FYI:

I've changed to use ayatana-appindicator.
I hope attached patch will solve this issue.
--- a/configure.ac
+++ b/configure.ac
@@ -363,27 +363,27 @@
 
 APPINDICATOR_REQUIRED=0.3
 
-AC_ARG_ENABLE(appindicator,
-                        AS_HELP_STRING([--enable-appindicator[=@<:@no/auto/yes@:>@]],[Build support for application indicators ]),
-                        [enable_appindicator=$enableval],
-                        [enable_appindicator="auto"])
-
-if test x$enable_appindicator = xauto ; then
-        PKG_CHECK_EXISTS([appindicator-0.1 >= $APPINDICATOR_REQUIRED],
-                         enable_appindicator="yes",
-                         enable_appindicator="no")
+AC_ARG_ENABLE(ayatana-appindicator,
+                        AS_HELP_STRING([--enable-appindicator[=@<:@no/auto/yes@:>@]],[Build support for ayatana application indicators ]),
+                        [enable_ayatana_appindicator=$enableval],
+                        [enable_ayatana_appindicator="auto"])
+
+if test x$enable_ayatana_appindicator = xauto ; then
+        PKG_CHECK_EXISTS([ayatana-appindicator-0.1 >= $APPINDICATOR_REQUIRED],
+                         enable_ayatana_appindicator="yes",
+                         enable_ayatana_appindicator="no")
 fi
 
-if test x$enable_appindicator = xyes ; then
-        PKG_CHECK_EXISTS([appindicator-0.1 >= $APPINDICATOR_REQUIRED],,
-                         AC_MSG_ERROR([appindicator-0.1 is not installed]))
+if test x$enable_ayatana_appindicator = xyes ; then
+        PKG_CHECK_EXISTS([ayatana-appindicator-0.1 >= $APPINDICATOR_REQUIRED],,
+                         AC_MSG_ERROR([ayatana-appindicator-0.1 is not installed]))
         PKG_CHECK_MODULES(APP_INDICATOR,
-                        appindicator-0.1 >= $APPINDICATOR_REQUIRED)
+                        ayatana-appindicator-0.1 >= $APPINDICATOR_REQUIRED)
         AC_SUBST(APP_INDICATOR_CFLAGS)
         AC_SUBST(APP_INDICATOR_LIBS)
         AC_DEFINE(HAVE_APP_INDICATOR, 1, [Have AppIndicator])
 fi
-AM_CONDITIONAL(HAVE_APP_INDICATOR, test x"$enable_appindicator" = xyes)
+AM_CONDITIONAL(HAVE_APP_INDICATOR, test x"$enable_ayatana_appindicator" = xyes)
 
 AC_ARG_ENABLE([shave],
             [  --disable-shave			Use shave output cleaner when building.],
@@ -524,7 +524,7 @@
 else
 	echo "Multimedia keys support is:       disabled"
 fi
-if test x"$enable_appindicator" = xyes; then
+if test x"$enable_ayatana_appindicator" = xyes; then
     echo "AppIndicator Support is:          enabled"
 else
     echo "AppIndicator Support is:          disabled"
--- a/src/tray-icon2.c
+++ b/src/tray-icon2.c
@@ -36,7 +36,7 @@
 #define TRAY_ICON2_ID "tray-icon2"
 
 #ifdef HAVE_APP_INDICATOR
-    #include <libappindicator/app-indicator.h>
+    #include <libayatana-appindicator/app-indicator.h>
     AppIndicator *indicator;
 #endif
 

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