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Is it possible to hide just update messages for deactivated plugins in WP 3.4+?

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yes, it is possible (answer above), but that doesn't address the problem. a plugin, even deactivated, can pose a security issue if left out of date. if you don't need the plugin, best to remove it from the site all together. – Norcross Dec 24 '12 at 19:15

Yep Its possible if you hook a function to site_transient_update_plugins filter hook and check if plugin is activated using is_plugin_active like this:

add_filter('site_transient_update_plugins', 'remove_update_nag_for_deactivated');
function remove_update_nag_for_deactivated($value) {
    foreach($value->response as $key => $val){
        if (!is_plugin_active($val))
            unset($value->response[ $key]);
    return $value;
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