LIBGLADE_CFLAGS) \
+ @GTK_CFLAGS@ \
+ $(GLUT_CFLAGS) \
+- $(MMDBSSM_CXXFLAGS) \
+- $(MMDB_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS)
++ $(MMDBSSM_CFLAGS) \
++ $(MMDB_CFLAGS) \
++ $(CLIPPER_CFLAGS)
+
+ # $(WITH_SCRIPT_CFLAGS)
+
+Index: ccp4mg-utils/util/Makefile.am
+===================================================================
+--- ccp4mg-utils/util/Makefile.am (revision 4651)
++++ ccp4mg-utils/util/Makefile.am (working copy)
+@@ -73,9 +73,9 @@
+ $(LIBGLADE_CFLAGS) \
+ @GTK_CFLAGS@ \
+ $(GLUT_CFLAGS) \
+- $(MMDBSSM_CXXFLAGS) \
+- $(MMDB_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS)
++ $(MMDBSSM_CFLAGS) \
++ $(MMDB_CFLAGS) \
++ $(CLIPPER_CFLAGS)
+
+ # $(WITH_SCRIPT_CFLAGS)
+
+Index: configure.in
+===================================================================
+--- configure.in (revision 4651)
++++ configure.in (working copy)
+@@ -108,14 +108,18 @@
+
+
+ dnl Check for MMDB.
+-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2],,[AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)])
+
+-AM_WITH_MMDBSSM
++PKG_CHECK_MODULES([MMDBSSM],[ssm],,[AM_WITH_MMDBSSM])
+ AM_WITH_CCP4SRS
+
+ dnl Check for Clipper. we exit if clipper is not found.
+ #
+-AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
++PKG_CHECK_MODULES([CLIPPER], [clipper libccp4c], [
++ CLIPPER_LIBS="${CLIPPER_LIBS} -lrfftw -lfftw"; AC_SUBST([CLIPPER_LIBS])
++ ], [
++ AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
++ ])
+
+ # we set default coot_guile to true
+ coot_guile=true
+@@ -189,11 +193,15 @@
+
+ dnl =========================== GooCanvas ================================
+
+-AM_PATH_GOOCANVAS
+-# give something for the preprocessor to chew on...
+-if test "$GOOCANVAS_CFLAGS" != "" ; then
+- GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
+-fi
++PKG_CHECK_MODULES([GOOCANVAS], [goocanvas],
++ [GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"; AC_SUBST(GOOCANVAS_CFLAGS)],
++ [
++ AM_PATH_GOOCANVAS
++ # give something for the preprocessor to chew on...
++ if test "$GOOCANVAS_CFLAGS" != "" ; then
++ GOOCANVAS_CFLAGS="-DHAVE_GOOCANVAS $GOOCANVAS_CFLAGS"
++ fi
++ ])
+
+ AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ],
+ coot_enterprise_additions="true",
+Index: coords/Makefile.am
+===================================================================
+--- coords/Makefile.am (revision 4651)
++++ coords/Makefile.am (working copy)
+@@ -34,7 +34,7 @@
+ -I$(top_srcdir)/compat \
+ $(ENTERPRISE_TOOLS_CFLAGS) \
+ $(RDKIT_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+ AM_CXXFLAGS = \
+ -DPKGDATADIR='"$(pkgdatadir)"' \
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am (revision 4651)
++++ coot-surface/Makefile.am (working copy)
+@@ -21,7 +21,7 @@
+ INCLUDES = -I$(top_srcdir)/surface \
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/mini-mol \
+- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(GTKGL_CFLAGS) $(GLUT_CFLAGS)
+
+ lib_LTLIBRARIES = libcoot-surface.la
+
+Index: coot-utils/Makefile.am
+===================================================================
+--- coot-utils/Makefile.am (revision 4651)
++++ coot-utils/Makefile.am (working copy)
+@@ -38,8 +38,8 @@
+ -I$(top_srcdir)/geometry \
+ -I$(top_srcdir)/compat \
+ -I$(top_srcdir)/mini-mol \
+- $(CLIPPER_CXXFLAGS) \
+- $(MMDB_CXXFLAGS) \
++ $(CLIPPER_CFLAGS) \
++ $(MMDB_CFLAGS) \
+ $(GSL_CFLAGS) \
+ $(WITH_GUILE_CFLAGS) \
+ $(WITH_PYTHON_CFLAGS)
+Index: cootaneer/Makefile.am
