I am not working on the linked data topic at the moment, but I will consider a cooperation when I get back to it. Thanks for the tip! Nevertheless if there are any questions regarding wp-linked-data by the dev team that may help them with their plugin I am here to answer.
No, this is not related to WP LDP. Did not know it until now.
The plugin noticed that you have pecl_http (http://pecl.php.net/package/pecl_http) installed. Is this correct? If so, check if pecl_http version is at least 0.19.0.
If you do not have pecl_http installed, let me no, because this might indicate a bug in the checking logic.
The plugin works also without pecl_http, so you may also uninstall it, if you do not need it for other applications. wp-linked-data uses a simplified content negotiation then.
Best regards.