Luca, here are some of the other patches that I'm using on the Fedora ntop. Some by me, but some figured out by Patrice.

(order is important to some patches)

ntop-nolibs.patch (better detection of libraries)
ntop-fix-missing-js.patch (fix missing javascript files on installed directories)
ntop-configure-mysql.patch (fix detection of mysql)
ntop-fix-cflags.patch (disable extra cflags information)
ntop-rrd-cleanup.patch (cleanup rrd lib/include detection)
ntop-LINUXfedora.patch (fix LIBS vs LDFLAGS cleanup in LINUXfedora)

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--- ntop/configure.in.orig	2004-12-21 05:07:08.000000000 +0100
+++ ntop/configure.in	2005-05-19 11:07:21.000000000 +0200
@@ -2198,10 +2198,8 @@
 AC_CHECK_LIB([c], [ceil], , [AC_CHECK_LIB([m], [ceil])])
 
 dnl> Networking libraries
-AC_CHECK_LIB([nsl],    [main])
-AC_CHECK_LIB([xnet],   [main])
-AC_CHECK_LIB([socket], [main])
-AC_CHECK_LIB([resolv], [main])
+AC_SEARCH_LIBS([gethostbyname], [nsl resolv])
+AC_SEARCH_LIBS([socket], [xnet socket])
 
 dnl> Multithreading libraries
 AC_CHECK_LIB(pthread, pthread_create, , [
@@ -2223,9 +2223,9 @@
 dnl>AC_CHECK_LIB([wrap], [hosts_access])
 
 dnl> XML dump (plugin)
-AC_CHECK_LIB([glib], [g_date_julian])
-AC_CHECK_LIB([xml2], [xmlCheckVersion])
-AC_CHECK_LIB([gdome], [gdome_di_saveDocToFile])
+AC_CHECK_LIB([glib-2.0], [g_date_get_julian], [:])
+AC_CHECK_LIB([xml2], [xmlCheckVersion], [:])
+AC_CHECK_LIB([gdome], [gdome_di_saveDocToFile], [:])
 
 dnl> Functions and types
 AC_FUNC_ALLOCA
--- ntop/configure.in.orig	2007-02-06 14:50:26.000000000 -0700
+++ ntop/configure.in	2007-02-07 01:33:14.000000000 -0700
@@ -1924,7 +1924,7 @@
 if test ".${ac_cv_header_glib_h}" = ".yes"            &&
    test ".${ac_cv_header_glibconfig_h}" = ".yes"      &&
    test ".${ac_cv_header_gdome_h}" = ".yes"           &&
-   test ".${ac_cv_lib_glib_g_date_julian}" = ".yes"   &&
+   test ".${ac_cv_lib_glib_2_0_g_date_get_julian}" = ".yes"   &&
    test ".${ac_cv_lib_xml2_xmlCheckVersion}" = ".yes" &&
    test ".${ac_cv_lib_gdome_gdome_di_saveDocToFile}" = ".yes"; then
     AC_MSG_RESULT(ok)
@@ -1940,7 +1940,7 @@
     echo "*                  gdome.h...${ac_cv_header_gdome_h}"
     echo "*                  libgdome.so or libgdome.a...${ac_cv_lib_gdome_gdome_di_saveDocToFile}"
     echo "*                  glib.h...${ac_cv_header_glib_h}"
-    echo "*                  libglib.so or libglib.a...${ac_cv_lib_glib_g_date_julian}"
+    echo "*                  libglib.so or libglib.a...${ac_cv_lib_glib_2_0_g_date_get_julian}"
     echo "*                  glibconfig.h...${ac_cv_header_glibconfig_h}"
     echo "*"
     echo "*           (yes means it was found, no means it was not found)"

--- ntop/Makefile.am	2006-06-13 09:52:26.000000000 -0600
+++ ntop.edit/Makefile.am	2007-03-07 16:11:11.000000000 -0700
@@ -86,7 +86,9 @@
            html/*.css html/*.dtd \
            html/statsicons \
            html/statsicons/flags html/statsicons/os \
-           html/statsicons/flags/*.gif html/statsicons/os/*.gif
+           html/statsicons/flags/*.gif html/statsicons/os/*.gif \
+           html/PlotKit html/PlotKit/*.js \
+           html/MochiKit html/MochiKit/*.js
 
 WEBFILES       = `cat www/FILES`
 PLUGINSFILES   = `cat plugins/FILES`

--- ntop/configure.in.mysql	2007-03-07 12:32:30.000000000 +0100
+++ ntop/configure.in	2007-03-11 00:50:07.000000000 +0100
@@ -144,13 +144,13 @@
 
 AC_ARG_ENABLE(mysql,
               [  --enable-mysql                 Enable usage of mysql [[default=enabled]]],
-              if test "x$enableval" = xyes; then
-                  ac_with_mysql="no"
-              else
-	          echo "x$enableval"
+              [if test "x$enableval" = xyes; then
                   ac_with_mysql="yes"
-              fi,
-              ac_with_mysql="yes")
+              else
+dnl	          echo "x$enableval"
+                  ac_with_mysql="no"
+              fi],
+              [ac_with_mysql="yes"])
 
 AC_ARG_ENABLE(void,
               [  +----------------------------------------------------------------------------+])

