It's interesting to compare what is in the Memoirs of SSS and what Barrows presents in Life and Correspondence of SSS. Barrows completely skips over the ship debate between Cook and Smith. However, Barrows had the advantage of access to the private papers of Smith so we get things like this. Which I think is worthwhile posting here:

The departure of the Portuguese fleet on the morning of the 29th of November, with the Prince Royal of Brazil and the whole of the regal family of Braganza on board, and various adherents and others attached to his present fortunes, comprising a fleet of about thirty-six sail of vessels, exclusive of the four English ships of the line, was a novel and imposing, yet a melancholy sight, being calculated by the occasion to inspire the spectators, and especially the remaining inhabitants, with gloomy forebodings. A sight it was pronounced, unparalleled in history—a sovereign, his family, and friends voluntarily abandoning the conveniences, comforts, and luxuries of life, committing themselves to the care and confidence of those, who might have been considered in the light of enemies, to court dangers unknown, on an element untried; proceeding to a distant clime, to throw themselves into the arms of a rude, unpolished people; and all this to avoid French friendship and its concomitant curses, French cruelty and oppression; than which they had nothing better to hope by remaining at home.

The prince-regent had a slight specimen of what might be expected from French fraternity, had he remained, by a visit he had from one of Buonaparte’s generals, of which the following note, headed S. S. S. (the common mark of Sir Sidney Smith) gives an instance.

S. S. S.

“Lannes at Lisbon, in 1807, as ambassador from Napoleon, officially insulted the Prince-Regent of Portugal according to his instructions. He asked an audience to make an official communication, and was told by the prince-regent to go through the minister for foreign affairs, according to the general custom, as well of his court, as of others. He refused to do this; and wrote a manifesto, which he took himself to the palace, and desired the sentinel to have it delivered immediately. The sentinel refused; whereupon Lannes (Montebello) threw the paper at the foot of the sentry, who afterwards picked it up, and it thus found its way to the prince-regent. Whereupon his royal highness sent to see the ambassador; and Lannes took the occasion to say everything harsh and disagreeable to him, keeping his hat on the whole interview in the royal presence. After this had gone on for some time, the prince said to him, that it might be more agreeable, perhaps, to finish the conference in the garden, as he (the prince) had not yet taken his usual morning walk.”

”They accordingly went into the garden. The ambassador now uncovered his head, and assumed a very different manner, which the prince ventured to observe to him. ‘Yes,’ replied Lannes, ‘it is very true; you now see me as General Lannes, before I was l’ambassadeur.’ After this they had several conferences, and were apparently very good friends.”

This anecdote the prince related to Sir Sidney Smith, and he also told him that Lannes had frequently spoken of Sir Sidney to him in terms of the greatest admiration, for the cool bravery he displayed at the siege of Acre, where they had been in close contact. (my emphasis)

Sir Sidney was not relieved in his command immediately on the arrival of Sir Charles Cotton, but was sent by him to examine Gibraltar, Porta Praya, and Madeira, whether any French ships or cruising vessels had visited these ports. While in the Foudroyant at Gibraltar, on the 29th of February, 1808, he received an order from the board to resume the command of the squadron that had sailed to the coast of South America, and with three ships of the line, named therein, which Sir Charles Cotton had received orders to place under his command, to proceed in company with the Agamemnon and the Confiance to the Brazil coast; and, having taken under his orders the whole of the ships and vessels on and intended for that coast, to hoist his flag as commander-in-chief.