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Diffstat (limited to 'sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch')
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch395
1 files changed, 0 insertions, 395 deletions
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch
deleted file mode 100644
index c787df903dfc..000000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch
+++ /dev/null
@@ -1,395 +0,0 @@
- lib/DiffractionImage/DiffractionImageCBF.cpp | 8 ++--
- lib/DiffractionImage/MAR/Makefile.am | 3 +-
- lib/DiffractionImage/MAR/marcif.c | 3 +-
- lib/DiffractionImage/Makefile.am | 68 +++++++++++++++-----------
- lib/DiffractionImage/configure | 5 +--
- lib/DiffractionImage/configure.in | 7 +--
- lib/src/Makefile.in | 2 +-
- lib/ssm/Makefile.am | 10 ++--
- lib/ssm/configure.ac | 30 ++---------
- src/pisa/Makefile.am | 5 +-
- src/pisa/configure.ac | 30 ++----------
- src/rapper/Makefile.am | 2 +-
- src/rapper/configure.ac | 2 +-
- 13 files changed, 70 insertions(+), 105 deletions(-)
-
-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/src/Makefile.in b/lib/src/Makefile.in
-index c23f488..9579b3b 100755
---- a/lib/src/Makefile.in
-+++ b/lib/src/Makefile.in
-@@ -659,7 +659,7 @@ csymlib.o: $(srcdir)/csymlib.c $(srcdir)/csymlib.h
- csymlib_f.o: $(srcdir)/csymlib_f.c $(srcdir)/csymlib.h
- ccp4_unitcell.o: $(srcdir)/ccp4_unitcell.c $(srcdir)/ccp4_unitcell.h
- ccp4_unitcell_f.o: $(srcdir)/ccp4_unitcell_f.c $(srcdir)/ccp4_unitcell.h
--hybrid_36_f.o: $(srcdir)/hybrid_36_f.c $(mmdbsrcdir)/hybrid_36.h
-+hybrid_36_f.o: $(srcdir)/hybrid_36_f.c
- cvecmat.o: $(srcdir)/cvecmat.c $(srcdir)/cvecmat.h
- cmtzlib_python_wrap.o: $(srcdir)/cmtzlib_python_wrap.c $(srcdir)/mtzdata.h
- cmaplib_python_wrap.o: $(srcdir)/cmaplib_python_wrap.c
-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)