I have libtool 1.5.26 on Linux (seems to be same version as used for
1.3.9) but I see this difference in my test roll of 1.3.9:

diff -ru opensource/apr-1.3.9/build/libtool.m4 apr-1.3.9/build/libtool.m4
--- opensource/apr-1.3.9/build/libtool.m4       2009-09-21
17:59:31.000000000 -0400
+++ apr-1.3.9/build/libtool.m4  2010-02-04 15:36:25.000000000 -0500
@@ -6042,7 +6042,25 @@
       ;;

     darwin* | rhapsody*)
-      _LT_AC_TAGVAR(allow_undefined_flag, $1)="$_lt_dar_allow_undefined"
+      case $host_os in
+        rhapsody* | darwin1.[[012]])
+         _LT_AC_TAGVAR(allow_undefined_flag, $1)='${wl}-undefined
${wl}suppress'
+         ;;
+       *) # Darwin 1.3 on
+         if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then
+           _LT_AC_TAGVAR(allow_undefined_flag,
$1)='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+         else
+           case ${MACOSX_DEPLOYMENT_TARGET} in
+             10.[[012]])
+               _LT_AC_TAGVAR(allow_undefined_flag,
$1)='${wl}-flat_namespace ${wl}-undefined ${wl}suppress'
+               ;;
+             10.*)
+               _LT_AC_TAGVAR(allow_undefined_flag,
$1)='${wl}-undefined ${wl}dynamic_lookup'
+               ;;
+           esac
+         fi
+         ;;
+      esac
       _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no
       _LT_AC_TAGVAR(hardcode_direct, $1)=no
       _LT_AC_TAGVAR(hardcode_automatic, $1)=yes

Does anyone recognize that diff and know where it comes from?  Or, can
anybody confirm that the diff isn't important?

(similar diff in the generated configure)

Thanks!

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