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misterc-guest pushed a commit to branch master
in repository r-hms-dbmi-spp.

commit 5bb58375f60e602d463fb32680e9d921e369cd94
Author: Michael R. Crusoe <michael.cru...@gmail.com>
Date:   Sat Oct 15 05:12:44 2016 -0700

    propagate flags passed to configure
---
 debian/patches/propagate-flags | 10 ++++++++++
 debian/patches/series          |  1 +
 debian/rules                   | 29 +++++++++++++++--------------
 3 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/debian/patches/propagate-flags b/debian/patches/propagate-flags
new file mode 100644
index 0000000..8db4885
--- /dev/null
+++ b/debian/patches/propagate-flags
@@ -0,0 +1,10 @@
+From: Michael R. Crusoe <michael.cru...@gmail.com>
+Subject: Propogate flags passed to configure
+--- r-hms-dbmi-spp.orig/src/Makevars.in
++++ r-hms-dbmi-spp/src/Makevars.in
+@@ -1,4 +1,3 @@
+ PKG_LIBS=@LIBS@ -lz
+ PKG_CFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@  
+-PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS  @HAVE_LIBBZ2@  @BOOST_CPPFLAGS@
+-
++PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@  @BOOST_CPPFLAGS@ 
@CXXFLAGS@
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..ff2e5cd
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+propagate-flags
diff --git a/debian/rules b/debian/rules
index 803e2fe..07a3fa8 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,21 +1,22 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
-export CXXFLAGS=-std=c++98
 
-debRreposname=hms-dbmi
-include /usr/share/R/debian/r-cran.mk
+# Use hardening flags for linking
+export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+CXXFLAGS +=-std=c++98
+
+PKG_CFLAGS=$(CFLAGS)
+PKG_CXXFLAGS=$(CXXFLAGS)
+PKG_CPPFLAGS=$(CPPFLAGS)
+PKG_FFLAGS=$(FFLAGS)
 
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION        := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 
's/-.*//')
-#DEBFLAVOR      := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print 
$$2}')
-#DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' 
debian/gbp.conf)
-#GIT_TAG        := $(subst ~,_,$(VERSION))
+export PKG_CFLAGS PKG_CXXFLAGS PKG_CPPFLAGS PKG_FFLAGS
 
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+makeFlags="LDFLAGS=$(LDFLAGS)"  # Doesn't seem to work?
 
+debRreposname=hms-dbmi
+include /usr/share/R/debian/r-cran.mk

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