update configure

Author: Zilong-Li

.gitignore

@@ -21,3 +21,4 @@ README.html
 ## docs
 inst/doc
 /src/Makevars
+/src/Makevars.win

configure

@@ -1,33 +1,41 @@
 #!/bin/sh
 
-# Exit on any error
 set -e
 
+CC=`"${R_HOME}/bin/R" CMD config CC`
+AR=`"${R_HOME}/bin/R" CMD config AR`
+RANLIB=`"${R_HOME}/bin/R" CMD config RANLIB`
+R_CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+R_CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+R_CPICFLAGS=`"${R_HOME}/bin/R" CMD config CPICFLAGS`
+
+# -fPIC is ensential for shared lib
+CFLAGS="${R_CFLAGS} ${R_CPICFLAGS} -fPIC -D_FILE_OFFSET_BITS=64"
+# remove assert by defining NDEBUG
+CPPFLAGS="${R_CPPFLAGS} -D NDEBUG"
+
 HTSLIB_DIR="htslib-1.21"
 
 echo "Configuring HTSlib in $HTSLIB_DIR"
 cd src/$HTSLIB_DIR
 ## copy file instead of symbolic linking
 cp htscodecs_bundled.mk htscodecs.mk
-./configure CFLAGS="-g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -DNDEBUG"
+./configure \
+    --disable-shared \
+    --enable-static \
+    CFLAGS="${CFLAGS}" \
+    CPPFLAGS="${CPPFLAGS}"
+
+EXTRA_LIBS="-lz -lm -lbz2 -llzma -lcurl"
 
-hasdeflate="no"
 if grep -wq "#define HAVE_LIBDEFLATE 1" config.h;then
-    hasdeflate="yes"
+    EXTRA_LIBS="${EXTRA_LIBS} -ldeflate"
 fi
 
-make libhts.a
-
-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
-CPPFLAGS="${CPPFLAGS} -DNDEBUG"
-
 echo "Create Makevar file"
-cd ../../
-SRC_MAKEVAR="src/Makevars"
-echo "PKG_CPPFLAGS=-I${HTSLIB_DIR} -I../inst/include -DNDEBUG" >$SRC_MAKEVAR
-
-if [ $hasdeflate = "no" ]; then
-    echo "PKG_LIBS=${HTSLIB_DIR}/libhts.a -lz -lm -lbz2 -llzma -lcurl" >>$SRC_MAKEVAR
-else
-    echo "PKG_LIBS=${HTSLIB_DIR}/libhts.a -ldeflate -lz -lm -lbz2 -llzma -lcurl" >>$SRC_MAKEVAR
-fi    
+cd ..
+sed \
+    -e "s|@EXTRA_CPPFLAGS@|${CPPFLAGS}|g" \
+    -e "s|@EXTRA_LIBS@|${EXTRA_LIBS}|g" \
+    Makevars.in > Makevars
+

configure.win

@@ -1,21 +1,43 @@
 #!/bin/sh
 
-HTSLIB_DIR="src/htslib-1.21"
-echo "Configuring HTSlib in $HTSLIB_DIR"
-cd $HTSLIB_DIR
-## fix symbolic linking error
-cp htscodecs_bundled.mk htscodecs.mk 
-# CPPFLAGS="-DNDEBUG"  CFLAGS="-g -O2 -fPIC -D_FILE_OFFSET_BITS=64"
-./configure --without-libdeflate
+set -e
 
