A letter was received to-day from Mr. Ranney, president of the N. C., Jackson, and Great Northern Railroad Co., asking the protection of government from harm for violations of the Act of Congress of April 19th, 1862, prohibiting the transportation of cotton within the enemy’s lines. He incloses a number of peremptory orders from Lieut.-Gen. Pemberton, dated January 19th, February 16th and 19th, to take large amounts of cotton into the enemy’s lines for S. J. Josephs (Jew?), and for Messrs. Clarke, Ford, and Hust, etc. etc. He says Gen. P. threatened to seize the road if he did not comply, and asserted that he had authority from the Secretary of War to issue the orders. One of these orders was from Gov. Pettus, for a small lot not more than fifty bales, to be exchanged for salt. This was authorized by the President, who most positively forbid the others. The letter from Gen. Johnston the other day said this traffic was subjugating the people. Was that “allowed” to reach the Secretary and the President? I know not; it has not yet passed through my hands from the President back to the department.

May 12th.—The departments and all places of business are still closed in honor of Gen. Jackson, whose funeral will take place to-day. The remains will be placed in state at the Capitol, where the people will be permitted to see him. The grief is universal, and the victory involving such a loss is regarded as a calamity.

The day is bright and excessively hot; and so was yesterday.

Many letters are coming in from the counties in which the enemy’s cavalry replenished their horses. It appears that the government has sent out agents to collect the worn-down horses left by the enemy; and this is bitterly objected to by the farmers. It is the corn-planting season, and without horses, they say, they can raise no crops. Some of these writers are almost menacing in their remarks, and intimate that they are about as harshly used, in this war, by one side as the other.

To-day I observed the clerks coming out of the departments with chagrin and mortification. Seventy-five per cent. of them ought to be in the army, for they are young able-bodied men. This applies also to the chiefs of bureaus.

The funeral was very solemn and imposing, because the mourning was sincere and heartfelt. There was no vain ostentation. The pall bearers were generals. The President followed near the hearse in a carriage, looking thin and frail in health. The heads of departments, two and two, followed on foot—Benjamin and Seddon first—at the head of the column of young clerks (who ought to be in the field), the State authorities, municipal authorities, and thousands of soldiers and citizens. The war-horse was led by the general’s servant, and flags and black feathers abounded.

Arrived at the Capitol, the whole multitude passed the bier, and gazed upon the hero’s face, seen through a glass in the coffin.

Just previous to the melancholy ceremony, a very large body of prisoners (I think 3500) arrived, and were marched through Main Street, to the grated buildings allotted them. But these attracted slight attention,—Jackson, the great hero, was the absorbing thought. Yet there are other Jacksons in the army, who will win victories,—no one doubts it.

The following is Gen. Lee’s order to the army after the intelligence of Gen. Jackson’s death:

“Headquarters Army Northern Va.,
“May 11th, 1863.