diff -up Rsamtools/Rsamtools/src/Makevars.common.system-samtools Rsamtools/Rsamtools/src/Makevars.common
--- Rsamtools/Rsamtools/src/Makevars.common.system-samtools	2015-04-16 16:12:05.000000000 -0400
+++ Rsamtools/Rsamtools/src/Makevars.common	2015-05-29 23:21:11.475617539 -0400
@@ -10,7 +10,6 @@ BCFOBJ_0 = \
 BAMOBJ=$(BAMOBJ_0:%=samtools/%) $(PATCH_O)
 BCFOBJ=$(BCFOBJ_0:%=samtools/bcftools/%) $(PATCH_O)
 TABIXOBJ = \
-  samtools/bgzf.o samtools/kstring.o samtools/knetfile.o \
   tabix/index.o tabix/bedidx.o $(PATCH_O)
 
 DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \
@@ -21,11 +20,11 @@ DFLAGS = -D_USE_KNETFILE -D_FILE_OFFSET_
 
 PKG_CFLAGS0 = \
   $(SHLIB_OPENMP_CFLAGS) \
-  $(DFLAGS) -I./samtools -I./samtools/bcftools -I./tabix
+  $(DFLAGS) -I./samtools -I/usr/include/samtools -I./samtools/bcftools -I./tabix
 
 PKG_LIBS0 = -pthread \
   $(SHLIB_OPENMP_CFLAGS) \
-  "${R_PACKAGE_DIR}/usrlib${R_ARCH}/libbam.a" \
+  -lbam \
   "${R_PACKAGE_DIR}/usrlib${R_ARCH}/libbcf.a" \
   "${R_PACKAGE_DIR}/usrlib${R_ARCH}/libtabix.a"
 
@@ -38,13 +37,13 @@ $(SHLIB): libs
 libs: libs0
 	mkdir -p "${R_PACKAGE_DIR}/include/samtools/bcftools"
 	mkdir -p "${R_PACKAGE_DIR}/include/tabix"
-	cp samtools/*.h "${R_PACKAGE_DIR}/include/samtools/"
+	# cp samtools/*.h "${R_PACKAGE_DIR}/include/samtools/"
 	cp samtools/bcftools/*h "${R_PACKAGE_DIR}/include/samtools/bcftools/"
 	cp tabix/*h "${R_PACKAGE_DIR}/include/tabix/"
-	cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
-		"${R_PACKAGE_DIR}/include/tabix/"
+	# cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
+	#	"${R_PACKAGE_DIR}/include/tabix/"
 	mkdir -p "${R_PACKAGE_DIR}/usrlib${R_ARCH}"
-	cp libbam.a libbcf.a libtabix.a "${R_PACKAGE_DIR}/usrlib${R_ARCH}"
+	cp libbcf.a libtabix.a "${R_PACKAGE_DIR}/usrlib${R_ARCH}"
 
 clean:
 	rm -f $(BAMOBJ) $(BCFOBJ) $(TABIXOBJ) *.a *.o *.so *.dll
diff -up Rsamtools/Rsamtools/src/Makevars.system-samtools Rsamtools/Rsamtools/src/Makevars
--- Rsamtools/Rsamtools/src/Makevars.system-samtools	2015-05-29 23:19:32.582280914 -0400
+++ Rsamtools/Rsamtools/src/Makevars	2015-05-29 23:22:03.183270684 -0400
@@ -1,12 +1,9 @@
 include Makevars.common
 
 PKG_CFLAGS = ${PKG_CFLAGS0}
-PKG_LIBS = ${PKG_LIBS0} -lz
+PKG_LIBS = ${PKG_LIBS0} -lz -lbam
 
-libs0: libbam.a libbcf.a libtabix.a
-
-libbam.a: $(BAMOBJ)
-	$(AR) -crus $@ $(BAMOBJ)
+libs0: libbcf.a libtabix.a
 
 libbcf.a: $(BCFOBJ)
 	$(AR) -crus $@ $(BCFOBJ)
diff -up Rsamtools/Rsamtools/src/samtools/bcftools/bcf.h.system-samtools Rsamtools/Rsamtools/src/samtools/bcftools/bcf.h
--- Rsamtools/Rsamtools/src/samtools/bcftools/bcf.h.system-samtools	2015-05-17 22:25:45.000000000 -0400
+++ Rsamtools/Rsamtools/src/samtools/bcftools/bcf.h	2015-05-29 23:19:32.586280887 -0400
@@ -33,6 +33,8 @@
 #include <stdint.h>
 #include <zlib.h>
 
+#include <kstring.h>
+
 #ifndef BCF_LITE
 #include "bgzf.h"
 typedef BGZF *bcfFile;