 CC=`"${R_HOME}/bin/R" CMD config CC`
 AR=`"${R_HOME}/bin/R" CMD config AR`
 RANLIB=`"${R_HOME}/bin/R" CMD config RANLIB`
-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
-CPPFLAGS="${CPPFLAGS} -DNDEBUG"
-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
-CPICFLAGS=`"${R_HOME}/bin/R" CMD config CPICFLAGS`
-CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
+R_CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+R_CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+R_CPICFLAGS=`"${R_HOME}/bin/R" CMD config CPICFLAGS`
+
+# -fPIC is ensential for shared lib
+CFLAGS="${R_CFLAGS} ${R_CPICFLAGS} -fPIC -D_FILE_OFFSET_BITS=64"
+# remove assert by defining NDEBUG
+CPPFLAGS="${R_CPPFLAGS} -D NDEBUG"
+
+HTSLIB_DIR="htslib-1.21"
+
+echo "Configuring HTSlib in $HTSLIB_DIR"
+cd src/$HTSLIB_DIR
+## copy file instead of symbolic linking
+cp htscodecs_bundled.mk htscodecs.mk
+# ./configure --without-libdeflate
+./configure \
+    --disable-shared \
+    --enable-static \
+    CFLAGS="${CFLAGS}" \
+    CPPFLAGS="${CPPFLAGS}"
+
+EXTRA_LIBS="-lz"
+
+if grep -wq "#define HAVE_LIBDEFLATE 1" config.h;then
+    EXTRA_LIBS="${EXTRA_LIBS} -ldeflate"
+fi
+    
+echo "Create Makevar file"
+cd ..
+sed \
+    -e "s|@EXTRA_CPPFLAGS@|${CPPFLAGS}|g" \
+    -e "s|@EXTRA_LIBS@|${EXTRA_LIBS}|g" \
+    Makevars.in > Makevars
 
-make libhts.a CC="${CC}" CPPFLAGS="${CPPFLAGS}" CFLAGS="${CFLAGS} ${CPICFLAGS}" AR="${AR}" RANLIB="${RANLIB}"
 

src/Makevars.in

@@ -0,0 +1,13 @@
+HTSLIB_DIR='./htslib-1.21'
+PKG_CPPFLAGS=-I$(HTSLIB_DIR) -I../inst/include @EXTRA_CPPFLAGS@
+PKG_LIBS=-L$(HTSLIB_DIR) -lhts @EXTRA_LIBS@
+
+all: $(SHLIB)
+
+$(SHLIB): $(HTSLIB_DIR)/libhts.a
+
+$(HTSLIB_DIR)/libhts.a:
+	(cd $(HTSLIB_DIR) && $(MAKE) libhts.a CC=$(CC) CPPFLAGS=$(CPPFLAGS) CFLAGS=$(CFLAGS) $(CPICFLAGS) AR=$(AR) RANLIB=$(RANLIB))
+
+clean:
+	(cd $(HTSLIB_DIR) && $(MAKE) clean)

src/Makevars.win renamed to src/Makevars.win.in

@@ -1,11 +1,11 @@
-HTSLIB_DIR='htslib-1.21'
-PKG_CPPFLAGS = -I${HTSLIB_DIR} -I../inst/include -DNDEBUG
-PKG_LIBS=-L${HTSLIB_DIR} -lhts
+HTSLIB_DIR='./htslib-1.21'
+PKG_CPPFLAGS=-I$(HTSLIB_DIR) -I../inst/include @EXTRA_CPPFLAGS@
+PKG_LIBS=-L$(HTSLIB_DIR) -lhts @EXTRA_LIBS@
 
 ifeq (,$(shell pkg-config --version 2>/dev/null))
   LIBPSL = $(or $(and $(wildcard $(R_TOOLS_SOFT)/lib/libpsl.a),-lpsl),)
   LIBBROTLI = $(or $(and $(wildcard $(R_TOOLS_SOFT)/lib/libbrotlidec.a),-lbrotlidec -lbrotlicommon),)
-  PKG_LIBS += ${HTSLIB_DIR}/libhts.a -lm -lbz2 -llzma -lcurl $(LIBPSL) $(LIBBROTLI) -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -lz
+  PKG_LIBS += ${HTSLIB_DIR}/libhts.a -lm -lbz2 -llzma -lcurl $(LIBPSL) $(LIBBROTLI) -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex
 else
   PKG_LIBS += -llzma -lbz2 -lregex $(shell pkg-config --libs libcurl)
   PKG_CPPFLAGS += $(shell pkg-config --cflags libcurl)
@@ -15,5 +15,11 @@ endif
 
 all: $(SHLIB)
 
-$(SHLIB): htslib-1.21/libhts.a
+$(SHLIB): $(HTSLIB_DIR)/libhts.a
+
+$(HTSLIB_DIR)/libhts.a:
+	(cd $(HTSLIB_DIR) && $(MAKE) libhts.a CC=$(CC) CPPFLAGS=$(CPPFLAGS) CFLAGS=$(CFLAGS) $(CPICFLAGS) AR=$(AR) RANLIB=$(RANLIB))
+
+clean:
+	(cd $(HTSLIB_DIR) && $(MAKE) clean)