update configure and gitignore

Zilong-Li · Dec 15, 2024 · 08e1cf5 · 08e1cf5
1 parent 84532a4
commit 08e1cf5
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Showing 4 changed files with 24 additions and 4 deletions.
diff --git 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
@@ -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
@@ -2,4 +2,12 @@
 
 HTSLIB_DIR="src/htslib-1.21"
 echo "Configuring HTSlib in $HTSLIB_DIR"
-cd $HTSLIB_DIR && ./configure --without-libdeflate && make
+cd $HTSLIB_DIR
+./configure \
+    --disable-shared \
+    --enable-static \
+    --without-libdeflate \
+    CFLAGS="-O2 -fPIC"
+
+make
+
diff --git a/src/Makevars b/src/Makevars
@@ -1,6 +1,6 @@
 HTSLIB_DIR='htslib-1.21'
 PKG_CPPFLAGS = -I${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