[med-svn] [trinityrnaseq] 01/03: improve hardening & drop galaxy plugin

[Michael Crusoe]

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

misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 7118b195d80b1514a2d5e24b630ad568df0ed6c2
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Mon Feb 22 02:26:41 2016 -0800

    improve hardening & drop galaxy plugin
    
    Galaxy isn't packaged for Debian
---
 debian/changelog          |  7 +++++++
 debian/copyright          |  2 +-
 debian/patches/hardening  | 13 +++++++++++--
 debian/rules              |  7 ++++++-
 debian/trinityrnaseq.docs |  1 -
 5 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a595a64..a09ec99 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+trinityrnaseq (2.1.1+dfsg-3) UNRELEASED; urgency=medium
+
+  * Properly harden Chrysalis binaries
+  * Drop Galaxy plugin
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu>  Mon, 22 Feb 2016 03:57:48 -0800
+
 trinityrnaseq (2.1.1+dfsg-2) unstable; urgency=medium
 
   * Split install of arch-dependent & arch-independent files, fixes FTBFS
diff --git a/debian/copyright b/debian/copyright
index 8c20dd8..0152d6d 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -15,7 +15,7 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  trinity-plugins/htslib*tar*
  trinity-plugins/samtools*
  trinity-plugins/slclust/Makefile.bak
- galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
+ galaxy-plugin
  Analysis/GenomeViewPlugin/*
  Chrysalis/MakeDepend.dSYM/*
  util/R/noiseq.r
diff --git a/debian/patches/hardening b/debian/patches/hardening
index eefba7b..3803561 100644
--- a/debian/patches/hardening
+++ b/debian/patches/hardening
@@ -2,7 +2,7 @@ Description: Use LDFLAGS & CPPFLAGS to enable hardening
 Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 --- trinityrnaseq.orig/Chrysalis/Makefile
 +++ trinityrnaseq/Chrysalis/Makefile
-@@ -312,7 +312,7 @@
+@@ -308,7 +308,7 @@
  endif
  
  # Linking control (e.g. to link templates):
@@ -11,7 +11,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
  # Required libraries:
  SYS_LIBS	= -lm -pthread
-@@ -384,7 +384,8 @@
+@@ -380,7 +380,8 @@
  		$(SYS_LANG) \
  		$(SYS_INCS) \
  		$(OMP_OPTIONS) \
@@ -21,6 +21,15 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
  
  LINK_OPTIONS	= \
  		$(SYS_DEBUG) \
+@@ -466,7 +467,7 @@
+ # How to compile C++ files:
+ .cc.o:
+ 	@ mkdir -p $(OBJ)/${@D}
+-	$(CPLUSPLUS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o
++	$(CPLUSPLUS) $(CXXFLAGS) $(CPPC) -c $(SRC)/$*.cc -o $(OBJ)/$*.o
+ 
+ ##############################################################################
+ ## ADDITIONAL TARGETS:
 --- trinityrnaseq.orig/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
 +++ trinityrnaseq/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
 @@ -1,8 +1,7 @@
diff --git a/debian/rules b/debian/rules
index 9063482..55f3e86 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,13 +12,18 @@ EXBASEDIR=debian/trinityrnaseq-examples/usr/share/trinityrnaseq
 LAST_CHANGE := $(shell dpkg-parsechangelog -S Date)
 export BUILD_DATETIME := $(shell LC_ALL=C date -u -d '$(LAST_CHANGE)')
 
+DPKG_EXPORT_BUILDFLAGS = 1
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+include /usr/share/dpkg/buildflags.mk
+
 %:
 	dh $@ --parallel --with javahelper,autoreconf
 
 override_dh_auto_configure:
 	for target in ${SOURCE_DIRECTORIES}; do dh_auto_configure \
 		--sourcedirectory=$${target} -- \
-		--prefix=/usr/lib/trinityrnaseq/$${target}; done
+		--prefix=/usr/lib/trinityrnaseq/$${target} \
+		$(shell dpkg-buildflags --export=configure); done
 
 override_dh_auto_build:
 	for target in ${SOURCE_DIRECTORIES}; do dh_auto_build \
diff --git a/debian/trinityrnaseq.docs b/debian/trinityrnaseq.docs
index 837d1fc..c88e05d 100644
--- a/debian/trinityrnaseq.docs
+++ b/debian/trinityrnaseq.docs
@@ -1,5 +1,4 @@
 README
 Release.Notes
 debian/tests/run-tests
-galaxy-plugin
 hpc_conf

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git