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, 367 insertions, 0 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 new file mode 100644 index 000000000000..4271d5b76aec --- /dev/null +++ b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch @@ -0,0 +1,367 @@ +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) |