+===================================================================
+--- cootaneer/Makefile.am (revision 4651)
++++ cootaneer/Makefile.am (working copy)
+@@ -20,7 +20,7 @@
+ EXTRA_DIST = \
+ cootaneer-llk-2.40.dat
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+ cootaneer_demo_SOURCES = cootaneer-demo.cpp
+
+Index: cootilus/Makefile.am
+===================================================================
+--- cootilus/Makefile.am (revision 4651)
++++ cootilus/Makefile.am (working copy)
+@@ -20,7 +20,7 @@
+ EXTRA_DIST = \
+ nautilus_lib.pdb
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+ cootilus_demo_SOURCES = cootilus-demo.cpp
+
+Index: db-main/Makefile.am
+===================================================================
+--- db-main/Makefile.am (revision 4651)
++++ db-main/Makefile.am (working copy)
+@@ -6,7 +6,7 @@
+ -DDATADIR='"$(datadir)"'
+
+ INCLUDES = -I$(top_srcdir)/utils -I$(top_srcdir)/coot-utils -I$(top_srcdir)/mini-mol \
+- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+
+ include_HEADERS = db-main.hh db-strands.hh
+
+Index: db-main/Makefile.simple
+===================================================================
+--- db-main/Makefile.simple (revision 4651)
++++ db-main/Makefile.simple (working copy)
+@@ -19,7 +19,7 @@
+ MCCP4 = $(HOME)/crystal
+
+ CXX = g++
+-MMDB_CXXFLAGS = -I$(MMDB)/include
++MMDB_CFLAGS = -I$(MMDB)/include
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
+
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb
+@@ -28,9 +28,9 @@
+ -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
+
+ MCCP4_CFLAGS = -I$(MCCP4)/include
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
+
+ CXXFLAGS = -g $(INCLUDES)
+ LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS)
+@@ -44,4 +44,4 @@
+ db-main.o: db-main.cc db-main.hh
+
+ testmmdbbits: testmmdbbits.cc
+- $(CXX) $(MMDB_CXXFLAGS) $(MMDB_LIBS) $? -o $@
++ $(CXX) $(MMDB_CFLAGS) $(MMDB_LIBS) $? -o $@
+Index: density-contour/Makefile.am
+===================================================================
+--- density-contour/Makefile.am (revision 4651)
++++ density-contour/Makefile.am (working copy)
+@@ -20,7 +20,7 @@
+
+ COORD_INCLUDES = -I$(top_srcdir)/coords
+
+-INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CXXFLAGS)
++INCLUDES = $(COORD_INCLUDES) $(CLIPPER_CFLAGS)
+
+ lib_LTLIBRARIES = libcoot-isosurface.la
+
+Index: geometry/Makefile.am
+===================================================================
+--- geometry/Makefile.am (revision 4651)
++++ geometry/Makefile.am (working copy)
+@@ -29,7 +29,7 @@
+ -I$(top_srcdir)/mini-mol \
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/compat \
+- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS)
+
+ AM_CXXFLAGS = \
+ -DDATADIR='"$(datadir)"' \
+Index: geometry/Makefile.simple
+===================================================================
+--- geometry/Makefile.simple (revision 4651)
++++ geometry/Makefile.simple (working copy)
+@@ -46,7 +46,7 @@
+
+
+ CXX = g++
+-MMDB_CXXFLAGS = -I$(MMDB)/include
++MMDB_CFLAGS = -I$(MMDB)/include
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
+
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb
+@@ -55,9 +55,9 @@
+ -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
+
+ MCCP4_CFLAGS = -I$(MCCP4)/include
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) -I$(top_srcdir)/coords
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/coords
+
+ top_srcdir = ..
