From e6c2d8f74bf2a473825f4bacf1f6e70e97315a26 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Sat, 14 Dec 2024 21:21:58 +0100
Subject: [PATCH] fix configure, cleanup

---
 cleanup                  | 4 ++--
 cleanup.win              | 4 ++--
 configure.win            | 2 +-
 src/htslib-1.21/Makefile | 8 ++++----
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/cleanup b/cleanup
index 0582d76..8b57b8e 100755
--- a/cleanup
+++ b/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 -
diff --git a/cleanup.win b/cleanup.win
index 1675add..8b57b8e 100755
--- a/cleanup.win
+++ b/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 -
diff --git a/configure.win b/configure.win
index 6446244..6c9c0cc 100755
--- a/configure.win
+++ b/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
diff --git a/src/htslib-1.21/Makefile b/src/htslib-1.21/Makefile
index ef9b5a9..c97d2a3 100644
--- a/src/htslib-1.21/Makefile
+++ b/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