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gentoo-overlay/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch

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diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp
index 69b32b0..602e35f 100755
--- a/lib/DiffractionImage/DiffractionImageCBF.cpp
+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp
@@ -6,10 +6,10 @@
// images.
#include "DiffractionImage.h"
-#include "cbf.h"
-#include "cbf_simple.h"
-#include "cbf_string.h"
-#include "cbf_byte_offset.h"
+#include <cbflib/cbf.h>
+#include <cbflib/cbf_simple.h>
+#include <cbflib/cbf_string.h>
+#include <cbflib/cbf_byte_offset.h>
using namespace std;
diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am
index fedb7ac..89a048e 100755
--- a/lib/DiffractionImage/MAR/Makefile.am
+++ b/lib/DiffractionImage/MAR/Makefile.am
@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu
noinst_LTLIBRARIES = libmar.la
-AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include
+AM_CPPFLAGS =
libmar_la_SOURCES = mar300_header.c \
mar345_header.c \
@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \
utils.c \
pck.c
-libmar_la_LDFLAGS = -static
diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c
index d3f4212..2c37108 100755
--- a/lib/DiffractionImage/MAR/marcif.c
+++ b/lib/DiffractionImage/MAR/marcif.c
@@ -31,8 +31,7 @@
#include "marcif_header.h"
#include "mar345_header.h"
-#include <cbf.h>
-#include <img.h>
+#include <cbflib/cbf.h>
#define printe(x) printf("%s: %s: %s\n",prg,f,x)
#undef cbf_failnez
diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am
index 189a1d7..6652576 100755
--- a/lib/DiffractionImage/Makefile.am
+++ b/lib/DiffractionImage/Makefile.am
@@ -1,7 +1,9 @@
AUTOMAKE_OPTIONS = gnu
-SUBDIRS = CBFlib Bruker MAR Rigaku jpg
+SUBDIRS = Bruker MAR Rigaku
-AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg
+SYSLIBS = -ljpeg -lcbf
+
+AM_CPPFLAGS =-I./MAR
lib_LTLIBRARIES = libDiffImage.la
if WANT_PYTHONMOD
@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \
Profile.cpp \
Peak.cpp \
dps_peaksearch_cn.c
-libDiffImage_la_LDFLAGS = -static
+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
+libDiffImage_la_LIBADD = $(SYSLIBS) \
+ ./MAR/libmar.la ./Bruker/libbruker.la \
+ ./Rigaku/librigaku.la
-libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \
+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \
./Bruker/libbruker.la ./MAR/libmar.la \
- ./Rigaku/librigaku.la ./jpg/libjpeg.la
+ ./Rigaku/librigaku.la
libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp
-libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
- --no-whole-archive -rpath '$(libdir)'
+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \
+ libDiffImage.la \
+ ./Bruker/libbruker.la \
+ ./MAR/libmar.la ./Rigaku/librigaku.la
-lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \
./Bruker/libbruker.la ./MAR/libmar.la \
- ./Rigaku/librigaku.la ./jpg/libjpeg.la
+ ./Rigaku/librigaku.la
lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp
-lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
- --no-whole-archive -rpath '$(libdir)'
+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \
+ ./Bruker/libbruker.la \
+ ./MAR/libmar.la ./Rigaku/librigaku.la
-libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \
+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \
./Bruker/libbruker.la ./MAR/libmar.la \
- ./Rigaku/librigaku.la ./jpg/libjpeg.la
+ ./Rigaku/librigaku.la
libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp
-libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \
- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \
- --no-whole-archive -rpath '$(libdir)'
+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS)
+libDiffractionImaJ_la_LIBADD = libDiffImage.la \
+ ./Bruker/libbruker.la $(SYSLIBS) \
+ ./MAR/libmar.la ./Rigaku/librigaku.la
bin_PROGRAMS = automask diffdump printpeaks diff2jpeg
-automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \
+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
automask_SOURCES = automask.cpp
-diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
+automask_LDFLAGS = $(SHARED_LIB_FLAGS)
+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \
+ ./MAR/libmar.la ./Rigaku/librigaku.la
diffdump_SOURCES = diffdump.cpp
-printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS)
+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \
+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
printpeaks_SOURCES = printpeaks.cpp
-diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \
- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la
+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS)
+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \
+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS)
diff2jpeg_SOURCES = diff2jpeg.cpp
+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS)
install-data-local:
@INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC}
diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure
index 3fb5784..fdf9683 100755
--- a/lib/DiffractionImage/configure
+++ b/lib/DiffractionImage/configure
@@ -21768,7 +21768,7 @@ _ACEOF
fi
-ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile"
+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile "
cat >confcache <<\_ACEOF
@@ -22407,12 +22407,9 @@ do
