From 08e1cf5d48042dd0b629aa57d39524b7f22e5391 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Sun, 15 Dec 2024 10:41:35 +0100
Subject: [PATCH] update configure and gitignore

---
 .gitignore    |  2 +-
 configure     | 14 +++++++++++++-
 configure.win | 10 +++++++++-
 src/Makevars  |  2 +-
 4 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index b5107ab..919cb2e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,7 +6,7 @@
 *.tar.gz
 *.tbi
 vignettes/*_cache
-src/htslib-1.18
+src/htslib-1.21
 test-random.R
 
 ## lsp
diff --git a/configure b/configure
index 0f19d4e..4911ee7 100755
--- a/configure
+++ b/configure
@@ -1,5 +1,17 @@
 #!/bin/sh
+# Configure script for R package with htslib integration
+
+# Exit on any error
+set -e
 
 HTSLIB_DIR="src/htslib-1.21"
 echo "Configuring HTSlib in $HTSLIB_DIR"
-cd $HTSLIB_DIR && ./configure --enable-static --disable-shared --without-libdeflate && make
+cd $HTSLIB_DIR
+./configure \
+    --disable-shared \
+    --enable-static \
+    --without-libdeflate \
+    CFLAGS="-O2 -fPIC"
+
+make
+
diff --git a/configure.win b/configure.win
index 6c9c0cc..a173558 100755
--- a/configure.win
+++ b/configure.win
@@ -2,4 +2,12 @@
 
 HTSLIB_DIR="src/htslib-1.21"
 echo "Configuring HTSlib in $HTSLIB_DIR"
-cd $HTSLIB_DIR && ./configure --without-libdeflate && make
+cd $HTSLIB_DIR
+./configure \
+    --disable-shared \
+    --enable-static \
+    --without-libdeflate \
+    CFLAGS="-O2 -fPIC"
+
+make
+
diff --git a/src/Makevars b/src/Makevars
index ef8506a..e9c52e1 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -1,6 +1,6 @@
 HTSLIB_DIR='htslib-1.21'
 PKG_CPPFLAGS = -I${HTSLIB_DIR} -I../inst/include
-PKG_LIBS = ${HTSLIB_DIR}/libhts.a -lz -lm -lbz2 -llzma -lcurl
+PKG_LIBS = ${HTSLIB_DIR}/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl
 
 .PHONY: all clean