Well, I can only compare the builds of 2.59a-3 and 2.59a-4.

2.59a-3:
[...]
dh_testdir
make
make[1]: Entering directory `/source-orig/autoconf-2.59a'
Making all in bin
make[2]: Entering directory `/source-orig/autoconf-2.59a/bin'
rm -f autom4te autom4te.tmp
sed -e 's,@SHELL\@,/bin/sh,g' -e 's,@PERL\@,/usr/bin/perl,g' -e 
's,@bindir\@,/usr/bin,g' -e 's,@datadir\@,/usr/share/autoconf,g' -e 
's,@prefix\@,/usr,g' -e 's,@autoconf-name\@,'`echo autoconf | sed 's,x,x,'`',g' 
-e 's,@autoheader-name\@,'`echo autoheader | sed 's,x,x,'`',g' -e 
's,@autom4te-name\@,'`echo autom4te | sed 's,x,x,'`',g' -e 
's,@M4\@,/usr/bin/m4,g' -e 's,@AWK\@,awk,g' -e 's,@VERSION\@,2.59,g' -e 
's,@PACKAGE_NAME\@,GNU Autoconf,g' -e 's,@configure_input\@,Generated from 
autom4te.in; do not edit by hand.,g' ./autom4te.in >autom4te.tmp
chmod +x autom4te.tmp
chmod -w autom4te.tmp
mv -f autom4te.tmp autom4te
rm -f autoconf autoconf.tmp
[...]


2.59a-4:
dh_testdir
make
make[1]: Entering directory `/source-etch/autoconf-2.59a'
Making all in bin
make[2]: Entering directory `/source-etch/autoconf-2.59a/bin'
rm -f autom4te autom4te.tmp
sed -e 's,@SHELL\@,/bin/sh,g' -e 's,@PERL\@,/usr/bin/perl,g' -e 
's,@bindir\@,/usr/bin,g' -e 's,@datadir\@,/usr/share/autoconf,g' -e 
's,@prefix\@,/usr,g' -e 's,@autoconf-name\@,'`echo autoconf | sed 's,x,x,'`',g' 
-e 's,@autoheader-name\@,'`echo autoheader | sed 's,x,x,'`',g' -e 
's,@autom4te-name\@,'`echo autom4te | sed 's,x,x,'`',g' -e 
's,@M4\@,/usr/bin/m4,g' -e 's,@AWK\@,awk,g' -e 's,@VERSION\@,2.59,g' -e 
's,@PACKAGE_NAME\@,GNU Autoconf,g' -e 's,@configure_input\@,Generated from 
autom4te.in; do not edit by hand.,g' ./autom4te.in >autom4te.tmp
chmod +x autom4te.tmp
chmod -w autom4te.tmp
mv -f autom4te.tmp autom4te
../tests/autom4te --language M4sh --cache '' ./autoconf.as -o autoconf.in
autom4te: cannot open /source-etch/autoconf-2.59a/tests/.././lib/autom4te.cfg: 
No such file or directory



Obviuosly something changed between 2.59a-3 and -4.

After "mv -f autom4te.tmp autom4te" the command 
"../tests/autom4te --language M4sh --cache '' ./autoconf.as -o autoconf.in" 
occur, which complains about not finding
autoconf-2.59a/tests/.././lib/autom4te.cfg. This doesn't happen in 2.59a-3. 

A diff of the two configure scripts give me this:

@@ -2910,11 +2910,6 @@
   *) ac_INSTALL=$ac_top_builddir$INSTALL ;;
   esac
 
-  if test x"$ac_file" != x-; then
-    { echo "$as_me:$LINENO: creating $ac_file" >&5
-echo "$as_me: creating $ac_file" >&6;}
-    rm -f "$ac_file"
-  fi
   # Let's still pretend it is `configure' which instantiates (i.e., don't
   # use $as_me), people would be surprised to read:
   #    /* config.h.  Generated by config.status.  */
@@ -2953,6 +2948,12 @@
         fi;;
       esac
     done` || { (exit 1); exit 1; }
+
+  if test x"$ac_file" != x-; then
+    { echo "$as_me:$LINENO: creating $ac_file" >&5
+echo "$as_me: creating $ac_file" >&6;}
+    rm -f "$ac_file"
+  fi
 _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF


I would suspect that this change had some strange side effect. 

Regards,
Henry



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