Having had great success monitoring our Linux hosts with Ganglia I've
also managed to build version 3.1.2 on cygwin-1.5.25-15.

I had to modify configure.in however; a patch is attached.

On Cygwin the linker will ignore libraries encountered on the command
line that it yet sees the need for, ordering is therefore important.
After the attached patch is applied, conftest.c will be compiled with
-lintl and -iconv in LIBS rather than LDFLAGS, placing them after the
source file on the command line.

Other platforms should be unaffected.
--- configure.in	2009-10-02 16:21:29.000000000 -0700
+++ ganglia-3.1.2/configure.in	2009-01-28 15:23:20.000000000 -0800
@@ -345,11 +345,13 @@
 if test x"$ac_cv_lib_confuse_cfg_parse" = xno; then
   echo Trying harder including gettext
   unset ac_cv_lib_confuse_cfg_parse
-  AC_CHECK_LIB(confuse, cfg_parse, [LIBS="$LIBS -lconfuse -lintl"],,[-lintl])
+  LDFLAGS="$LDFLAGS -lintl"
+  AC_CHECK_LIB(confuse, cfg_parse)
   if test x"$ac_cv_lib_confuse_cfg_parse" = xno; then
     echo Trying harder including iconv
     unset ac_cv_lib_confuse_cfg_parse
-    AC_CHECK_LIB(confuse, cfg_parse, [LIBS="$LIBS -lconfuse -lintl -liconv"],,[-lintl -liconv])
+    LDFLAGS="$LDFLAGS -liconv"
+    AC_CHECK_LIB(confuse, cfg_parse)
     if test x"$ac_cv_lib_confuse_cfg_parse" = xno; then
       echo "libconfuse not found"
       exit
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