+
+Index: high-res/Makefile.am
+===================================================================
+--- high-res/Makefile.am (revision 4651)
++++ high-res/Makefile.am (working copy)
+@@ -36,8 +36,8 @@
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/lidia-core \
+ -I$(top_srcdir)/compat \
+- $(MMDB_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS)
++ $(MMDB_CFLAGS) \
++ $(CLIPPER_CFLAGS)
+
+ libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \
+ sequence-assignment.cc
+Index: ideal/Makefile.am
+===================================================================
+--- ideal/Makefile.am (revision 4651)
++++ ideal/Makefile.am (working copy)
+@@ -37,11 +37,11 @@
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/mini-mol \
+ -I$(top_srcdir)/geometry \
+- $(CLIPPER_CXXFLAGS) \
+- $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) \
++ $(MMDB_CFLAGS)
+
+ AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) $(COOT_WINDOWS_CFLAGS) \
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) $(COOT_GSL_FLAGS)
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) $(COOT_GSL_FLAGS)
+ AM_LDFLAGS = $(GSL_LIBS) $(MMDB_LIBS) $(CLIPPER_LIBS)
+
+
+Index: ideal/Makefile.simple
+===================================================================
+--- ideal/Makefile.simple (revision 4651)
++++ ideal/Makefile.simple (working copy)
+@@ -44,7 +44,7 @@
+
+
+ CXX = g++
+-MMDB_CXXFLAGS = -I$(MMDB)/include
++MMDB_CFLAGS = -I$(MMDB)/include
+ FFTW_LIBS = -L$(FFTW)/lib -lrfftw -lfftw
+
+ MMDB_LIBS = -L$(MMDB)/lib -lmmdb
+@@ -53,9 +53,9 @@
+ -L$(CLIPPER)lib -L/h/paule/mapview/lib $(FFTW_LIBS)
+
+ MCCP4_CFLAGS = -I$(MCCP4)/include
+-CLIPPER_CXXFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
++CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
+
+-INCLUDES = $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS) \
++INCLUDES = $(CLIPPER_CFLAGS) $(MMDB_CFLAGS) \
+ -I$(top_srcdir)/coords \
+ -I$(top_srcdir)/geometry
+
+Index: lbg/Makefile.am
+===================================================================
+--- lbg/Makefile.am (revision 4651)
++++ lbg/Makefile.am (working copy)
+@@ -11,7 +11,7 @@
+ $(GSL_CFLAGS) \
+ $(GOOCANVAS_CFLAGS) \
+ $(GTK_CFLAGS) \
+- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
++ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
+ $(COOT_WINDOWS_CFLAGS) \
+ $(ENTERPRISE_TOOLS_CFLAGS) \
+ $(RDKIT_CXXFLAGS) \
+Index: lbg/Makefile.simple
+===================================================================
+--- lbg/Makefile.simple (revision 4651)
++++ lbg/Makefile.simple (working copy)
+@@ -24,11 +24,11 @@
+ MMDB=$(CRYST)
+ # MMDB=$(HOME)/test/mmdb
+
+-MMDB_CXXFLAGS=-I$(MMDB)/include/mmdb
++MMDB_CFLAGS=-I$(MMDB)/include/mmdb
+ MMDB_LDFLAGS=$(MMDB)/lib/libmmdb.la
+
+ CLIPPER=$(CRYST)
+-CLIPPER_CXXFLAGS=-I$(CLIPPER)/include
++CLIPPER_CFLAGS=-I$(CLIPPER)/include
+ CLIPPER_LDFLAGS=$(CLIPPER)/lib/libclipper-core.la \
+ $(CLIPPER)/lib/librfftw.la \
+ $(CLIPPER)/lib/libfftw.la
+@@ -40,7 +40,7 @@
+ LIDIA_CORE_LDFLAGS = $(COOT_INSTALLED)/lib/libcoot-lidia-core.la
+
+
+-CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(LIDIA_CORE_CXXFLAGS) \
