Line 3846 in wp-includes/functions.php is in a function named _deprecated_function(), which warns about the use of deprecated functions. I did a quick search of my copy of 4.9.4 core and didn’t find any instances of wpdb->escape() or get_current_site_name(), the two functions you’re actually being warned about.
Most likely, the deprecated functions are in a plugin or a theme. If you disable all plugins and switch to a default theme (such as Twenty Seventeen), the Notices should go away.
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