Libtool generating flags incompatible with nvcc

[mahesh.mach]

Hello,

My friend and I are working on porting an existing library to NVIDIA CUDA.
The library has a GNU Build System defined for its compilation and
installation. We have suitably edited the configure.ac and Makefile.am files
to compile with nvcc instead of gcc. Our aim is to generate a shared
library.We call

$ aclocal
$ autoconf
$ automake
$ ./configure
$ make

But during the make step, flags such as -Wl,-soname ; --whole-archive and
--no-whole-archive are passed to the linker which is nvcc again, and these
flags are not recognized by it and generation of the shared library fails.
On further inspection, we found that these flags are passed from libtool.sh
which is autogenerated by config.status which in turn depends on
configure.ac

Is there any MACRO which we can use to get rid of these flags?

Thanks
Mahesh
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