[med-svn] [Git][med-team/vg][master] 3 commits: Restrict architectures to build for. Closes: #964039.
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Jul 14 19:33:46 BST 2020
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 <crusoe at debian.org> 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},
${misc:Depends}
Conflicts: cgvg
=====================================
debian/patches/series
=====================================
@@ -16,7 +16,6 @@ no_pg
use_packaged_fastahack
#use_packaged_vw # debian package is out of date, missing array_parameters.h, and not in testing/stable
#use_packaged_sdsl # fails many tests, local copy is a newer snapshot than Debian's
-#use_packaged_protobuf ?
hardening_flags
use_packaged_smithwaterman
static
=====================================
debian/patches/use_packaged_protobuf deleted
=====================================
@@ -1,73 +0,0 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
-Description: Use the Debian packaged version of protobuf
---- vg.orig/Makefile
-+++ vg/Makefile
-@@ -35,7 +35,7 @@
- # Define libraries to link against. Make sure to always link statically against
- # htslib and libdeflate and Protobuf so that we can use position-dependent code
- # there for speed.
--LD_LIB_FLAGS:= -L$(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 <michael.crusoe at gmail.com>
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
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