diff options
Diffstat (limited to 'sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch')
| -rw-r--r-- | sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch | 367 |
1 files changed, 0 insertions, 367 deletions
diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch deleted file mode 100644 index 4271d5b76aec..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch +++ /dev/null @@ -1,367 +0,0 @@ -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) |