case $ac_config_target in
"depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
"Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;;
- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;;
"MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;;
"Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;;
"Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;;
- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;;
*) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in
index 7f54b4b..16efc64 100755
--- a/lib/DiffractionImage/configure.in
+++ b/lib/DiffractionImage/configure.in
@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then
HAVE_PYTHON=1
CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}"
])
+ PYLIB="-lpython${PYTHON_VER}"
+ AC_SUBST(PYLIB)
fi
AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1])
@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z)
AC_CHECK_LIB([m], [sqrt])
AC_CONFIG_FILES([Makefile
- CBFlib/Makefile
- CBFlib/src/Makefile
MAR/Makefile
Rigaku/Makefile
- Bruker/Makefile
- jpg/Makefile])
+ Bruker/Makefile])
AC_OUTPUT
diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am
index e9554e1..a3ba33d 100755
--- a/lib/ssm/Makefile.am
+++ b/lib/ssm/Makefile.am
@@ -1,7 +1,11 @@
+ACLOCAL_AMFLAGS = -I macros
#libtool
lib_LTLIBRARIES = libssm.la
+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS)
+libssm_la_CFLAGS = @MMDB_CFLAGS@
libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \
ssm_align.cpp ss_graph.cpp
+libssm_la_LIBADD = @MMDB_LIBS@
#non libtool
#lib_LIBRARIES = libssm.a
@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp
bin_PROGRAMS = superpose
-INCLUDES = $(MMDB_CXXFLAGS)
-
-AM_LDFLAGS = $(MMDB_LIBS)
+INCLUDES = @MMDB_CFLAGS@
EXTRA_DIST = macros/mmdb.m4
-superpose_LDADD = libssm.la
+superpose_LDADD = libssm.la @MMDB_LIBS@
libssm_a_AR = $(AR) $(AR_FLAGS)
diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac
index 783cb46..d637d11 100755
--- a/lib/ssm/configure.ac
+++ b/lib/ssm/configure.ac
@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug,
[ac_cv_enable_debug=no ] )
dnl Optional: Check for MMDB.
-AM_PATH_MMDB(,
- [ if test "x$mmdb_prefix" != x ; then
- if test "x$ac_MMDB_CXXFLAGS" != x ; then
- case "$ac_MMDB_CXXFLAGS" in
- *src/mmdb )
- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
- ;;
- *include/mmdb )
- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
- ;;
- *)
- esac
- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
- else
- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb"
- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb"
- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
- fi
- else
- AC_MSG_WARN([mmdb not found])
- fi
- ]
-)
+
+PKG_CHECK_MODULES([MMDB],[mmdb])
+AC_SUBST([MMDB_CFLAGS])
+AC_SUBST([MMDB_LIBS])
# Checks for typedefs, structures, and compiler characteristics.
#
@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
# test for function in m
AC_CHECK_LIB([m], [sqrt])
+
AC_SUBST(AR_FLAGS)
AC_SUBST(superpose_LDFLAGS)
AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes)
diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am
index 094fd6b..922a131 100755
--- a/src/pisa/Makefile.am
+++ b/src/pisa/Makefile.am
@@ -1,3 +1,4 @@
+ACLOCAL_AMFLAGS = -I macros
SUBDIRS = molref pisastore sbase
pkgdatadir = $(datadir)/pisa
@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp
bin_PROGRAMS = pisa
-INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS)
+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS)
-pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS)
+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@
EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in
diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
index 81afdda..4f99df6 100755
--- a/src/pisa/configure.ac
+++ b/src/pisa/configure.ac
@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
AC_CHECK_LIB([m], [sqrt])
dnl Optional: Check for MMDB.
-AM_PATH_MMDB(,
- [ if test "x$mmdb_prefix" != x ; then
- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then
- case "$ac_MMDB_CXXFLAGS" in
- *src/mmdb )
- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
- ;;
- *include/mmdb )
- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
- ;;
- *)
- esac
- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
- else
- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
- fi
- else
- AC_MSG_ERROR([mmdb not found])
- fi
- ]
-)
+PKG_CHECK_MODULES([MMDB],[mmdb])
+AC_SUBST([MMDB_CFLAGS])
+AC_SUBST([MMDB_LIBS])
ac_saved_CXXFLAGS=$CXXFLAGS
ac_saved_LIBS=$LIBS
-CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS"
LIBS="$MMDB_LIBS $LIBS"
AM_PATH_SSM(,
[ if test "x$ssm_prefix" != x ; then
diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
index e78b10d..486b931 100755
--- a/src/rapper/Makefile.am
+++ b/src/rapper/Makefile.am
@@ -1,3 +1,3 @@
-SUBDIRS = libxml2 gc7.0 LOOP data
+SUBDIRS = LOOP data
EXTRA_DIST =
diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
index 5e4ef69..11b63ec 100755
--- a/src/rapper/configure.ac
+++ b/src/rapper/configure.ac
@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
AC_SUBST(rapper_LDFLAGS)
-AC_CONFIG_SUBDIRS([gc7.0 libxml2])
+#AC_CONFIG_SUBDIRS([gc7.0 libxml2])
#AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
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