fix configure, cleanup

cleanup

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-rm -f src/htslib-1.19.1/config.h src/*.o src/*.so src/*.dll src/*.dylib 
-cd src/htslib-1.19.1/ && make clean && cd -
+rm -f src/htslib-1.21/config.h src/*.o src/*.so src/*.dll src/*.dylib 
+cd src/htslib-1.21/ && make clean && cd -

cleanup.win

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-rm -f src/htslib-1.18/config.h src/*.o src/*.so src/*.dll src/*.dylib 
-cd src/htslib-1.18/ && make clean && cd -
+rm -f src/htslib-1.21/config.h src/*.o src/*.so src/*.dll src/*.dylib 
+cd src/htslib-1.21/ && make clean && cd -

configure.win

@@ -2,4 +2,4 @@
 
 HTSLIB_DIR="src/htslib-1.21"
 echo "Configuring HTSlib in $HTSLIB_DIR"
-cd $HTSLIB_DIR && ./configure && make
+cd $HTSLIB_DIR && ./configure --without-libdeflate && make

src/htslib-1.21/Makefile

@@ -22,9 +22,9 @@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
-AR     = ar
-RANLIB = ranlib
+CC       := $(shell ${R_HOME}/bin/R CMD config CC)
+AR       := $(shell ${R_HOME}/bin/R CMD config AR)
+RANLIB   := $(shell ${R_HOME}/bin/R CMD config RANLIB)
 
 # Default libraries to link if configure is not used
 htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl
@@ -35,7 +35,7 @@ CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
-CFLAGS   = -g -Wall -O2 -fvisibility=hidden
+CFLAGS   = -g -Wall -O2 -fvisibility=hidden -fPIC
 EXTRA_CFLAGS_PIC = -fpic
 TARGET_CFLAGS =
 LDFLAGS  = -fvisibility=hidden