diff options
Diffstat (limited to 'sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch')
| -rw-r--r-- | sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch | 131 |
1 files changed, 131 insertions, 0 deletions
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch new file mode 100644 index 000000000000..107cfd740238 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch @@ -0,0 +1,131 @@ + src/Makefile.in | 14 +++++----- + src/pisa/configure.ac | 67 +++++++++---------------------------------------- + 2 files changed, 19 insertions(+), 62 deletions(-) + +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b11db04 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs) + eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS) + pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; +- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ++ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; ++ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp + + ### bp3, afro, gcx + +@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs) + + $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ +- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ++ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ ++ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C + + ### crunch2 pmf + +@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs) + cross_validate : $(cross_validateobjs) + @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS) + cif2xml.o cross_validate.o : # dependencies at end +- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp ++ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp + + pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract + pdb_extract_suite : +@@ -873,8 +873,8 @@ $(dev_tools_ctargets) : + $(dev_tools_cxxtargets) : + @$(SETFLAGS) xxx=1; \ + rm -f $@; \ +- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\ +- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ++ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\ ++ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) + + ### mlphare + mlphare: +diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac +index 81afdda..044b6f8 100755 +--- a/src/pisa/configure.ac ++++ b/src/pisa/configure.ac +@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) + # test for function in m + AC_CHECK_LIB([m], [sqrt]) + +-dnl Optional: Check for MMDB. +-AM_PATH_MMDB(, +- [ if test "x$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 $MMDB_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([mmdb not found]) +- fi +- ] +-) ++PKG_CHECK_MODULES([MMDB],[mmdb]) ++PKG_CHECK_MODULES([SSM],[ssm]) ++ ++MMDB_CXXFLAGS=${MMDB_CFLAGS} ++ ++AC_SUBST([MMDB_CFLAGS]) ++AC_SUBST([MMDB_CXXFLAGS]) ++AC_SUBST([SSM_CFLAGS]) ++ ++AC_SUBST([MMDB_LIBS]) ++AC_SUBST([SSM_LIBS]) + +-ac_saved_CXXFLAGS=$CXXFLAGS +-ac_saved_LIBS=$LIBS + CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" + LIBS="$MMDB_LIBS $LIBS" +-AM_PATH_SSM(, +- [ if test "x$ssm_prefix" != x ; then +- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then +- case "$ac_SSM_CXXFLAGS" in +- *lib/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g` +- ;; +- *include/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g` +- ;; +- *) +- esac +- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS" +- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- else +- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm" +- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm" +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([ssm not found]) +- fi +- ] +-) +-CXXFLAGS=$ac_saved_CXXFLAGS +-LIBS=$ac_saved_LIBS ++ + + # Checks for typedefs, structures, and compiler characteristics. + # |