--- ntop/Makefile.am.orig	2007-03-14 15:19:34.000000000 -0600
+++ ntop/Makefile.am	2007-03-16 10:26:31.000000000 -0600
@@ -44,7 +44,7 @@
 AWK       = @AWK@
 CC        = @CC@
 CCLD      = @CCLD@
-AM_CFLAGS = @CFLAGS@
+AM_CFLAGS =
 AM_LDFLAGS= @LDFLAGS@
 
 

--- ntop/plugins/Makefile.am.rrd	2007-03-16 23:15:08.000000000 +0100
+++ ntop/plugins/Makefile.am	2007-03-16 23:15:16.000000000 +0100
@@ -32,10 +32,6 @@
 
 SUFFIXES    = .so
 
[EMAIL PROTECTED]@
-RRD_INC=-I${RRD_HOME}/include
-RRD_LIB=-L${RRD_HOME}/lib -lrrd_th
-
 # 
 # Where to install the plugin 
 # 
--- ntop/Makefile.am.rrd	2007-03-16 23:01:00.000000000 +0100
+++ ntop/Makefile.am	2007-03-16 23:01:00.000000000 +0100
@@ -33,10 +33,6 @@
 DEFS      = @DEFS@
 INCS      = @INCS@
 
[EMAIL PROTECTED]@
-RRD_INC=-I${RRD_HOME}/include
-RRD_LIB=-L${RRD_HOME}/lib -lrrd_th
-
 INCLUDES  = -I. $(INCS) ${RRD_INC}
 LIBS      = 
 BASE_LIBS = @LIBS@ ${RRD_LIB}
@@ -44,8 +40,9 @@
 AWK       = @AWK@
 CC        = @CC@
 CCLD      = @CCLD@
-AM_CFLAGS =
-AM_LDFLAGS= @LDFLAGS@
+
+#AM_CFLAGS =
+#AM_LDFLAGS= 
 
 
 DISTCLEANFILES = trivialcompilemessage *.db #* *~ *.log
--- ntop/configure.in.rrd	2007-03-16 23:01:00.000000000 +0100
+++ ntop/configure.in	2007-03-16 23:01:00.000000000 +0100
@@ -1229,6 +1229,8 @@
    RRD_HOME=/usr/local/rrdtool
 fi
 
+RRD_LIB="-L${RRD_HOME}/lib -lrrd_th"
+
 if test -f "$RRD_HOME/lib/librrd_th.so"; then
    AC_MSG_RESULT(Found RRD)
 else
@@ -1242,11 +1244,18 @@
        if test ".${ac_cv_lib_rrd_th_main}" != ".yes"; then
          AC_MSG_ERROR(Unable to find RRD at $RRD_HOME: please use --with-rrd-home=DIR);
 	 AC_MSG_ERROR(RRD source can be downloaded from http://www.rrdtool.org/);
-        fi
+       else
+         RRD_LIB=
+       fi
      fi
   fi
 fi
 
+RRD_INC=
+if test -d "${RRD_HOME}/include"; then
+  RRD_INC="-I${RRD_HOME}/include"
+fi
+
 dnl> The failed recheck stuff below is courtesy of Chris Turbeville [EMAIL PROTECTED]
 dnl> Chris developed this for Solaris 9, confirming work I had done earlier for FreeBSD
 dnl> And thank to Julien TOUCHE [EMAIL PROTECTED] for the OpenBSD dependencies
@@ -2328,7 +2337,8 @@
 AC_SUBST(CFG_RUN_DIR)
 AC_SUBST(SCRIPTVER)
 AC_SUBST(SO_VERSION_PATCH)
-AC_SUBST(RRD_HOME)
+AC_SUBST(RRD_LIB)
+AC_SUBST(RRD_INC)
 
 AC_CONFIG_FILES([Makefile])
 

--- ntop/configureextra/LINUXfedora.fix	2007-03-16 22:54:56.000000000 +0100
+++ ntop/configureextra/LINUXfedora	2007-03-16 22:59:31.000000000 +0100
@@ -16,12 +16,12 @@
 #  Note - this assumes you've installed the RH rpms:
 #         glib, glib-devel, libxml2, libxml2-devel
 #         and the gdome2 and gdome2-devel rpms from http://gdome2.cs.unibo.it/
-if test -f /usr/lib/pkgconfig/glib-2.0.pc; then
-  LDFLAGS="${LDFLAGS} "`pkg-config --libs glib-2.0`
+if pkg-config --exists --print-errors glib-2.0; then
+  LIBS="${LIBS} "`pkg-config --libs glib-2.0`
   CPPFLAGS="${CPPFLAGS} "`pkg-config --cflags-only-I glib-2.0`
 else
   if test -f /usr/lib/libglib.so; then
-    LDFLAGS="${LDFLAGS} -lglib"
+    LIBS="${LIBS} -lglib"
   fi
   if test -d /usr/include/glib-1.2; then
     CPPFLAGS="${CPPFLAGS} -I/usr/include/glib-1.2"
@@ -33,8 +33,8 @@
     CPPFLAGS="${CPPFLAGS} -I/usr/lib/glib/include"
   fi
 fi
-if test -f /usr/lib/pkgconfig/gdome2.pc; then
-  LDFLAGS="${LDFLAGS} "`pkg-config --libs gdome2`
+if pkg-config --exists --print-errors gdome2; then
+  LIBS="${LIBS} "`pkg-config --libs gdome2`
   CPPFLAGS="${CPPFLAGS} "`pkg-config --cflags-only-I gdome2`
 else
   if test -d /usr/include/libgdome; then

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