++CXXFLAGS=-g -O2 $(EXTRA_FLAGS) $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(LIDIA_CORE_CXXFLAGS) \
+ -I$(top_srcdir)/compat
+
+ lbg: lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
+Index: lidia-core/Makefile.am
+===================================================================
+--- lidia-core/Makefile.am (revision 4651)
++++ lidia-core/Makefile.am (working copy)
+@@ -22,7 +22,7 @@
+
+ # 20110408 I add a CResidue,dictionary_residue_restraints_t constructor to molfile_molecule_t
+ # simple
+-#INCLUDES = $(CLIPPER_CXXFLAGS)
++#INCLUDES = $(CLIPPER_CFLAGS)
+ #
+ INCLUDES = \
+ -I$(top_srcdir)/geometry \
+@@ -31,7 +31,7 @@
+ -I$(top_srcdir)/utils \
+ $(ENTERPRISE_TOOLS_CFLAGS) \
+ $(RDKIT_CXXFLAGS) \
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+ libcoot_lidia_core_la_SOURCES = lbg-shared.cc lbg-molfile.cc lig-build.cc rdkit-interface.cc \
+ cod-types.cc
+Index: ligand/Makefile.am
+===================================================================
+--- ligand/Makefile.am (revision 4651)
++++ ligand/Makefile.am (working copy)
+@@ -36,7 +36,7 @@
+ -I$(top_srcdir)/db-main \
+ $(COOT_GSL_FLAGS) \
+ $(GSL_CFLAGS) \
+- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+ include_HEADERS = ligand.hh residue_by_phi_psi.hh wligand.hh monomer-utils.hh \
+ chi-angles.hh dunbrack.hh helix-placement.hh fast-ss-search.hh \
+Index: macros/clipper.m4
+===================================================================
+--- macros/clipper.m4 (revision 4651)
++++ macros/clipper.m4 (working copy)
+@@ -56,7 +56,7 @@
+ #
+ # should use clipper-config --cflags
+ #
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/include"
++ CLIPPER_CFLAGS="-I$clipper_prefix/include"
+ # -I$clipper_prefix/cctbx
+
+ # yes, libmmtz.a is in -L$clipper_prefix/umtz!
+@@ -75,7 +75,7 @@
+ #
+ ccp4c=ccp4c
+
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
++ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -l$ccp4c $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx
+
+
+@@ -102,8 +102,8 @@
+ # this needs to be 'configured' - typically either s or blank.
+ fftw_pre=
+
+- CLIPPER_CXXFLAGS="$CCP4_CFLAGS"
+- CLIPPER_LDOPTS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
++ CLIPPER_CFLAGS="$CCP4_CFLAGS"
++ CLIPPER_LIBS="-lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-minimol -lclipper-cns -lclipper-core $CCP4_LIBS $MMDB_LIBS -l${fftw_pre}rfftw -l${fftw_pre}fftw -lz -lm"
+ fi
+
+ # BL: workaround needed for new MinGW
+@@ -113,17 +113,17 @@
+ case $ac_cv_build_alias in
+ # BL says:: same as for cygwin in mingw
+ MINGW*|Mingw*|*mingw*|Cygwin*|CYGWIN*|*cygwin*)
+- CLIPPER_LDOPTS=$CLIPPER_LDOPTS
++ CLIPPER_LIBS=$CLIPPER_LIBS
+ ;;
+ *)
+- CLIPPER_LDOPTS=$CLIPPER_LDOPTS" -lpthread"
++ CLIPPER_LIBS=$CLIPPER_LIBS" -lpthread"
+ ;;
+ esac
+
+ AC_MSG_CHECKING([for Clipper])
+
+- LIBS="$save_LIBS $CLIPPER_LDOPTS"
+- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
++ LIBS="$save_LIBS $CLIPPER_LIBS"
++ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
+ # AC_TRY_LINK uses the c compiler, so we will temporarily
+ # reassign $CC to the c++ compiler.
