refactor configuration

Author: Zilong-Li

.gitignore

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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: vcfppR
 Title: Rapid Manipulation of the Variant Call Format (VCF)
-Version: 0.7.7
+Version: 0.8.0
 Authors@R: c(
     person("Zilong", "Li", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5859-2078")),

cleanup.win

@@ -1,5 +1,5 @@
 #!/bin/sh
 
 HTSLIB_DIR="src/htslib-1.21"
-rm -f ${HTSLIB_DIR}/config.h src/*.o src/*.so src/*.dll src/*.dylib 
+rm -f ${HTSLIB_DIR}/config.h src/*.o src/*.dll src/*.so src/*.dylib 
 cd $HTSLIB_DIR && make clean && cd -

configure

@@ -1,30 +1,43 @@
 #!/bin/sh
 
-# Exit on any error
 set -e
 
+MAKE=`"${R_HOME}/bin/R" CMD config MAKE`
+CC=`"${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} ${R_CPICFLAGS} -fPIC -D_FILE_OFFSET_BITS=64"
+CFLAGS="-Wall -g -O2 -fvisibility=hidden -fPIC -D_FILE_OFFSET_BITS=64"
+# remove assert by defining NDEBUG
+CPPFLAGS="${R_CPPFLAGS} -DNDEBUG"
+
 HTSLIB_DIR="htslib-1.21"
 
 echo "Configuring HTSlib in $HTSLIB_DIR"
 cd src/$HTSLIB_DIR
+./configure \
+    CFLAGS="${CFLAGS}"
+
 ## copy file instead of symbolic linking
-cp htscodecs_bundled.mk htscodecs.mk
-./configure CFLAGS="-g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -DNDEBUG"
+rm -f htscodecs.mk && cp htscodecs_bundled.mk htscodecs.mk
+
+${MAKE} libhts.a CC="${CC}" CPPFLAGS="${CPPFLAGS}"  AR="${AR}" RANLIB="${RANLIB}"
+
+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
-
 echo "Create Makevar file"
-cd ../../
-SRC_MAKEVAR="src/Makevars"
-echo "PKG_CPPFLAGS=-I${HTSLIB_DIR} -I../inst/include" >$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

@@ -1,11 +1,46 @@
 #!/bin/sh
 
-HTSLIB_DIR="src/htslib-1.21"
+set -e
+
+MAKE=`"${R_HOME}/bin/R" CMD config MAKE`
+CC=`"${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=`"${R_HOME}/bin/R" CMD config CPICFLAGS`
+
+# -fPIC is ensential for shared lib
+CFLAGS="-Wall -g -O2 -fvisibility=hidden -fPIC -D_FILE_OFFSET_BITS=64"
+# CFLAGS="${R_CFLAGS} ${R_CPICFLAGS} -fPIC -D_FILE_OFFSET_BITS=64"
+# remove assert by defining NDEBUG
+CPPFLAGS="${R_CPPFLAGS} -DNDEBUG"
+
+HTSLIB_DIR="htslib-1.21"
+
 echo "Configuring HTSlib in $HTSLIB_DIR"
-cd $HTSLIB_DIR
-## fix symbolic linking error
-cp htscodecs_bundled.mk htscodecs.mk 
-./configure --without-libdeflate  CFLAGS="-g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -DNDEBUG"
+cd src/$HTSLIB_DIR
+# ./configure --without-libdeflate
+./configure \
+    --without-libdeflate \
+    CFLAGS="${CFLAGS}"
+
+## copy file instead of symbolic linking
+rm -f htscodecs.mk && cp htscodecs_bundled.mk htscodecs.mk
+
+${MAKE} libhts.a CC="${CC}" CPPFLAGS="${CPPFLAGS}"  AR="${AR}" RANLIB="${RANLIB}"
+
+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.win.in > Makevars.win
 
-make libhts.a
 

src/Makevars.in

@@ -0,0 +1,7 @@
+HTSLIB_DIR='./htslib-1.21'
+PKG_CPPFLAGS=-I$(HTSLIB_DIR) -I../inst/include @EXTRA_CPPFLAGS@
+PKG_LIBS=-L$(HTSLIB_DIR) -lhts @EXTRA_LIBS@
+
+.PHONY: all
+
+all: $(SHLIB)

src/Makevars.win

@@ -0,0 +1,17 @@
+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 += -lm -llzma -lbz2 -lcurl $(LIBPSL) $(LIBBROTLI) -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex
+else
+  PKG_LIBS += -lm -llzma -lbz2 -lregex $(shell pkg-config --libs libcurl)
+  PKG_CPPFLAGS += $(shell pkg-config --cflags libcurl)
+endif
+
+.PHONY: all
+
+all: $(SHLIB)
+

src/Makevars.win.in

@@ -3,3 +3,4 @@ files <- c(files, dir("htslib-1.21/", pattern="a$", full.names=TRUE))
 dest <- file.path(R_PACKAGE_DIR, paste0('libs', R_ARCH))
 dir.create(dest, recursive = TRUE, showWarnings = FALSE)
 file.copy(files, dest, overwrite = TRUE)
+