Michael R. Crusoe pushed to branch master at Debian Med / vg
Commits: c4d49fac by Michael R. Crusoe at 2020-07-14T15:14:27+02:00 Restrict architectures to build for. Closes: #964039. - - - - - 0e905b0e by Michael R. Crusoe at 2020-07-14T18:44:38+02:00 remove old, unused protobuf patch - - - - - b9f084f9 by Michael R. Crusoe at 2020-07-14T18:44:38+02:00 release 1.25.0+ds-2 - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/series - − debian/patches/use_packaged_protobuf - debian/patches/use_packaged_vcflib Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +vg (1.25.0+ds-2) unstable; urgency=medium + + * Restrict architectures to build for. Closes: #964039. + + -- Michael R. Crusoe <[email protected]> Tue, 14 Jul 2020 15:15:28 +0200 + vg (1.25.0+ds-1) unstable; urgency=medium * New upstream version ===================================== debian/control ===================================== @@ -72,7 +72,7 @@ Rules-Requires-Root: no Package: vg Built-Using: ${simde:Built-Using} -Architecture: any +Architecture: amd64 i386 arm64 ppc64el s390x riscv64 x32 Depends: ${shlibs:Depends}, ${misc:Depends} Conflicts: cgvg ===================================== debian/patches/series ===================================== @@ -16,7 +16,6 @@ no_pg use_packaged_fastahack #use_packaged_vw # debian package is out of date, missing array_parameters.h, and not in testing/stable #use_packaged_sdsl # fails many tests, local copy is a newer snapshot than Debian's -#use_packaged_protobuf ? hardening_flags use_packaged_smithwaterman static ===================================== debian/patches/use_packaged_protobuf deleted ===================================== @@ -1,73 +0,0 @@ -Author: Michael R. Crusoe <[email protected]> -Description: Use the Debian packaged version of protobuf ---- vg.orig/Makefile -+++ vg/Makefile -@@ -35,7 +35,7 @@ - # Define libraries to link against. Make sure to always link statically against - # htslib and libdeflate and Protobuf so that we can use position-dependent code - # there for speed. --LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw $(CWD)/$(LIB_DIR)/libprotobuf.a -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg -+LD_LIB_FLAGS:= -L$(CWD)/$(LIB_DIR) $(CWD)/$(LIB_DIR)/libvgio.a -lhandlegraph -lvcflib -lgssw -lssw -lprotobuf -lsublinearLS $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lpthread -ljansson -lncurses -lgcsa2 -lgbwt -ldivsufsort -ldivsufsort64 -lvcfh -lgfakluge -lraptor2 -lsdsl -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -llz4 -lstructures -lvw -lboost_program_options -lallreduce -lbdsg - # Use pkg-config to find Cairo and all the libs it uses - LD_LIB_FLAGS += $(shell pkg-config --libs --static cairo jansson) - -@@ -173,7 +173,6 @@ - - - RAPTOR_DIR:=deps/raptor --PROTOBUF_DIR:=deps/protobuf - LOCKFREE_MALLOC_DIR:=deps/lockfree-malloc - SDSL_DIR:=deps/sdsl-lite - SNAPPY_DIR:=deps/snappy -@@ -211,7 +210,6 @@ - # But that requires fancy ar scripting. - # If you just pass them to ar it puts the library *file* in libvg where nothing can read it. - LIB_DEPS = --LIB_DEPS += $(LIB_DIR)/libprotobuf.a - LIB_DEPS += $(LIB_DIR)/libsdsl.a - LIB_DEPS += $(LIB_DIR)/libssw.a - LIB_DEPS += $(LIB_DIR)/libsnappy.a -@@ -291,13 +289,6 @@ - ln -s `which shuf` $(BIN_DIR)/shuf - endif - --# Make sure we have protoc built, and the protobuf lib --bin/protoc: $(LIB_DIR)/libprotobuf.a --$(LIB_DIR)/libprotobuf.a: deps/protobuf/src/google/protobuf/*.cc -- rm -rf $(LIB_DIR)/libprotobuf* $(LIB_DIR)/libprotoc* -- rm -Rf include/google/protobuf/ -- +. ./source_me.sh && cd $(PROTOBUF_DIR) && ./autogen.sh && export DIST_LANG=cpp && ./configure --prefix="$(CWD)" $(FILTER) && $(MAKE) $(FILTER) && $(MAKE) install && export PATH=$(CWD)/bin:$$PATH -- - test/build_graph: test/build_graph.cpp $(LIB_DIR)/libvg.a $(SRC_DIR)/json2pb.h $(SRC_DIR)/vg.hpp - . ./source_me.sh && $(CXX) $(INCLUDE_FLAGS) $(CXXFLAGS) -o test/build_graph test/build_graph.cpp -lvg $(LD_LIB_FLAGS) $(FILTER) - -@@ -347,7 +338,7 @@ - # But we don't delete libvgio.dylib; Mac insists on it for some reason. - # We also need to clear out the old Protobuf header in case Protobuf updated; - # we don't want to accidentally build against it. --$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIB_DIR)/libprotobuf.a $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp -+$(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp - +rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h - +rm -Rf $(CWD)/$(INC_DIR)/vg/io/ - +. ./source_me.sh && cd $(LIBVGIO_DIR) && PKG_CONFIG_PATH=$(CWD)/$(LIB_DIR)/pkgconfig:$(PKG_CONFIG_PATH) cmake -DCMAKE_PREFIX_PATH=$(CWD) -DCMAKE_LIBRARY_PATH=$(CWD)/$(LIB_DIR) -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib . $(FILTER) && $(MAKE) clean && VERBOSE=1 $(MAKE) $(FILTER) && $(MAKE) install && rm -f $(CWD)/$(LIB_DIR)/libvgio.so -@@ -579,7 +570,7 @@ - $(RM) -r $(OBJ_DIR)/*.o $(OBJ_DIR)/*.d - $(RM) -f $(INC_DIR)/vg_git_version.hpp $(INC_DIR)/vg_system_version.hpp - --clean: clean-protobuf clean-vcflib -+clean: clean-vcflib - $(RM) -r $(BIN_DIR) - $(RM) -r $(LIB_DIR) - $(RM) -r $(UNITTEST_OBJ_DIR) -@@ -612,11 +603,6 @@ - # lru_cache is never built because it is header-only. - # bash-tap is never built either. - --clean-protobuf: -- cd $(DEP_DIR) && cd protobuf && $(MAKE) clean -- rm -f $(LIB_DIR)/libprotobuf.a -- rm -rf $(INC_DIR)/google/protobuf/ -- - clean-vcflib: - cd $(DEP_DIR) && cd vcflib && $(MAKE) clean - rm -f $(LIB_DIR)/libvcfh.a ===================================== debian/patches/use_packaged_vcflib ===================================== @@ -1,6 +1,5 @@ Author: Michael R. Crusoe <[email protected]> Description: Attempt to use the Debian version of vcflib -but this fails due to the difference between the bundled htslib and the htslib used in Debian's vcflib --- vg.orig/Makefile +++ vg/Makefile @@ -31,12 +31,12 @@ View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/b048884e3843f507c33840d5583d10f0e7532358...b9f084f91e6a0ccbd44159fb208e0928d18f4432 -- View it on GitLab: https://salsa.debian.org/med-team/vg/-/compare/b048884e3843f507c33840d5583d10f0e7532358...b9f084f91e6a0ccbd44159fb208e0928d18f4432 You're receiving this email because of your account on salsa.debian.org.
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