+ #
+@@ -140,7 +140,7 @@
+
+ LIBS="$saved_LIBS"
+ CFLAGS="$saved_CFLAGS"
+- CLIPPER_LIBS="$CLIPPER_LDOPTS"
++ CLIPPER_LIBS="$CLIPPER_LIBS"
+ ifelse([$1], , :, [$1])
+
+ else
+@@ -148,12 +148,12 @@
+ LIBS="$saved_LIBS"
+ CFLAGS="$saved_CFLAGS"
+ CLIPPER_LIBS=""
+- CLIPPER_CXXFLAGS=""
++ CLIPPER_CFLAGS=""
+ ifelse([$2], , :, [$2])
+
+ fi
+
+-AC_SUBST(CLIPPER_CXXFLAGS)
++AC_SUBST(CLIPPER_CFLAGS)
+ AC_SUBST(CLIPPER_LIBS)
+
+ ])
+Index: macros/clipper.m4.old
+===================================================================
+--- macros/clipper.m4.old (revision 4651)
++++ macros/clipper.m4.old (working copy)
+@@ -34,7 +34,7 @@
+ # should ideally be CLIPPER_CFLAGS="-I$clipper_prefix/include", and the like
+ # when clipper and dependencies get installed.
+ #
+- CLIPPER_CXXFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
++ CLIPPER_CFLAGS="-I$clipper_prefix/mccp4 -I$clipper_prefix/fftw/include -I$clipper_prefix/boost -I$clipper_prefix/include"
+ # -I$clipper_prefix/cctbx
+
+ # yes, libmmtz.a is in -L$clipper_prefix/umtz!
+@@ -45,20 +45,20 @@
+ # HACK! FIXME
+ # added lz, we should have proper autoconf check for this.
+ #
+- CLIPPER_LDOPTS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
++ CLIPPER_LIBS="-L$clipper_prefix/lib -lclipper-mtz -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-mmdb -lclipper-mmdbold -lclipper -L$clipper_prefix/mccp4 -lmccp4 $MMDB_LIBS -L$clipper_prefix/fftw/lib -lrfftw -lfftw -lz -lm"
+ # -L$clipper_prefix/boost/lib -lclipper-cctbx -L$clipper_prefix/cctbx/lib -lsgtbx -luctbx
+ else
+ # the compiler looks in the "standard" places for clipper. In real life,
+ # it would be quite unlikely that clipper would be installed in /usr/include,
+ # /usr/lib etc. so this code will not usually find the right dependencies.
+- CLIPPER_CXXFLAGS=""
+- CLIPPER_LDOPTS=""
++ CLIPPER_CFLAGS=""
++ CLIPPER_LIBS=""
+ fi
+
+ AC_MSG_CHECKING([for Clipper])
+
+- LIBS="$save_LIBS $CLIPPER_LDOPTS"
+- CFLAGS="$save_CFLAGS $CLIPPER_CXXFLAGS"
++ LIBS="$save_LIBS $CLIPPER_LIBS"
++ CFLAGS="$save_CFLAGS $CLIPPER_CFLAGS"
+ # AC_TRY_LINK uses the c compiler, so we will temporarily
+ # reassign $CC to the c++ compiler.
+ #
+@@ -72,7 +72,7 @@
+
+ LIBS="$saved_LIBS"
+ CFLAGS="$saved_CFLAGS"
+- CLIPPER_LIBS="$CLIPPER_LDOPTS"
++ CLIPPER_LIBS="$CLIPPER_LIBS"
+ ifelse([$1], , :, [$1])
+
+ else
+@@ -80,12 +80,12 @@
+ LIBS="$saved_LIBS"
+ CFLAGS="$saved_CFLAGS"
+ CLIPPER_LIBS=""
+- CLIPPER_CXXFLAGS=""
++ CLIPPER_CFLAGS=""
+ ifelse([$2], , :, [$2])
+
+ fi
+
+-AC_SUBST(CLIPPER_CXXFLAGS)
++AC_SUBST(CLIPPER_CFLAGS)
+ AC_SUBST(CLIPPER_LIBS)
+
+ ])
+Index: macros/goo-canvas.m4
+===================================================================
+--- macros/goo-canvas.m4 (revision 4651)
++++ macros/goo-canvas.m4 (working copy)
+@@ -36,9 +36,9 @@
+ # GCC c++ does not.
