Setting up configure/makevars for libcouchbase in R? - r

Question

I am creating a new R package where I would like to call an external c library(libcouchbase).
My problem is how to get the package build system to find the libraries during linking. I am using a linux/ubuntu like system.
This is what I had so far do :
create an configure.ac
AC_INIT(rcouchbase, version-0.1)
AC_CHECK_LIB([couchbase], [lcb_create], [],
[AC_MSG_ERROR(Failed to locate libcouchbase >= 2.0.0)])
COUCHBASE_LIBS="$LIBS"
AC_SUBST(COUCHBASE_LIBS)
AC_OUTPUT(src/Makevars)
generate a configure using autoconf
system("autoconf configure.ac > configure | chmod +x configure")
create a makevars.in
# set by configure
COUCHBASE_LIBS = #COUCHBASE_LIBS#
PKG_LIBS = $(COUCHBASE_LIBS)
build my package:
When I build my package, the configure file sucess to find the
==> R CMD INSTALL --no-multiarch --with-keep.source rcouchbase
Here the some significant output:
==> R CMD INSTALL --no-multiarch --with-keep.source rcouchbase
* installing to library ‘/home/agstudy/R/packages’
* installing *source* package ‘rcouchbase’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for lcb_create in -lcouchbase... yes
configure: creating ./config.status
config.status: creating src/Makevars
make: Nothing to be done for `all'.
** libs
installing to /home/agstudy/R/packages/rcouchbase/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/agstudy/R/packages/rcouchbase/libs/rcouchbase.so':
/home/agstudy/R/packages/rcouchbase/libs/rcouchbase.so: undefined symbol: lcb_destroy
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/agstudy/R/packages/rcouchbase’
Exited with status 1.
So does anyone know what I should add to my makevars/config file to solve the linkng problem?
EDIT add shared library dependencies:
ldd libcouchbase.so
linux-vdso.so.1 => (0x00007fff0a7fe000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fea0a26e000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fea0a06a000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fea09ca1000)
/lib64/ld-linux-x86-64.so.2 (0x00007fea0a7c5000)

Answer 1

When you say COUCHBASE_LIBS="$LIBS", who is filling in $LIBS for you?
At a first step, try to decompose the issue. You should us pieces: src/Makevars.in, but
not the generated src/Makevars. Does it have the correct library listed?
Also, look at / show us R CMD INSTALL ... output. Is there a link step with the library?
What you posted suggests not as the lcb_destroy symbol is missing.
In case you want to learn about Autotools / Automake, I have gone back to this (older) tutorial a few times; you may find it useful.
Edit: You are still confused. We don't want to see ldd libcouchbase; we presume that one is fine. Your package does not load so we need its linking step and its ldd output.
I.e. my RQuantLib package ends its R CMD INSTALL on
g++ -shared -o RQuantLib.so [many .o files removed] \
-L/usr/lib -lQuantLib -L/usr/lib/R/lib -lR
which clearly shows that it does link with the (required) QuantLib library.