The Pontiff said that God had made Juan Carlos Cruz gay and that his sexuality "does not matter".
In his meeting with Francis on a Sunday at his Santa Marta residence, Mr. Cruz said he had told the pope that he was anxious he would think less of him.
Cruz reportedly told El Pais, a Spanish newspaper, that the two had a conversation about his homosexuality and said he was told, "Juan Carlos, I don't care about you being gay. All material and spiritual poverty, every form of discrimination against our brothers and sisters, is always a effect of the rejection of God and his love", he said. "You should not discriminate against or marginalise these people, and the Catechism says this as well". "You have to be happy with who you are".
"Basing itself on Sacred Scripture, which presents homosexual acts as acts of grave depravity, tradition has always declared that 'homosexual acts are intrinsically disordered.' They are contrary to the natural law".
Catholics believe that God creates all human persons in love, but all people are also called to use their freedom responsibly, following positive inspirations and resisting attractions that are sinful.
In a commentary piece in United Kingdom newspaper The Independent, however, Douglas Robertson pointed out that what Francis said "doesn't really contradict the church's teaching in any way".More news: Warriors run riot in Game 3
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Salvadoran Cardinal Gregorio Rosa Chavez told TV2000, the Italian bishops' television station, that he hoped Pope Francis would make a brief trip to San Salvador in January to pray at the tomb of by-then St. Oscar Romero.
A spokesperson for the Vatican did not comment on the conversation Cruz had with the Pope. Given this situation, the archdiocese is not able to offer further comment on these reports.
The resignation of the bishops appears to stem from the numerous cases against Fr. Fernando Karadima, who was found guilty in a Vatican investigation of abusing boys in Santiago in the 1970s and 1980s. In coming forward, Cruz was depicted as a pervert by some bishops in Chile. "I don't think he has changed church teaching but he's demonstrating an affirmation of gay Catholics, something that has been missing over the years in Rome".
This week, Pope Francis made worldwide headlines potentially stating the most progressive views towards homosexuality in the history of the Catholic Church. The revised edition says: "This inclination, which is objectively disordered, constitutes for a lot of them a trial".
"I welcome any statement from Pope Francis which reminds people that gay people (like anyone) should love themselves", wrote Douglas Robertson at the Independent.
Since his election in 2013, the pope has dramatically shifted the language the Church has used about homosexuality, which was once seen as a taboo subject.