Change way of installation, fixed insecure runpaths

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 143 insertions, 15 deletions

diff --git a/sci-libs/ccp4-libs/files/6.1.3-destdir.patch b/sci-libs/ccp4-libs/files/6.1.3-destdir.patch
new file mode 100644
index 000000000000..e69de29bb2d1
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-destdir.patch
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
index b3fefacdac54..ac52001245e6 100644
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
+++ b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
@@ -9,18 +9,3 @@
  # maybe create shared library
  	$(SHARE_LIB)
  
---- lib/src/Makefile.in	2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new	2009-08-11 12:17:53.000000000 +0200
-@@ -716,11 +716,9 @@
- 	  rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- 	done
- 
--install : all install-ccp4HEADERS install-mmdbHEADERS
--	$(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
-+install : all install-ccp4HEADERS
- 	$(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
- 	$(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
--	$(RANLIB) $(libdir)/$(LMMDB)
- 	$(RANLIB) $(libdir)/$(LC)
- 	$(RANLIB) $(libdir)/$(LF)
- 	$(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch
new file mode 100644
index 000000000000..bfb526c35661
--- /dev/null
+++ b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch
@@ -0,0 +1,143 @@
+diff --git a/Makefile.in b/Makefile.in
+index ac552fe..fab1a87 100755
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -30,8 +30,7 @@ lapacklib : FORCE
+ 
+ cciflib : FORCE
+ 	if test -n "$(ccifdir)"; then cd $(ccifdir); \
+-	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi; \
+-           $(MAKE) install
++	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
+ 
+ cctbx: FORCE
+ 	if test -n "$(cctbxdir)"; then cd $(top_srcdir)/$(cctbxdir); \
+@@ -40,8 +39,7 @@ cctbx: FORCE
+ libdir : FORCE lapacklib cciflib libccp4 clipper ssm diffractionImg
+ 
+ libccp4: FORCE
+-	cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) ; \
+-	$(MAKE) install
++	cd lib/src; $(MAKE) $(MFLAGS) $(MVARS)
+ 
+ share : FORCE
+ 	cd share; $(MAKE) $(MFLAGS) $(MVARS)
+@@ -51,18 +49,15 @@ ccp4i : FORCE
+ 
+ clipper: FORCE fftw
+ 	if test -n "$(clipperdir)"; then cd $(top_srcdir)/lib/clipper/clipper; \
+-	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
+-	$(MAKE) install
++	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
+ 
+ diffractionImg: 
+ 	if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \
+-	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
+-        $(MAKE) install
++	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
+ 
+ ssm: 
+ 	if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \
+-	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \
+-	$(MAKE) install
++	$(MAKE) -i $(MFLAGS) $(MVARS); else true; fi
+ 
+ fftw: FORCE
+ 	if test -n "$(fftwdir)"; then cd $(top_srcdir)/lib/fftw; \
+@@ -79,7 +74,7 @@ unsupported :  FORCE libdir
+ 	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
+ 
+ datadir : FORCE libdir
+-	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS)
++	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) font84.dat
+ 
+ xwindir : FORCE libdir
+ 	if test -f x-windows/Makefile; then cd x-windows; \
+diff --git a/lib/ccif/Makefile.in b/lib/ccif/Makefile.in
+index 975f1d9..75eda9f 100755
+--- a/lib/ccif/Makefile.in
++++ b/lib/ccif/Makefile.in
+@@ -371,11 +371,11 @@ condition.h condition_list.h: $(srcdir)/condition.list $(srcdir)/condition.awk
+ #
+ 
+ install : all
+-	$(INSTALL_DATA) `pwd`/$L $(libdir)/$L
+-	$(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(libdir)/$(CIFMMLIB)
+-	$(RANLIB) $(libdir)/$L
++	$(RANLIB) $L
++	$(INSTALL_DATA) `pwd`/$L $(DESTDIR)/$(libdir)/$L
++	$(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(DESTDIR)$(libdir)/$(CIFMMLIB)
+ 	if (test -f $(SHARED_LIB_NAME)); then \
+-	  $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(libdir)/$(SHARED_LIB_NAME); \
++	  $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(DESTDIR)/$(libdir)/$(SHARED_LIB_NAME); \
+         fi
+ 
+ uninstall :
+diff --git a/lib/data/Makefile.in b/lib/data/Makefile.in
+index cc25c5c..7445ca5 100755
+--- a/lib/data/Makefile.in
++++ b/lib/data/Makefile.in
+@@ -30,9 +30,9 @@ font84.dat : fontpack $(srcdir)/font84.ascii
+ 
+ install : all 
+ 	-rm -f font84.dat
+-	test -f font84.ascii || $(LNS) $(srcdir)/font84.ascii .
++	test -f font84.ascii || $(LNS) $(DESTIDIR)/$(srcdir)/font84.ascii .
+ 	./fontpack
+-	$(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat 
++	$(INSTALL) `pwd`/font84.dat $(DESTDIR)/$(libdir)/font84.dat 
+ 
+ uninstall :
+ 	-rm -f $(libdir)/font84.dat
+diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in
+index c23f488..3a611f1 100755
+--- a/lib/src/Makefile.in
++++ b/lib/src/Makefile.in
+@@ -685,7 +685,7 @@ testlib : $(srcdir)/testlib.f  $(LF)
+ #
+ 
+ install-ccp4HEADERS: $(ccp4_HEADERS)
+-	if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir $(DESTDIR)$(includedir)/ccp4; fi
++	if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir -p $(DESTDIR)$(includedir)/ccp4; fi
+ 	@list='$(ccp4_HEADERS)'; for p in $$list; do \
+ 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ 	  f="`echo $$p | sed -e 's|^.*/||'`"; \
+@@ -716,13 +716,11 @@ uninstall-mmdbHEADERS:
+ 	  rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
+ 	done
+ 
+-install : all install-ccp4HEADERS install-mmdbHEADERS
+-	$(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
+-	$(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
+-	$(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
+-	$(RANLIB) $(libdir)/$(LMMDB)
+-	$(RANLIB) $(libdir)/$(LC)
+-	$(RANLIB) $(libdir)/$(LF)
++install : all install-ccp4HEADERS
++	$(RANLIB) $(LC)
++	$(RANLIB) $(LF)
++	$(INSTALL_DATA) `pwd`/$(LC) $(DESTDIR)/$(libdir)/$(LC)
++	$(INSTALL_DATA) `pwd`/$(LF) $(DESTDIR)/$(libdir)/$(LF)
+ 	$(SHARE_INST)
+ 
+ uninstall : uninstall-ccp4HEADERS uninstall-mmdbHEADERS
+diff --git a/lib/ssm/Makefile.in b/lib/ssm/Makefile.in
+index 27d3aa2..0a14fe5 100755
+--- a/lib/ssm/Makefile.in
++++ b/lib/ssm/Makefile.in
+@@ -375,12 +375,12 @@ distclean-libtool:
+ uninstall-info-am:
+ install-library_includeHEADERS: $(library_include_HEADERS)
+ 	@$(NORMAL_INSTALL)
+-	test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)"
++	test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)/ssm"
+ 	@list='$(library_include_HEADERS)'; for p in $$list; do \
+ 	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+ 	  f=$(am__strip_dir) \
+-	  echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/$$f'"; \
+-	  $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/$$f"; \
++	  echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/ssm/$$f'"; \
++	  $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/ssm/$$f"; \
+ 	done
+ 
+ uninstall-library_includeHEADERS: