See http://gcc.gnu.org/PR22541

From: Dan Kegel

When building gcc-3.4.3 or gcc-4.0.[01] into a clean $PREFIX (the only two I've tried like this),
the configure script happily copies the glibc include files from include to sys-include;
here's the line from the log file (with $PREFIX instead of the real prefix):

Copying $PREFIX/i686-unknown-linux-gnu/include to $PREFIX/i686-unknown-linux-gnu/sys-include

But later, when running fixincludes, it gives the error message
 The directory that should contain system headers does not exist:
  $PREFIX/lib/gcc/i686-unknown-linux-gnu/3.4.3/../../../../i686-unknown-linux-gnu/sys-include

Nevertheless, it continues building; the header files it installs in
 $PREFIX/lib/gcc/i686-unknown-linux-gnu/3.4.3/include
do not include the boilerplate that would cause it to #include_next the
glibc headers in the system header directory.
Thus the resulting toolchain can't compile the following program:
#include <limits.h>
int x = PATH_MAX;
because its limits.h doesn't include the glibc header.

That's not nice.  I suspect the problem is that gcc/Makefile.in assumes that
it can refer to $PREFIX/i686-unknown-linux-gnu  with the path 
                $PREFIX/lib/../i686-unknown-linux-gnu, but
that fails because the directory $PREFIX/lib doesn't exist during 'make all';
it is only created later, during 'make install'.  (Which makes this problem
confusing, since one only notices the breakage well after 'make install',
at which point the path configure complained about does exist, and has the
right stuff in it.)

A possible fix is to replace the line in gcc/Makefile.in that says
    SYSTEM_HEADER_DIR = @SYSTEM_HEADER_DIR@
with a version that gets rid of extra ..'s, e.g.
    SYSTEM_HEADER_DIR = `echo @SYSTEM_HEADER_DIR@ | sed -e :a -e "s,[^/]*/\.\.\/,,;ta"`
(hey, that's the first time I've ever used a label in a sed script; thanks to the sed faq
for explaining the :a ... ta method of looping to repeat a search-and-replace until it doesn't match.)

[rediffed against gcc-4.0.0]

--- gcc-4.0.0/gcc/Makefile.in.orig	2005-04-04 12:45:13.000000000 -0700
+++ gcc-4.0.0/gcc/Makefile.in	2005-05-20 12:33:43.000000000 -0700
@@ -378,7 +378,10 @@
 CROSS_SYSTEM_HEADER_DIR = @CROSS_SYSTEM_HEADER_DIR@
 
 # autoconf sets SYSTEM_HEADER_DIR to one of the above.
-SYSTEM_HEADER_DIR = @SYSTEM_HEADER_DIR@
+# Purge it of unneccessary internal relative paths
+# to directories that might not exist yet.
+# The sed idiom for this is to repeat the search-and-replace until it doesn't match, using :a ... ta.
+SYSTEM_HEADER_DIR = `echo @SYSTEM_HEADER_DIR@ | sed -e :a -e "s,[^/]*/\.\.\/,," -e ta`
 
 # Control whether to run fixproto and fixincludes.
 STMP_FIXPROTO = @STMP_FIXPROTO@
@@ -2838,13 +2841,15 @@
 ../$(build_subdir)/fixincludes/fixincl: ; @ :
 
 # Build fixed copies of system files.
+# Abort if no system headers available, unless building a crosscompiler.
+# FIXME: abort unless building --without-headers would be more accurate and less ugly
 stmp-fixinc: gsyslimits.h macro_list \
   ../$(build_subdir)/fixincludes/fixincl \
   ../$(build_subdir)/fixincludes/fixinc.sh
 	@if test ! -d ${SYSTEM_HEADER_DIR}; then \
 	  echo The directory that should contain system headers does not exist: >&2 ; \
 	  echo "  ${SYSTEM_HEADER_DIR}" >&2 ; \
-	  if test "x${SYSTEM_HEADER_DIR}" = "x${gcc_tooldir}/sys-include"; \
+	  if test "x${SYSTEM_HEADER_DIR}" = "x`echo "${gcc_tooldir}/sys-include" | sed -e :a -e "s,[^/]*/\.\.\/,," -e ta`"; \
 	  then sleep 1; else exit 1; fi; \
 	fi
 	rm -rf include; mkdir include