It seems unnecessary to patch both configure and configure.in.  The
following diff against python-modules svn HEAD eliminates the patch
against configure and runs autoconf after configure.in has been patched.
Build-tested.

-- 
Robert Edmonds
[EMAIL PROTECTED]
Index: debian/patches/01_configure.diff
===================================================================
--- debian/patches/01_configure.diff    (revision 1164)
+++ debian/patches/01_configure.diff    (working copy)
@@ -14,51 +14,6 @@
 exit 0
 
 @DPATCH@
-diff -Nur mod_python-3.2.8.orig/configure mod_python-3.2.8/configure
---- mod_python-3.2.8.orig/configure    2005-10-28 11:06:22.000000000 -0500
-+++ mod_python-3.2.8/configure 2006-05-16 08:38:20.000000000 -0500
-@@ -2706,19 +2706,21 @@
-   ALL="dso"
- 
-   # check Apache version
--  echo "$as_me:$LINENO: checking Apache version" >&5
--echo $ECHO_N "checking Apache version... $ECHO_C" >&6
--  HTTPD="`${APXS} -q SBINDIR`/`${APXS} -q TARGET`"
--  ver=`$HTTPD -v | awk '/version/ {print $3}' | awk -F/ '{print $2}'`
--  echo "$as_me:$LINENO: result: $ver" >&5
--echo "${ECHO_T}$ver" >&6
-+# peterh: Remove apache version check for debian package, since we don't
-+# want to build-depend on apache2.
-+#  echo "$as_me:$LINENO: checking Apache version" >&5
-+#echo $ECHO_N "checking Apache version... $ECHO_C" >&6
-+#  HTTPD="`${APXS} -q SBINDIR`/`${APXS} -q TARGET`"
-+#  ver=`$HTTPD -v | awk '/version/ {print $3}' | awk -F/ '{print $2}'`
-+#  echo "$as_me:$LINENO: result: $ver" >&5
-+#echo "${ECHO_T}$ver" >&6
- 
-   # make sure version begins with 2
--  if test -z "`echo $ver | egrep \^2`"; then
--    { { echo "$as_me:$LINENO: error: This version of mod_python only works 
with Apache 2. The one you have seems to be $ver." >&5
--echo "$as_me: error: This version of mod_python only works with Apache 2. The 
one you have seems to be $ver." >&2;}
--   { (exit 1); exit 1; }; }
--  fi
-+#  if test -z "`echo $ver | egrep \^2`"; then
-+#    { { echo "$as_me:$LINENO: error: This version of mod_python only works 
with Apache 2. The one you have seems to be $ver." >&5
-+#echo "$as_me: error: This version of mod_python only works with Apache 2. 
The one you have seems to be $ver." >&2;}
-+#   { (exit 1); exit 1; }; }
-+#  fi
- 
-   # determine LIBEXEC
-   echo "$as_me:$LINENO: checking for Apache libexec directory" >&5
-@@ -3035,7 +3037,7 @@
- # get the mod_python version
- 
- MP_VERSION=`awk '/MPV_STRING/ {print $3}' src/include/mpversion.h`
--MP_VERSION=`echo $MP_VERSION | sed s/\\"//g`
-+MP_VERSION=`echo $MP_VERSION | sed 's/"//g'`
- 
- # get --with-python-src. The python src is required to generate the 
documentation
- # It is not required to compile or install mod_python itself
 diff -Nur mod_python-3.2.8.orig/configure.in mod_python-3.2.8/configure.in
 --- mod_python-3.2.8.orig/configure.in 2005-10-28 11:06:22.000000000 -0500
 +++ mod_python-3.2.8/configure.in      2006-05-16 08:40:23.000000000 -0500
Index: debian/changelog
===================================================================
--- debian/changelog    (revision 1164)
+++ debian/changelog    (working copy)
@@ -8,6 +8,10 @@
   [ Piotr Ozarowski ]
   * Added watch file
 
+  [ Robert S. Edmonds ]
+  * Patching the generated configure script is wrong and unnecessary.
+    (closes: #370234)
+
  -- Piotr Ozarowski <[EMAIL PROTECTED]>  Tue,  6 Jun 2006 13:39:06 +0200
 
 libapache2-mod-python (3.2.8-1) unstable; urgency=low
Index: debian/rules
===================================================================
--- debian/rules        (revision 1164)
+++ debian/rules        (working copy)
@@ -16,7 +16,6 @@
        dh_testdir
        # Add here commands to configure the package.
        
-       autoconf
        # Don't configure here (see install)
 #      -./configure --enable-EAPI --prefix=/usr --mandir=\$${prefix}/share/man 
--infodir=\$${prefix}/share/info
        touch configure-stamp
@@ -54,6 +53,8 @@
        # Add here commands to install the package into 
debian/libapache-mod-python.
        #$(MAKE) install DESTDIR=$(CURDIR)/debian/libapache-mod-python
 
+       autoconf
+
        # python 2.3
        rm -f config.cache config.status
        export PYTHON_BIN=/usr/bin/python2.3

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