From: "Michael R. Crusoe" <crusoe@debian.org>
Date: Fri, 6 Sep 2019 14:16:07 +0900
Subject: Use the Debian package for libdeflate

Forwarded: not-needed
---
 Makefile | 21 ++-------------------
 1 file changed, 2 insertions(+), 19 deletions(-)

diff --git a/Makefile b/Makefile
index 9dbfe97..4d65db8 100644
--- a/Makefile
+++ b/Makefile
@@ -77,7 +77,7 @@ LD_LIB_FLAGS := -lvcflib -ltabixpp -lgssw -lssw -lsublinearLS -lpthread -lncurse
 # By default it has no suffix
 BOOST_SUFFIX=""
 # We define some more libraries to link against at the end, in static linking mode if possible, so we can use faster non-PIC code.
-LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a $(CWD)/$(LIB_DIR)/libdeflate.a -lz -lbz2 -llzma
+LD_STATIC_LIB_FLAGS := -lvgio $(CWD)/$(LIB_DIR)/libtabixpp.a $(CWD)/$(LIB_DIR)/libhts.a -ldeflate -lz -lbz2 -llzma
 # Some of our static libraries depend on libraries that may not always be avilable in static form.
 LD_STATIC_LIB_DEPS := -lpthread -lm
 # Use pkg-config to find dependencies.
@@ -356,7 +356,6 @@ STRUCTURES_DIR:=deps/structures
 BACKWARD_CPP_DIR:=deps/backward-cpp
 DOZEU_DIR:=deps/dozeu
 ELFUTILS_DIR:=deps/elfutils
-LIBDEFLATE_DIR:=deps/libdeflate
 LIBVGIO_DIR:=deps/libvgio
 LIBHANDLEGRAPH_DIR:=deps/libhandlegraph
 LIBBDSG_DIR:=deps/libbdsg
@@ -398,7 +397,6 @@ LIB_DEPS += $(LIB_DIR)/libraptor2.a
 LIB_DEPS += $(LIB_DIR)/libfml.a
 LIB_DEPS += $(LIB_DIR)/libsublinearLS.a
 LIB_DEPS += $(LIB_DIR)/libstructures.a
-LIB_DEPS += $(LIB_DIR)/libdeflate.a
 LIB_DEPS += $(LIB_DIR)/libvgio.a
 LIB_DEPS += $(LIB_DIR)/libhandlegraph.a
 LIB_DEPS += $(LIB_DIR)/libbdsg.a
@@ -648,21 +646,6 @@ $(LIB_DIR)/libhandlegraph.a: $(LIBHANDLEGRAPH_DIR)/src/include/handlegraph/*.hpp
 	+. ./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
 
 
-# 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-# We don't just leave it as .so because we need to deal with outdated .so files with no paths set.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 $(LIBDEFLATE_DIR) && V=1 LDFLAGS="$(LDFLAGS) $(LD_RENAMEABLE_FLAGS)" $(MAKE) $(FILTER) && cp libdeflate.a $(CWD)/$(LIB_DIR) && cp libdeflate.h $(CWD)/$(INC_DIR)
-
 # We build htslib after libdeflate so it can use libdeflate.
 # We need to do some wizardry to get it to pick up the right build and target system types on modern autotools.
 # We have to do a full build in order to install, to get the pkg-config file so libvgio can link against it.
@@ -673,7 +656,7 @@ $(LIB_DIR)/libdeflate.a: $(LIBDEFLATE_DIR)/*.h $(LIBDEFLATE_DIR)/lib/*.h $(LIBDE
 # We also need to make sure that htslib searches itself before system paths, as
 # a system path, in case another htslib is installed on the system. Some HTSlib
 # headers look for the current HTSlib with <>.
-$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(LIB_DIR)/libdeflate.a $(LIB_DIR)/libdeflate.$(SHARED_SUFFIX) $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
+$(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h
 	+. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoreconf -i && autoheader && autoconf || true
 	+. ./source_me.sh && cd $(HTSLIB_DIR) && (./configure -n 2>&1 || true) | grep "build system type" | rev | cut -f1 -d' ' | rev >systype.txt
 	+. ./source_me.sh && cd $(HTSLIB_DIR) && CFLAGS="-I$(CWD)/$(HTSLIB_DIR) -isystem $(CWD)/$(HTSLIB_DIR) -I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="$(LDFLAGS) -L$(CWD)/$(LIB_DIR) $(LD_UTIL_RPATH_FLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) --host=$$(cat systype.txt) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install