+ #
+ if test -e $goocanvas_prefix/lib/libgoocanvas.la ; then
+- GOOCANVAS_LDOPTS="$goocanvas_prefix/lib/libgoocanvas.la"
++ GOOCANVAS_LIBS="$goocanvas_prefix/lib/libgoocanvas.la"
+ else
+- GOOCANVAS_LDOPTS="-L$goocanvas_prefix/lib -lgoocanvas"
++ GOOCANVAS_LIBS="-L$goocanvas_prefix/lib -lgoocanvas"
+ fi
+ else
+ # the compiler looks in the "standard" places for GOOCANVAS. (or uses pkgconfig)
+@@ -57,19 +57,19 @@
+ break;;
+ esac
+ if test -e /usr/lib/libgoocanvas.la ; then
+- GOOCANVAS_LDOPTS="libgoocanvas.la"
++ GOOCANVAS_LIBS="libgoocanvas.la"
+ else
+ if test -z "${PKG_CONFIG}"; then
+- GOOCANVAS_LDOPTS="-lgoocanvas"
++ GOOCANVAS_LIBS="-lgoocanvas"
+ else
+- GOOCANVAS_LDOPTS=`$PKG_CONFIG goocanvas --libs`
++ GOOCANVAS_LIBS=`$PKG_CONFIG goocanvas --libs`
+ fi
+ fi
+ fi
+
+ AC_MSG_CHECKING([for Goocanvas])
+
+-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
+ CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
+ #
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
+@@ -95,7 +95,7 @@
+ if test x$have_goocanvas = xyes; then
+
+ GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
+- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
+
+ ifelse([$1], , :, [$1])
+
+Index: macros/mmdb-ssm.m4
+===================================================================
+--- macros/mmdb-ssm.m4 (revision 4651)
++++ macros/mmdb-ssm.m4 (working copy)
+@@ -32,7 +32,7 @@
+
+ if test x$with_ssmlib_prefix != x; then
+
+- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
++ MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
+ MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+
+ ac_mmdb_dirs='
+@@ -47,16 +47,16 @@
+
+ for ac_dir in $ac_mmdb_dirs; do
+ if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
+- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
++ ac_MMDBSSM_CFLAGS="-I$with_ssmlib_prefix/$ac_dir"
+ break
+ fi
+ done
+
+- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
++ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
+
+ else
+
+- MMDBSSM_CXXFLAGS=""
++ MMDBSSM_CFLAGS=""
+ MMDBSSM_LIBS=""
+ with_ssmlib_prefix=no
+
+@@ -64,6 +64,6 @@
+
+ AC_MSG_RESULT([$with_ssmlib_prefix])
+
+-AC_SUBST(MMDBSSM_CXXFLAGS)
++AC_SUBST(MMDBSSM_CFLAGS)
+ AC_SUBST(MMDBSSM_LIBS)
+ ])
+Index: macros/mmdb.m4
+===================================================================
+--- macros/mmdb.m4 (revision 4651)
++++ macros/mmdb.m4 (working copy)
+@@ -55,7 +55,7 @@
+ # --with-mmdb=/some/thing
+ #
+
+- # should ideally be MMDB_CXXFLAGS="-I$MMDB_prefix/include", and the like
++ # should ideally be MMDB_CFLAGS="-I$MMDB_prefix/include", and the like
+ # when MMDB and dependencies get installed - we infact, include both
+ # directories.
