[med-svn] [trinityrnaseq] 02/03: add hardening

Michael Crusoe misterc-guest at moszumanska.debian.org
Wed Sep 16 21:10:05 UTC 2015 

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

commit 7e2bc8b65b281d235680f1db9623844396bcba41
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Sep 16 11:01:16 2015 -0700

    add hardening
---
 debian/autoreconf            |  1 +
 debian/control               |  1 +
 debian/copyright             |  1 +
 debian/lintian-overrides     |  2 -
 debian/patches/hardening     | 89 ++++++++++++++++++++++++++++++++++++++++++++
 debian/patches/series        |  1 +
 debian/rules                 |  8 ++--
 debian/trinityrnaseq.install |  1 -
 8 files changed, 96 insertions(+), 8 deletions(-)

diff --git a/debian/autoreconf b/debian/autoreconf
new file mode 100644
index 0000000..97ab876
--- /dev/null
+++ b/debian/autoreconf
@@ -0,0 +1 @@
+Inchworm
diff --git a/debian/control b/debian/control
index 1af3396..637dfd2 100644
--- a/debian/control
+++ b/debian/control
@@ -5,6 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                autotools-dev,
+               dh-autoreconf,
                automake1.11,
                jellyfish (>= 2.1.4),
                libjung-free-java,
diff --git a/debian/copyright b/debian/copyright
index 0615a0f..bebb07c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -14,6 +14,7 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  trinity-plugins/TransDecoder*
  trinity-plugins/collectl
  trinity-plugins/GAL*
+ trinity-plugins/slclust/Makefile.bak
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
index 6fb9c91..3cb29c6 100644
--- a/debian/lintian-overrides
+++ b/debian/lintian-overrides
@@ -1,4 +1,2 @@
 trinityrnaseq: executable-not-elf-or-script usr/lib/trinityrnaseq/*
 trinityrnaseq: image-file-in-usr-lib usr/lib/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/*
-trinityrnaseq: package-contains-timestamped-gzip usr/lib/trinityrnaseq/Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
-trinityrnaseq: package-contains-timestamped-gzip usr/lib/trinityrnaseq/sample_data/*
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 0000000..22ac52d
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,89 @@
+Description: Use LDFLAGS & CPPFLAGS to enable hardening
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+--- trinityrnaseq.orig/Chrysalis/Makefile
++++ trinityrnaseq/Chrysalis/Makefile
+@@ -309,7 +309,7 @@
+ endif
+ 
+ # Linking control (e.g. to link templates):
+-SYS_LINK	=
++SYS_LINK	=  $(LDFLAGS)
+ 
+ # Required libraries:
+ SYS_LIBS	= -lm -pthread
+@@ -381,7 +381,8 @@
+ 		$(SYS_LANG) \
+ 		$(SYS_INCS) \
+ 		$(OMP_OPTIONS) \
+-		$(PTHREAD_OPTIONS)
++		$(PTHREAD_OPTIONS) \
++		$(CPPFLAGS)
+ 
+ LINK_OPTIONS	= \
+ 		$(SYS_DEBUG) \
+--- trinityrnaseq.orig/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
++++ trinityrnaseq/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
+@@ -1,8 +1,7 @@
+-CC     = gcc
+-CFLAGS = -O2 -std=c99 -Werror
++CFLAGS += -O2 -std=c99 -Werror
+ 
+ all:kseq.h fastool.c
+-	$(CC) $(CFLAGS) fastool.c -o fastool
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) fastool.c -o fastool
+ 
+ clean:
+ 	rm -f *.o fastool
+--- trinityrnaseq.orig/trinity-plugins/slclust/src/Makefile
++++ trinityrnaseq/trinity-plugins/slclust/src/Makefile
+@@ -17,11 +17,8 @@
+ # use ${LIBDIR} defined above if appropriate
+ LIBS           = 
+ 
+-# How they are invoked on the compile line (eg: -lspecial)
+-LLIBS          =
+-
+ # Local additions for the CFLAG options
+-LOCAL_CFLAGS   = -Wall 
++LOCAL_CXXFLAGS   = -Wall 
+ #-static
+ 
+ 
+@@ -34,20 +31,11 @@
+ INCLUDE       = ${PROJECT_ROOT}/include
+ 
+ DEBUG         = DEBUG
+-CFLAGS        = -I${INCLUDE} ${LOCAL_CFLAGS}
+-CC            = g++ ${CFLAGS}
++CXXFLAGS        += -I${INCLUDE} ${LOCAL_CXXFLAGS}
+ 
+ MAKEFILE      = Makefile
+ 
+ 
+-# Suffix rules
+-
+-.cc.o:
+-	${CC} -c $<
+-
+-.cpp.o:
+-	${CC} -c $<
+-
+ # Target dependencies
+ 
+ 
+@@ -59,12 +47,13 @@
+ 
+ 
+ clean :
+-	rm -f ${OBJS} core a.out *~ \#* ${EXECUTABLE} ${MAKEFILE}.bak
++	rm -f ${OBJS} core a.out *~ \#* ${EXECUTABLE} ${MAKEFILE}.bak \
++		${BIN}/${EXECUTABLE}
+ 
+ 
+ ${OBJ} : ${MAKEFILE}
+ 
+ ${EXECUTABLE} : ${OBJS}
+-	${CC} ${OBJS} ${LIBS} -o ${EXECUTABLE}	
++	${CXX} ${LDFLAGS} ${OBJS} ${LIBS} -o ${EXECUTABLE}	
+ 	chmod 755 ${EXECUTABLE}
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 7daf669..b7c5342 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ collections15-to-4
 0002-fix_istream_failure_call.patch
 fix-jsquery
 fix_system_paths
+hardening
diff --git a/debian/rules b/debian/rules
index 394c18d..aa5fd46 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,11 +9,10 @@ SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugin
 BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
 
 %:
-	dh $@ --parallel --with javahelper
+	dh $@ --parallel --with javahelper,autoreconf
 
 override_dh_auto_configure:
-	for target in ${SOURCE_DIRECTORIES}; do dh_autotools-dev_updateconfig \
-		-O--sourcedirectory=$${target}; dh_auto_configure \
+	for target in ${SOURCE_DIRECTORIES}; do dh_auto_configure \
 		--sourcedirectory=$${target} -- \
 		--prefix=/usr/lib/trinityrnaseq/$${target}; done
 
@@ -22,8 +21,7 @@ override_dh_auto_build:
 		-O--sourcedirectory=$${target}; done
 
 override_dh_auto_clean:
-	for target in ${SOURCE_DIRECTORIES}; do dh_autotools-dev_restoreconfig \
-		-O--sourcedirectory=$${target}; dh_auto_clean \
+	for target in ${SOURCE_DIRECTORIES}; do dh_auto_clean \
 		--sourcedirectory=$${target}; done
 	rm Chrysalis/Makefile_auto
 
diff --git a/debian/trinityrnaseq.install b/debian/trinityrnaseq.install
index d824aa2..8c6270f 100644
--- a/debian/trinityrnaseq.install
+++ b/debian/trinityrnaseq.install
@@ -15,7 +15,6 @@ Chrysalis/GraphFromFasta /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/CreateIwormFastaBundle /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/Chrysalis /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/BreakTransByPairs /usr/lib/trinityrnaseq/Chrysalis/
-Chrysalis/checkLock /usr/lib/trinityrnaseq/Chrysalis/
 Trinity /usr/lib/trinityrnaseq
 PerlLib /usr/lib/trinityrnaseq/
 sample_data /usr/lib/trinityrnaseq/

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