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.cru...@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.cru...@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.cru...@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 You're receiving this email because of your account on salsa.debian.org.
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