[med-svn] [subread] 03/04: d/rules: export EXTRA_FLAGS with hardening flags d/patches/inject_hardening_flags.patch: add EXTRA_FLAGS to LDFLAGS d/patches/fix_syntax.patch: fix syntax error

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository subread.

commit f40148dd2830a23242123fbf1be751c5ba936454
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Feb 23 14:45:54 2015 +0100

    d/rules: export EXTRA_FLAGS with hardening flags
    d/patches/inject_hardening_flags.patch: add EXTRA_FLAGS to LDFLAGS
    d/patches/fix_syntax.patch: fix syntax error
---
 debian/control                              |  2 +-
 debian/patches/fix_syntax.patch             | 13 +++++++++++++
 debian/patches/inject_hardening_flags.patch | 13 +++++++++++++
 debian/patches/series                       |  2 ++
 debian/rules                                |  8 ++------
 5 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/debian/control b/debian/control
index 2b18b5a..0da9d85 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               zlib1g-dev
+               zlib1g-dev,
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/subread.git
 Vcs-Git: git://anonscm.debian.org/debian-med/subread.git
diff --git a/debian/patches/fix_syntax.patch b/debian/patches/fix_syntax.patch
new file mode 100644
index 0000000..94b8ae0
--- /dev/null
+++ b/debian/patches/fix_syntax.patch
@@ -0,0 +1,13 @@
+Subject: spelling-error-in-binary subread-buildindex sucessfully successfully
+Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+--- subread.orig/src/index-builder.c
++++ subread/src/index-builder.c
+@@ -958,7 +958,7 @@
+ 	if(tmp_file_for_signal[0])
+ 	{
+ 		unlink(tmp_file_for_signal);
+-		SUBREADprintf("\n\nReceived a terminal signal. The temporary file was removed. The index was NOT built sucessfully. Please DO NOT use the new index until they are rebuilt.\n\n");
++		SUBREADprintf("\n\nReceived a terminal signal. The temporary file was removed. The index was NOT built successfully. Please DO NOT use the new index until they are rebuilt.\n\n");
+ 	}
+ 
+ 	exit(param);
diff --git a/debian/patches/inject_hardening_flags.patch b/debian/patches/inject_hardening_flags.patch
new file mode 100644
index 0000000..7a0de01
--- /dev/null
+++ b/debian/patches/inject_hardening_flags.patch
@@ -0,0 +1,13 @@
+Subject: Patch injects hardening LDFLAGS
+Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+--- subread.orig/src/Makefile.Linux
++++ subread/src/Makefile.Linux
+@@ -4,7 +4,7 @@
+ 
+ CCFLAGS = -mtune=core2 ${MACOS} -O9 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
+ #CCFLAGS =  -D_FORTIFY_SOURCE=2 -mtune=core2 ${MACOS} -O2 -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  # -DREPORT_ALL_THE_BEST
+-LDFLAGS = ${STATIC_MAKE} -lpthread -lz -lm ${MACOS} -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
++LDFLAGS = ${STATIC_MAKE} ${EXTRA_FLAGS} -lpthread -lz -lm ${MACOS} -O9 -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+ CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 
+ 
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c3feeb9
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix_syntax.patch
+inject_hardening_flags.patch
diff --git a/debian/rules b/debian/rules
index e6f24f0..762920d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,17 +3,13 @@ DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/default.mk
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-
-export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
-export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
-CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
-LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+export EXTRA_FLAGS := $(shell dpkg-buildflags --get LDFLAGS)
 
 %:
 	dh $@
 
 override_dh_clean:
-	cd src; DEB_BUILD_HARDENING=1 make -f  Makefile.Linux clean
+	cd src; make -f Makefile.Linux clean
 	dh_clean
 
 override_dh_auto_build:

-- 
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