[med-svn] [Git][med-team/trinityrnaseq][master] CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq


Commits:
10f51f60 by Michael R. Crusoe at 2019-01-04T15:59:16Z
CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs

and add LDFALGS CPPFLAGS and unshadow CFALGS for seqtk-trinity-0.0.2

- - - - -


5 changed files:

- debian/changelog
- + debian/patches/hardening
- + debian/patches/seqtk-trinity-hardening
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+trinityrnaseq (2.6.6+dfsg-7) UNRELEASED; urgency=medium
+
+  * Eliminate warning about missing hardening flags
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Fri, 04 Jan 2019 07:58:22 -0800
+
 trinityrnaseq (2.6.6+dfsg-6) unstable; urgency=medium
 
   * -examples: Don't hardcode number of --CPU (especially above 2). Fixes the


=====================================
debian/patches/hardening
=====================================
@@ -0,0 +1,24 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs
+--- trinityrnaseq.orig/Chrysalis/Makefile
++++ trinityrnaseq/Chrysalis/Makefile
+@@ -466,7 +466,7 @@
+ # 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/scaffold_iworm_contigs/Makefile
++++ trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/Makefile
+@@ -2,7 +2,7 @@
+ prefix = ../htslib
+ 
+ ScaffoldIwormContigs:
+-	$(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
++	$(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) $(CPPFLAGS) $(CXXFLAGS) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
+ 
+ clean:
+ 	rm -f scaffold_iworm_contigs


=====================================
debian/patches/seqtk-trinity-hardening
=====================================
@@ -0,0 +1,18 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Add LDFALGS CPPFLAGS and unshadw CFALGS for seqtk-trinity-0.0.2
+
+--- trinityrnaseq.orig/trinity-plugins/seqtk-trinity-0.0.2/Makefile
++++ trinityrnaseq/trinity-plugins/seqtk-trinity-0.0.2/Makefile
+@@ -1,10 +1,10 @@
+ CC=gcc
+-CFLAGS=-g -Wall -O2 -Wno-unused-function
++CFLAGS+=-g -Wall -O2 -Wno-unused-function
+ 
+ all:seqtk-trinity
+ 
+ seqtk-trinity:seqtk.c khash.h kseq.h
+-		$(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
++		$(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) seqtk.c -o $@ -lz -lm
+ 
+ clean:
+ 		rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*


=====================================
debian/patches/series
=====================================
@@ -14,3 +14,4 @@ disable-libieee
 python3
 better_java_version_check
 unfix_num_of_cores
+hardening


=====================================
debian/rules
=====================================
@@ -27,9 +27,11 @@ override_dh_auto_configure:
 		$(shell dpkg-buildflags --export=configure); done
 
 override_dh_auto_build:
+	patch -p1 < debian/patches/seqtk-trinity-hardening
 	for target in ${SOURCE_DIRECTORIES_ALL}; do dh_auto_build \
 		-O--sourcedirectory=$${target}; done
 
+
 override_dh_auto_clean:
 	for target in ${SOURCE_DIRECTORIES}; do dh_auto_clean \
 		--sourcedirectory=$${target}; done



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/commit/10f51f605b9ad837d8c6cbecc1863b12519246d6
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