I haven’t found out too much about this ship but the following is a quote from a South African website:
Page 15 of the 'History of South Africa 1486 - 1691 recounts that the first English ships to put into a harbor on the South African coast were the Penelope, Merchant Royal, and the Edward Bonaventure on the 10th of April, 1591. So many men had died of scurvy that it was advisable to send the Merchant Royal back to England short handed.
This seems to be backed up by this quote on another website:
1591
Abraham Kendall, captain of the Royal Merchant, part of the first fleet of English East Indiamen on their way east, landed with a crew suffering from scurvy.
They later recovered.
Any further information would be welcome.