# C++11 syntax used throughout
CXX_STD = CXX11

## Add these to your global Makevars if you want to build with OpenMP
## The global Makevars is located inside the home directory at `.R/Makevars`
# PKG_CPPFLAGS += $(SHLIB_OPENMP_CXXFLAGS)
# PKG_CFLAGS += $(SHLIB_OPENMP_CFLAGS)
# PKG_LIBS += $(SHLIB_OPENMP_CFLAGS)



# Access to pgc RNG and htslib headers:
RHTSLIB_CPPFLAGS = $(shell echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\
    "${R_HOME}/bin/R" --vanilla --slave)
PKG_CPPFLAGS += -D_FILE_OFFSET_BITS=64 -I../inst/include/ $(RHTSLIB_CPPFLAGS)

# For htslib:
RHTSLIB_LIBS = $(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\
    "${R_HOME}/bin/R" --vanilla --slave)

# Compression library and others
PKG_LIBS += -lz -llzma $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(RHTSLIB_LIBS)
