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 +#include +#include +#include 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 -#include +#include #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)