[med-svn] r15034 - in trunk/packages/loki/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-10-28 17:00:32 +0000 (Mon, 28 Oct 2013)
New Revision: 15034

Added:
   trunk/packages/loki/trunk/debian/patches/hardening.patch
Modified:
   trunk/packages/loki/trunk/debian/changelog
   trunk/packages/loki/trunk/debian/control
   trunk/packages/loki/trunk/debian/patches/series
   trunk/packages/loki/trunk/debian/rules
Log:
Fixed some hardening issues and uploaded to unstable


Modified: trunk/packages/loki/trunk/debian/changelog
===================================================================
--- trunk/packages/loki/trunk/debian/changelog	2013-10-28 16:48:12 UTC (rev 15033)
+++ trunk/packages/loki/trunk/debian/changelog	2013-10-28 17:00:32 UTC (rev 15034)
@@ -1,4 +1,4 @@
-loki (2.4.7.4-5) UNRELEASED; urgency=low
+loki (2.4.7.4-5) unstable; urgency=low
 
   * debian/upstream: added citation information
   * debian/control:
@@ -12,6 +12,7 @@
   * debian/copyright: DEP5
   * debian/rules: switch from cdbs to dh
   * debhelper 9 to enable hardening flags
+  * debian/patches/hardening.patch
 
  -- Andreas Tille <tille at debian.org>  Mon, 28 Oct 2013 17:08:17 +0100
 

Modified: trunk/packages/loki/trunk/debian/control
===================================================================
--- trunk/packages/loki/trunk/debian/control	2013-10-28 16:48:12 UTC (rev 15033)
+++ trunk/packages/loki/trunk/debian/control	2013-10-28 17:00:32 UTC (rev 15034)
@@ -11,7 +11,6 @@
 
 Package: loki
 Architecture: any
-Section: science
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Suggests: loki-doc
@@ -21,16 +20,18 @@
  traits only, although this restriction will be lifted in later versions.
  Joint estimation of QTL number, position and effects uses Reversible Jump
  MCMC. It is also possible to perform affected only IBD sharing analyses.
- .
- The homepage of this project used to be at http://loki.homeunix.net
- but the project is dead now and the homepage vanished.  The Homepage
- field above points to the web archive.
 
 Package: loki-doc
 Architecture: all
 Section: doc
 Depends: ${misc:Depends}
 Enhances: loki
-Description: Postscript manual for loki
+Description: MCMC linkage analysis on general pedigrees (PS manual)
+ Performs Markov chain Monte Carlo multipoint linkage analysis on large,
+ complex pedigrees.  The current package supports analyses on quantitative
+ traits only, although this restriction will be lifted in later versions.
+ Joint estimation of QTL number, position and effects uses Reversible Jump
+ MCMC. It is also possible to perform affected only IBD sharing analyses.
+ .
  Documentation on how to use Simon Heath's "prep" and "loki" tools 
  for MCMC genetic linkage and IBD analysis on general pedigrees.

Added: trunk/packages/loki/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/loki/trunk/debian/patches/hardening.patch	                        (rev 0)
+++ trunk/packages/loki/trunk/debian/patches/hardening.patch	2013-10-28 17:00:32 UTC (rev 15034)
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Mon, 28 Oct 2013 17:08:17 +0100
+Description: Propagate hardening for linker also into subdirectory utils
+
+--- a/utils/Makefile.in
++++ b/utils/Makefile.in
+@@ -12,7 +12,7 @@ bindir = @bindir@
+ INSTALL_PERM = 755
+ 
+ CFLAGS = $(MY_CFLAGS) -I../include
+-LDFLAGS = 
++LDFLAGS := $(LDFLAGS) 
+ LIBS = -lm 
+ ALL_LIBS = $(LIBS)
+ 
+@@ -26,7 +26,7 @@ qavg: qavg.c
+ 	$(CC) $(CFLAGS) -o $@ qavg.c $(LDFLAGS) $(ALL_LIBS)
+ 
+ hist: hist.c
+-	$(CC) $(CFLAGS) -o $@ hist.c
++	$(CC) $(CFLAGS) -o $@ hist.c $(LDFLAGS)
+ 
+ ../bin:
+ 	mkdir ../bin

Modified: trunk/packages/loki/trunk/debian/patches/series
===================================================================
--- trunk/packages/loki/trunk/debian/patches/series	2013-10-28 16:48:12 UTC (rev 15033)
+++ trunk/packages/loki/trunk/debian/patches/series	2013-10-28 17:00:32 UTC (rev 15034)
@@ -1,2 +1,3 @@
 10_utils.patch
 10_lex
+hardening.patch

Modified: trunk/packages/loki/trunk/debian/rules
===================================================================
--- trunk/packages/loki/trunk/debian/rules	2013-10-28 16:48:12 UTC (rev 15033)
+++ trunk/packages/loki/trunk/debian/rules	2013-10-28 17:00:32 UTC (rev 15034)
@@ -22,4 +22,4 @@
 	for man in $(MANPAGES) ; do \
 	    ln -s loki.1.gz debian/$(pkg)/usr/share/man/man1/$${man}.gz ; \
 	done
-	make install prefix=$(CURDIR)/debian/loki/usr bindir=$(CURDIR)/debian/loki/usr/bin
+	make install prefix=$(CURDIR)/debian/loki/usr bindir=$(CURDIR)/debian/loki/usr/bin LDFLAGS="$(LDFLAGS)"