To use these libraries, the third party package developer needs to (1) discover the appropriate header files when their package is built, and (2) link in the libraries. Note that in order to link correctly across platforms your package must provide both the respective src/Makevars and src/Makevars.win files.
To discover appropriate header files at package installation time, add
LinkingTo: Rgin
to the DESCRIPTION file, and reference the relevant include files as, for instance,
#include "gin/bam.h"
The content of the include files can be found in the Rgin source (under src/include/gin) or at their installed location.
Linking to the static libraries is accomplished by including the following code in src/Makevars.win for Windows:
GINVARS=$(shell echo 'cat(Rgin:::.pkgMk())' |\
"${R_HOME}/bin/R" --vanilla --slave)
include $(GINVARS)
PKG_LIBS=$(GIN_LIBS)
PKG_CPPFLAGS=$(GIN_CPPFLAGS)and with the following code in src/Makevars for all other platforms:
GIN_PATH=`${R_HOME}/bin/Rscript -e "cat(Rgin:::.pkgLd())"`
GIN_LIBS="$(GIN_PATH)/libgin.a" "$(GIN_PATH)/libcephes.a"\
"$(GIN_PATH)/libmaxflow.a" -lz -pthread
GIN_CPPFLAGS=-D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE64_SOURCE
PKG_LIBS=$(GIN_LIBS)
PKG_CPPFLAGS=$(GIN_CPPFLAGS)This updates the environment variables $PKG_CPPFLAGS and $PKG_LIBS; if your Makevars/Makevars.win modifies these also, do so by adding to the respecitve line, e.g.,
PKG_LIBS=$(GIN_LIBS) -lfoo
PKG_CPPFLAGS=$(GIN_CPPFLAGS) -I/path/bar