@@ -13,7 +13,7 @@ GSTRUCT_INCLUDE_DIR = $(INCLUDE_DIR)/gstruct

 SAMTOOLS_LIB = samtools/libbam.a

-PKG_CPPFLAGS += -I$(INCLUDE_DIR) -g -O3

+PKG_CPPFLAGS += -I$(INCLUDE_DIR)

 PKG_CFLAGS += -g -O3

 PKG_LIBS += $(GSTRUCT_LIB) $(SAMTOOLS_LIB) -lz

@@ -28,8 +28,8 @@ $(OBJECTS): $(GSTRUCT_INCLUDE_DIR) $(OBJECTS:%.o=%.c)

 $(GSTRUCT_LIB) $(GSTRUCT_INCLUDE_DIR): gstruct

-RSAMTOOLS_PATH := $(shell R_LIBS_USER=$(R_LIBRARY_DIR) $(R_HOME)/bin/Rscript --vanilla -e \

-                    'cat(system.file(package="Rsamtools"))')

+RSAMTOOLS_PATH := $(shell R_LIBS=$(R_LIBRARY_DIR) $(R_HOME)/bin/Rscript \

+		    --vanilla -e 'cat(system.file(package="Rsamtools"))')

 ${R_SRC_DIR}/samtools: $(RSAMTOOLS_PATH)

 ## gmap/gstruct assume samtools headers and libs are in one directory,

 ## so we need to create one and populate it with links to Rsamtools.

@@ -45,7 +45,7 @@ $(SUBDIRS): %: %/Makefile

 gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools 

 	cd $(dir $@); \

-	CFLAGS="-g" ./configure --enable-static --disable-shared \

+	./configure --enable-static --disable-shared \

 	            --prefix=${PREFIX} --includedir=${GSTRUCT_INCLUDE_DIR} \

 	            --libdir=${PREFIX}/${LIBnn} \

 	            --with-samtools-lib=${R_SRC_DIR}/samtools \

@@ -57,8 +57,7 @@ gstruct/Makefile: gstruct/configure ${R_SRC_DIR}/samtools

 gmap/Makefile: gmap/configure

 	cd $(dir $@); \

 	 ./configure --with-gmapdb=${GMAPDB} --prefix=${PREFIX} \

-	            --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode \

-		    CFLAGS=-g #added by gabe 5/14/14

+	            --libdir=${PREFIX}/${LIBnn} --disable-maintainer-mode

 clean:

 	for dir in $(SUBDIRS); do \