In the month of August a very malignant fever made its appearance at Thompsons Island, which threatened the destruction of our station there.  Many perished, and the commanding officer was severely attacked.  Uncertain as to his fate and knowing that most of the medical officers had been rendered incapable of discharging their duties, it was thought expedient to send to that post an officer of rank and experience, with several skilled surgeons, to ascertain the origin of the fever and the probability of its recurrence there in future seasons; to furnish every assistance to those who were suffering, and, if practicable, to avoid the necessity of abandoning so important a station.  Commodore Rodgers, with a promptitude which did him honor, cheerfully accepted that trust, and has discharged it in the manner anticipated from his skill and patriotism.  Before his arrival Commodore Porter, with the greater part of the squadron, had removed from the island and returned to the United States in consequence of the prevailing sickness.  Much useful information has, however, been obtained as to the state of the island and great relief afforded to those who had been necessarily left there.

Although our expedition, cooperating with an invigorated administration of the government of the island of Cuba, and with the corresponding active exertions of a British naval force in the same seas, have almost entirely destroyed the unlicensed piracies from that island, the success of our exertions has not been equally effectual to suppress the same crime, under other pretenses and colors, in the neighboring island of Porto Rico.  They have been committed there under the abusive issue of Spanish commissions.

At an early period of the present year remonstrances were made to the governor of that island, by an agent who was sent for the purpose, against those outrages on the peaceful commerce of the United States, of which many had occurred.  That officer, professing his own want of authority to make satisfaction for our just complaints, answered only by a reference of them to the Government of Spain.  The minister of the United States to that court was specially instructed to urge the necessity of immediate and effectual interposition of that Government, directing restitution and indemnity for wrongs already committed and interdicting the repetition of them.  The minister, as has been seen, was debarred access to the Spanish Government, and in the mean time several new cases of flagrant outrage have occurred, and citizens of the United States in the island of Porto Rico have suffered, and others been threatened with assassination for asserting their unquestionable rights even before the lawful tribunals of the country.

The usual orders have been given to all our public ships to seize American vessels in the slave trade and bring them in for adjudication, and I have the gratification to state that not one so employed has been discovered, and there is good reason to believe that our flag is now seldom, if at all, disgraced by that traffic.