Can't change the libdeflate install_name on MacOS "because larger updated load commands do not fit" about vg

[adamnovak]

I think adding that flag to LD_LIB_FLAGS doesn't work because those flags also get passed to the compiler in the vg makefile, and in that context you might need a -Wl, on the front.

Maybe we need to pass those flags specifically to the libdeflate build?

vg/Makefile

Lines 646 to 659 in 963d8d9

	# On Linux, libdeflate builds a .so.
	# On Mac, it *still* builds an so, which is just a dylib with .so extension.
	# On Mac we need to make sure to set the install name. We do that by renaming to dylib.
	# We don't just leave it as .so because we need to deal with outdated .so files with no paths set.
	$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX): $(LIB_DIR)/libdeflate.a
	+cd $(LIBDEFLATE_DIR) && cp libdeflate.so $(CWD)/$(LIB_DIR)
	+touch $(CWD)/$(LIB_DIR)/libdeflate.so
	ifeq ($(shell uname -s),Darwin)
	+mv $(LIB_DIR)/libdeflate.so $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
	+install_name_tool -id $(CWD)/$(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX)
	endif
	$(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
	+. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)

Once you get libdeflate.dylib to build with those flags, you can probably take them out and complete the vg build.

[stacy-l]

Managed to resolve this:

vg/Makefile

Lines 658 to 659 in 963d8d9

	$(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDEFLATE_DIR)/lib/*/*.h $(LIBDEFLATE_DIR)/lib/*.c $(LIBDEFLATE_DIR)/lib/*/*.c
	+. ./source_me.sh && cd $(LIBDEFLATE_DIR) && V=1 $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)

Drop in change, doesn't need to be reverted to finish building.

$(LIB_DIR)/libhandlegraph.a: $(LIBHANDLEGRAPH_DIR)/src/include/handlegraph/*.hpp $(LIBHANDLEGRAPH_DIR)/src/*.cpp
	+. ./source_me.sh && cd $(LIBHANDLEGRAPH_DIR) && rm -Rf build CMakeCache.txt CMakeFiles && mkdir build && cd build && CXXFLAGS="$(CXXFLAGS) $(CPPFLAGS)" cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=$(CWD) -DCMAKE_INSTALL_LIBDIR=lib .. && $(MAKE) $(FILTER) && $(MAKE) install

[adamnovak]

I'm not sure those are the right lines? But I have a PR that I think will do what I think you did, on Mac.