diff --git a/configure b/configure index 2544557..97ef24a 100755 --- a/configure +++ b/configure @@ -8,8 +8,8 @@ HTSLIB_DIR="src/htslib-1.21" echo "Configuring HTSlib in $HTSLIB_DIR" cd $HTSLIB_DIR ./configure \ - --without-libdeflate \ - CFLAGS="-O2 -fPIC" - + CFLAGS="-O2 -fPIC" \ + LDFLAGS=$(${R_HOME}/bin/R CMD config LDFLAG) + make libhts.a diff --git a/configure.win b/configure.win index 4034c55..ddace16 100755 --- a/configure.win +++ b/configure.win @@ -3,9 +3,11 @@ HTSLIB_DIR="src/htslib-1.21" echo "Configuring HTSlib in $HTSLIB_DIR" cd $HTSLIB_DIR +## fix symbolic linking error +cp htscodecs_bundled.mk htscodecs.mk ./configure \ - --without-libdeflate \ - CFLAGS="-O2 -fPIC" + CFLAGS="-O2 -fPIC" \ + LDFLAGS=$(${R_HOME}/bin/R CMD config LDFLAG) make libhts.a