Problem with AC_SEARCH_LIBS macro in configure.ac file - gnu

Question

I'm trying to setup a few --with arguments in my configure script. However, I'm experiencing a weird behavior with following code:
AC_MSG_CHECKING([FFTW library directory])
AC_ARG_WITH(fftw-lib, [AC_HELP_STRING([--with-fftw-lib], [path to FFTW directory containing library file])], withfftwlib=$withval, withfftwlib="")
if test "$withfftwlib" != ""; then
if test "$fourlib" != "fftw"; then AC_MSG_ERROR([Only choose one Fourier transform library!])
fi
AC_MSG_RESULT([$withfftwlib])
if [[ -d "$withfftwlib" ]]; then
AC_SEARCH_LIBS([fftw_plan_dft], [fftw3], [AC_SUBST(FFTW_LIB, "-L${withfftwlib} -lfftw3")], [AC_MSG_ERROR([libfftw3 not found])])
AC_SEARCH_LIBS([fftwf_execute_r2r], [fftw3f], [AC_SUBST(FFTWF_LIB, "-lfftw3f")], [AC_MSG_ERROR([libfftw3f not found])])
fi
else
AC_MSG_RESULT([none])
if test "$fftwval" = "yes"; then AC_MSG_ERROR([location to FFTW library directory was not given!])
fi
fi
AC_MSG_CHECKING([CUDA directory])
AC_ARG_WITH(cuda, [AC_HELP_STRING([--with-cuda], [path to location of CUDA library])], withcuda=$withval, withcuda="")
if test "withcuda" != "yes" && test "$withcuda" != "" && test "$withcuda" != "no"; then
if test "$fourlib" != "cuda"; then AC_MSG_ERROR([Only choose one Fourier transform library!])
fi
AC_MSG_RESULT([$withcuda])
if [[ -d "$withcuda/samples/common/inc" ]]; then
AC_SUBST(CUDA_INC, "-I$withcuda/samples/common/inc")
CUDA_LIB="-lcuda -lcufft"
else
AC_MSG_ERROR([cuda library was not found in given location!])
fi
if test "$cublasval" = "yes"; then
CUDA_LIB+=" -lcublas"
fi
AC_SUBST(CUDA_LIB, "$CUDA_LIB")
else
AC_MSG_RESULT([none])
if test "$cudaval" = "yes"; then AC_MSG_ERROR([location to CUDA was not given!])
fi
fi
Here, users are expected to use either --with-fftw-lib or --with-cuda flag. The problem is, somehow, those two AC_SEARCH_LIBS macros cause unexpected output when using --with-cuda flag.
This is what it should be when I use --with-cuda (I removed the two AC_SEARCH_LIBS macros).
...
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 mpiCC accepts -g... yes
checking whether we are using the GNU Fortran compiler... yes
checking whether mpif90 accepts -g... yes
checking for gcc... mpicc
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking whether make sets $(MAKE)... (cached) yes
checking how to run the C preprocessor... mpicc -E
checking for ar... ar
checking the archiver (ar) interface... ar
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for size_t... yes
checking for stdlib.h... (cached) yes
...
verses what I get (when I keep the macros)
...
checking whether we are using the GNU C++ compiler... no
checking whether mpiCC accepts -g... no
checking whether we are using the GNU Fortran compiler... no
checking whether mpif90 accepts -g... no
checking for gcc... mpicc
checking whether we are using the GNU C compiler... no
checking whether mpicc accepts -g... no
checking for mpicc option to accept ISO C89... unsupported
checking whether make sets $(MAKE)... (cached) yes
checking how to run the C preprocessor... mpicc -E
checking for ar... ar
checking the archiver (ar) interface... ar
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... no
checking for sys/stat.h... no
checking for stdlib.h... no
checking for string.h... no
checking for memory.h... no
checking for strings.h... no
checking for inttypes.h... no
checking for stdint.h... no
checking for unistd.h... no
checking for stdlib.h... (cached) no
checking for string.h... (cached) no
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... no
checking for size_t... no
checking for stdlib.h... (cached) no
...
I removed those identical parts where I do other checks. Notice how it does less checks, ex) no checking whether the C++ compiler works, and it also affects other checks that are not depends on either of the --with flags.
The other weird part is that it works just fine when I use --with-fftw-lib instead of --with-cuda.
I have tried remove small portions of codes to see what segment of the codes causes it, and it seems the two AC_SEARCH_LIBS macros are doing it.
Is it possible that an unused macro can have effects on the configure script? If then, what should I do in this case? If not, what could be the possible cause of it?