test configure

configure

@@ -1,5 +1,96 @@
-#!/bin/sh
+#!/bin/bash
+# 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 --without-libdeflate && make libhts.a
+# cd $HTSLIB_DIR && ./configure --without-libdeflate && make libhts.a
+
+# Determine the package source directory
+PKG_SOURCE_DIR=$(pwd)
+
+# Create a directory for htslib build
+HTSLIB_BUILD_DIR="${PKG_SOURCE_DIR}/src/htslib_build"
+mkdir -p "${HTSLIB_BUILD_DIR}"
+
+# Function to check for compilation tools
+check_tools() {
+    # Check for essential build tools
+    command -v gcc >/dev/null 2>&1 || { 
+        echo "Error: GCC compiler not found" >&2
+        exit 1
+    }
+    command -v make >/dev/null 2>&1 || {
+        echo "Error: Make not found" >&2
+        exit 1
+    }
+}
+
+# Function to configure and build htslib
+build_htslib() {
+    echo "Configuring htslib..."
+
+    # Go to the htslib source directory
+    cd "${PKG_SOURCE_DIR}/${HTSLIB_DIR}"
+
+    # Clean any previous builds
+    make clean || true
+
+    # Configure htslib
+    # Customize these options as needed
+    ./configure \
+        --disable-shared \
+        --enable-static \
+        --prefix="${HTSLIB_BUILD_DIR}" \
+        CFLAGS="-O2 -fPIC"
+
+    # Build htslib
+    make
+    make install
+}
+
+# Function to create Makevars files
+create_makevars() {
+    echo "Creating Makevars files..."
+
+    # Unix Makevars
+    cat > "${PKG_SOURCE_DIR}/src/Makevars" << EOL
+# Paths and flags for htslib
+PKG_CPPFLAGS = -I${HTSLIB_BUILD_DIR}/include -I${PKG_SOURCE_DIR}/inst/include
+PKG_LIBS = -L${HTSLIB_BUILD_DIR}/lib -lhts -lz
+
+# Ensure static linking
+STATICALLY_LINKED_LIBS = ${HTSLIB_BUILD_DIR}/lib/libhts.a
+EOL
+
+    # Windows Makevars
+    cat > "${PKG_SOURCE_DIR}/src/Makevars.win" << EOL
+# Windows-specific paths and flags for htslib
+PKG_CPPFLAGS = -I${HTSLIB_BUILD_DIR}/include -I${PKG_SOURCE_DIR}/inst/include
+PKG_LIBS = -L${HTSLIB_BUILD_DIR}/lib -lhts -lz
+
+# Ensure static linking
+STATICALLY_LINKED_LIBS = ${HTSLIB_BUILD_DIR}/lib/libhts.a
+EOL
+}
+
+# Main script execution
+main() {
+    # Check for necessary build tools
+    check_tools
+
+    # Build htslib
+    build_htslib
+
+    # Create Makevars files
+    # create_makevars
+
+    echo "htslib configuration complete."
+    exit 0
+}
+
+# Run the main function
+main
+