In libgcrypt-1.6.2/m4/gpg-error.m4, it is stated that --with-gpg-error-prefix
(without 'lib') is depcrecated:

  dnl Accept --with-gpg-error-prefix and make it work the same as
  dnl --with-libgpg-error-prefix above, for backwards compatibility,
  dnl but do not document this old, inconsistently-named option.

However, when passing --with-libgpg-error-prefix to ./configure, it is ignored
because the deprecated option is empty. This is obvious when looking in the
resulting configure script (line 13964):

2. gpg-error is required.
4. Check whether --with-libgpg-error-prefix was given. if test "${with_libgpg_error_prefix+set}" = set; then : withval=$with_libgpg_error_prefix; gpg_error_config_prefix="$withval" else gpg_error_config_prefix="" fi
5. Check whether --with-gpg-error-prefix was given. if test "${with_gpg_error_prefix+set}" = set; then : withval=$with_gpg_error_prefix; gpg_error_config_prefix="$withval" else gpg_error_config_prefix="" fi if test x$gpg_error_config_prefix != x ; then if test x${GPG_ERROR_CONFIG+set} != xset ; then GPG_ERROR_CONFIG=$gpg_error_config_prefix/bin/gpg-error-config fi fi

The result is after running 'autoreconf' (version 2.69-6) on ubuntu 14.04.