From eb7653c7d0b2c1ec08a436154d5d5623ad3ad3d1 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sun, 2 Jun 2013 18:42:24 +0200 Subject: sci-chemistry/coot: Update pc patches Package-Manager: portage-2.2.0_alpha177 --- sci-chemistry/coot/ChangeLog | 5 + sci-chemistry/coot/Manifest | 2 +- 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 -- 8 files changed, 1055 insertions(+), 128 deletions(-) delete mode 100644 sci-chemistry/coot/files/9999-clipper-config.patch delete mode 100644 sci-chemistry/coot/files/9999-goocanvas.patch delete mode 100644 sci-chemistry/coot/files/9999-mmdb-config.patch create mode 100644 sci-chemistry/coot/files/9999-pc.patch delete mode 100644 sci-chemistry/coot/files/9999-ssm.patch (limited to 'sci-chemistry') diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog index c729aceb7..2bbf002da 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 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 coot-9999.ebuild: Fix PYTHON() -> ${EPYTHON} for new eclasses diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest index ae71a3d6c..947b27422 100644 --- a/sci-chemistry/coot/Manifest +++ b/sci-chemistry/coot/Manifest @@ -1 +1 @@ -DIST greg-data.tar.gz 8046569 SHA256 3680a4a3c8e2f36a53a3e5cf67bbce567513e9a782cc14a2029a331257497631 SHA512 7ccafb493a4b14e0fd15f7df68b479456fd5d6d5981a869cf3b0fd5af246cea969718eda83e308b5298fef0e5d47a73474c529357fce80e1204a0df7c5cc4410 WHIRLPOOL 20cf48c8e60b0c3bad80581f42e5778183f83ee4c44432486ef95c549b54e984bb76bc8739577548fb2a742e44c108dbd8393c4dc8594e0687ef446834fbfbcb +DIST greg-data.tar.gz 8202091 SHA256 b82743b1d3c2d3acaa4adb4901368d46e0638733364963ad62044f79111f21f7 SHA512 71ab00869df074660103b824130776ceeaad398b1df8bbc30c9fc41660cc08a66998a406c5cfc93f4605cc5052aae414bd79b6e6de2ae46acd9c6997dbd5361b WHIRLPOOL 87deff25e864f55b316f432b9a9b595e23352720d08257e2b69bbe7946bf8ab5d1fcc9d13205354a0edd3fbea89422952df5f6fa0c05f9707167b544494b2c14 diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild index 4a7ee5520..c8831ad82 100644 --- a/sci-chemistry/coot/coot-9999.ebuild +++ b/sci-chemistry/coot/coot-9999.ebuild @@ -37,9 +37,9 @@ SCIDEPS=" >=sci-libs/gsl-1.3 >=sci-libs/mmdb-1.23 sci-libs/ssm - = 1.2]) -+ac_MMDB_LDOPTS="${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 000000000..a6bc18e5d --- /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 + + * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in +- MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel ++ MMDBSSM_CFLAGS [Oops]. Hopefully fixes problems spotted by Joel + Bard and Joseph Toth. + + * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add +@@ -2252,14 +2252,14 @@ + + 2004-11-20 Paul Emsley + +- * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for ++ * coords/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS [for + coot-close.cc usage]. + + 2004-11-19 Paul Emsley + +- * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS ++ * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CFLAGS + +- * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS ++ * analysis/Makefile.am (INCLUDES): Added CLIPPER_CFLAGS + + 2004-11-16 Paul Emsley + +@@ -2269,7 +2269,7 @@ + + 2004-11-15 Paul Emsley + +- * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks ++ * coot-utils/Makefile.am: add MMDB_CFLAGS to INCLUDE [thanks + Joseph Toth]. + + * surface/CXXSphereNode.h: removed the ; again! +Index: analysis/Makefile.am +=================================================================== +--- analysis/Makefile.am (revision 4651) ++++ analysis/Makefile.am (working copy) +@@ -11,8 +11,8 @@ + -I$(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 = $(OPENMP_CFLAGS) + diff --git a/sci-chemistry/coot/files/9999-ssm.patch b/sci-chemistry/coot/files/9999-ssm.patch deleted file mode 100644 index c801da724..000000000 --- a/sci-chemistry/coot/files/9999-ssm.patch +++ /dev/null @@ -1,56 +0,0 @@ - macros/mmdb-ssm.m4 | 42 +----------------------------------------- - 1 files changed, 1 insertions(+), 41 deletions(-) - -diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4 -index 1937a16..6ef547c 100644 ---- a/macros/mmdb-ssm.m4 -+++ b/macros/mmdb-ssm.m4 -@@ -22,47 +22,7 @@ - AC_DEFUN([AM_WITH_MMDBSSM], - [AC_PROVIDE([AM_USE_MMDBSSM]) - -- --AC_ARG_WITH(ssmlib-prefix, -- AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ), -- [ with_ssmlib_prefix="$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) -- cgit v1.2.3-65-gdbad