+ #
+@@ -69,7 +69,7 @@
+ lib/src/mmdb'
+ for ac_dir in $ac_mmdb_dirs; do
+ if test -r "$mmdb_prefix/$ac_dir/mmdb/mmdb_manager.h"; then
+- ac_MMDB_CXXFLAGS="-I$mmdb_prefix/$ac_dir"
++ ac_MMDB_CFLAGS="-I$mmdb_prefix/$ac_dir"
+ break
+ fi
+ done
+@@ -82,14 +82,14 @@
+ # the compiler looks in the "standard" places for MMDB. In real life,
+ # it would be quite unlikely that MMDB would be installed in /usr/include,
+ # /usr/lib etc. so this code will not usually find the right dependencies.
+- ac_MMDB_CXXFLAGS=""
++ ac_MMDB_CFLAGS=""
+ ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+
+ AC_MSG_CHECKING([for MMDB])
+
+ LIBS="$save_LIBS $ac_MMDB_LDOPTS"
+- CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
++ CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CFLAGS"
+ #
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
+ # temporarily reassign $CC to the c++ compiler.
+@@ -118,7 +118,7 @@
+ CLINKR_FLAG=-DMMDB_WITHOUT_LINKR
+ fi
+ CXXFLAGS="$saved_CXXFLAGS"
+- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
++ MMDB_CFLAGS="$ac_MMDB_CFLAGS $HASH_FLAG $CISPEP_FLAG $CLINKR_FLAG"
+ MMDB_LIBS="$ac_MMDB_LDOPTS"
+ ifelse([$1], , :, [$1])
+
+@@ -134,12 +134,12 @@
+ LIBS="$saved_LIBS"
+ CXXFLAGS="$saved_CXXFLAGS"
+ MMDB_LIBS=""
+- MMDB_CXXFLAGS=""
++ MMDB_CFLAGS=""
+ ifelse([$2], , :, [$2])
+
+ fi
+
+-AC_SUBST(MMDB_CXXFLAGS)
++AC_SUBST(MMDB_CFLAGS)
+ AC_SUBST(MMDB_LIBS)
+
+ ])
+Index: mini-mol/Makefile.am
+===================================================================
+--- mini-mol/Makefile.am (revision 4651)
++++ mini-mol/Makefile.am (working copy)
+@@ -25,8 +25,8 @@
+ INCLUDES = \
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/compat \
+- $(CLIPPER_CXXFLAGS) \
+- $(MMDB_CXXFLAGS)
++ $(CLIPPER_CFLAGS) \
++ $(MMDB_CFLAGS)
+
+ AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
+
+Index: protein_db/Makefile.am
+===================================================================
+--- protein_db/Makefile.am (revision 4651)
++++ protein_db/Makefile.am (working copy)
+@@ -19,7 +19,7 @@
+
+ lib_LTLIBRARIES=libcoot-protein-db.la
+
+-INCLUDES= $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
++INCLUDES= $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
+
+ include_HEADERS=protein_db.h protein_db_utils.h rna_db.h
+
+Index: sequence-view/Makefile.am
+===================================================================
+--- sequence-view/Makefile.am (revision 4651)
++++ sequence-view/Makefile.am (working copy)
+@@ -55,9 +55,9 @@
+ -I$(top_srcdir)/analysis \
+ -I$(top_srcdir)/cootaneer \
+ -I$(top_srcdir)/src \
+- $(CLIPPER_CXXFLAGS) \
+- $(MMDB_CXXFLAGS) \
+- $(MMDBSSM_CXXFLAGS) \
++ $(CLIPPER_CFLAGS) \
++ $(MMDB_CFLAGS) \
++ $(MMDBSSM_CFLAGS) \
+ $(GLUT_CFLAGS) \
+ $(CANVAS_CFLAGS) \
+ $(GTKGL_CONTEXT_CFLAGS) \
+Index: skeleton/Makefile.am
+===================================================================
+--- skeleton/Makefile.am (revision 4651)
++++ skeleton/Makefile.am (working copy)
+@@ -28,7 +28,7 @@
+ -I$(top_srcdir)/angles \
