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Allen related that Allen possessed enormous wealth, and lived in great pomp and luxury; but it is certain that these statements are incorrect. Allen, when he was created a cardinal, had neither private fortune nor ecclesiastical revenues with which to support his new dignity; but Philip II soon afterwards conferred upon him a rich abbey in Calabria, and an annual pension charged upon the revenues of the archbishopric of Palermo. Whatever this may have brought in, he still remained one of the poorer cardinals, as appears from the circumstance that Urban VII, on his elevation to the papacy (1590), bestowed upon Allen one thousand crowns, and released him from the obligation of repaying three thousand crowns, which he had borrowed from the preceding pontiff. His biographer, Nicholas Fitzherbert, also speaks expressly of his being in ‘straitened circumstances.’

In November 1589 Philip II nominated him archbishop of Mechlin and metropolitan of Belgium, but he was not preconised by the pope. He did not visit Mechlin, and at length, in 1591, Philip gave up all hope of inducing Allen to accept the archbishopric, and nominated another ecclesiastic to the vacant see.

On the death of Cardinal Antonio Carafa Gregory XIV made Allen apostolic librarian. The same pontiff charged him, in conjunction with Cardinal Marc' Antonio Colonna and several consultors, to revise the edition of the Vulgate which Sixtus V had published just before his death. Allen also undertook, in conjunction with others, to correct the text of St. Augustine's works, but death prevented him from completing so vast an undertaking.

Long before he became a member of the Sacred College he had received from the holy see extensive faculties for the benefit of the English mission, and these were enlarged when he was made cardinal. For many years the most cordial relations subsisted between him and the jesuits, and he had always thankfully availed himself of their co-operation in promoting the good of the English seminaries, but it is clear that towards the end of his life a change came over these relations, and that there was no longer the same unanimity between the cardinal and the fathers of the society. It does not plainly appear what were the causes of this estrangement; but it is probable that the points of disagreement related to the English seminaries and mission, and not to political affairs.

Allen died at Rome on 16 Oct. 1594, and was buried in the church of the Holy Trinity, attached to the English college.

In forming an estimate of Cardinal Allen's character it is but fair to take into account the peculiar position in which he was placed, and the opinions generally entertained in his day by catholic theologians concerning the pope's deposing power. By many admirers of Queen Elizabeth and her policy Allen has been denounced in unmeasured terms as a traitor to his sovereign and his country. This feeling is forcibly expressed by Godwin (Catalogue of the Bishops of England, 698), who describes Allen as ‘a man by birth English, but so ill deserving to be accounted English, as that, like another Herostratus, he endeavoured by raising a combustion in our church, the most glorious and renowned of the world, to make himself known to posterity.’ On the other hand, catholic writers speak of Allen in terms of the highest commendation, and John Pits, who had studied in the English colleges of Douay and Rheims, passes this splendid eulogium on his character: ‘He had a handsome countenance and dignified gait, and was on all occasions courteous; as regards mental endowments he was pious, learned, discreet, serious, and of great authority; humble, modest, patient, meek, of a peaceful disposition: in a word, graced by every species of virtue’ (Relationes Historicæ de Rebus Anglicis, 792). Cardinal Allen and his fellow-exiles considered the catholic religion to be most essential to the welfare of their countrymen; they regarded Elizabeth as the capital enemy of their faith, and likewise as a usurper; and they never questioned the justice of those temporal and civil deprivations and forfeitures which, during so many ages, had been connected with the spiritual sentence of excommunication. That they committed a grave political error in urging the Spanish king to invade England cannot be denied, and the event proved that they had entirely mistaken the temper of their co-religionists at home. In Mary's reign Philip II was king of England, and loyalty to him was then a proper sentiment; but Allen preserved throughout life his allegiance to the monarch to whose liberality he was so largely indebted, and this led him to adopt a course of action which it is difficult to justify. All his political schemes ended in disastrous failure; but, on the other hand, it is certain that by the opportune establishment of Douay College for the education of missioners he prevented the catholic religion from being completely destroyed in England, as was the case in Sweden, Norway, and Denmark.

There is a fine portrait of Allen in Lodge's ‘Portraits of Illustrious Personages.’

His works are: 1. ‘Certain brief Reasons concerning Catholic Faith,’ Douay, 1564. 2. ‘A Defense and Declaration of the Catholike Churches Doctrine touching