+ -I$(top_srcdir)/coot-utils \
+ -I$(top_srcdir)/compat \
+- $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS)
++ $(MMDB_CFLAGS) $(CLIPPER_CFLAGS)
+
+ AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
+
+Index: src/Makefile.am
+===================================================================
+--- src/Makefile.am (revision 4651)
++++ src/Makefile.am (working copy)
+@@ -220,11 +220,11 @@
+ $(GOOCANVAS_CFLAGS) \
+ @GTK_CFLAGS@ \
+ $(GLUT_CFLAGS) \
+- $(MMDBSSM_CXXFLAGS) \
+- $(MMDB_CXXFLAGS) \
++ $(MMDBSSM_CFLAGS) \
++ $(MMDB_CFLAGS) \
+ $(CCP4SRS_CXXFLAGS) \
+ $(GSL_CFLAGS) \
+- $(CLIPPER_CXXFLAGS) \
++ $(CLIPPER_CFLAGS) \
+ $(PYGTK_CFLAGS) \
+ $(GLOB_CFLAGS) \
+ $(CURL_CFLAGS)
+Index: surface/Makefile.am
+===================================================================
+--- surface/Makefile.am (revision 4651)
++++ surface/Makefile.am (working copy)
+@@ -1,5 +1,5 @@
+
+-INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CXXFLAGS) $(CLIPPER_CXXFLAGS) $(FFTW_CXXFLAGS)
++INCLUDES = -I$(top_srcdir)/coot-utils $(MMDB_CFLAGS) $(CLIPPER_CFLAGS) $(FFTW_CXXFLAGS)
+
+ AM_CXXFLAGS = $(OPENMP_CFLAGS)
+
diff --git a/sci-chemistry/coot/files/9999-ssm.patch b/sci-chemistry/coot/files/9999-ssm.patch
deleted file mode 100644
index c801da7..0000000
--- a/sci-chemistry/coot/files/9999-ssm.patch
+++ /dev/null
@@ -1,56 +0,0 @@
- macros/mmdb-ssm.m4 | 42 +-----------------------------------------
- 1 files changed, 1 insertions(+), 41 deletions(-)
-
-diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 1937a16..6ef547c 100644
---- a/macros/mmdb-ssm.m4
-+++ b/macros/mmdb-ssm.m4
-@@ -22,47 +22,7 @@
- AC_DEFUN([AM_WITH_MMDBSSM],
- [AC_PROVIDE([AM_USE_MMDBSSM])
-
--
--AC_ARG_WITH(ssmlib-prefix,
-- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
-- [ with_ssmlib_prefix="$withval" ],
-- with_ssmlib_prefix="")
--
--AC_MSG_CHECKING([for SSMLib])
--
--if test x$with_ssmlib_prefix != x; then
--
-- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-- MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
--
--ac_mmdb_dirs='
--.
--include
--include/ssm
--include/mmdb
--lib
--src
--lib/src
--lib/src/mmdb'
--
-- for ac_dir in $ac_mmdb_dirs; do
-- if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
-- ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
-- break
-- fi
-- done
--
-- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
--
--else
--
-- MMDBSSM_CXXFLAGS=""
-- MMDBSSM_LIBS=""
-- with_ssmlib_prefix=no
--
--fi
--
--AC_MSG_RESULT([$with_ssmlib_prefix])
-+PKG_CHECK_MODULES([MMDBSSM],[ssm])
-
- AC_SUBST(MMDBSSM_CXXFLAGS)
- AC_SUBST(MMDBSSM_LIBS)
next reply other threads:[~2013-06-02 16:49 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-06-02 16:48 Justin Lecher [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-22 13:40 [gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/ Aisha Tammy
2015-09-15 13:34 Justin Lecher
2014-06-30 19:02 Justin Lecher
2013-11-25 18:48 Justin Lecher
2013-10-02 6:49 Justin Lecher
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