In his first public appearance in New York, Pope Francis stood beneath the soaring vaulted ceilings of St. Patrick’s Cathedral and told nearly 2,500 priests and nuns that their shared religious vocation was meant to be “lived in joy.”

“There is a cause for rejoicing here,” Francis told the crowd at an evening Vespers prayer service, quoting the words of St. Peter, the Catholic Church’s first pope, while standing in the splendor of an American religious landmark that has recently undergone a $177 million renovation.

But amid the prayerful ceremony, filled with recitations of the Hail Mary and the Lord’s Prayer and deeply evocative hymns, Francis also touched on some of the reasons that many American Catholics have lost the sense of joy that Francis is hoping to rekindle, including the sexual abuse scandal and strained relations between the Vatican and American religious women.

To his call for joy, Francis added the rest of St. Peter’s quote, warning that the clergy “may for a time have to suffer the distress of many trials.”

As he did in Washington, Francis referred to the sexual abuse scandal, telling the gathered clergy that “you suffered greatly in the not distant past by having to bear the shame of some of your brothers who harmed and scandalized the Church in the most vulnerable of her members.”

The pope’s statements seemed consistent with his earlier remarks on his U.S. trip, which have angered some victims’ groups who complain that his public expressions of sympathy seem to focus more on priests and bishops than on victims.

“I know that many of you are in the front lines in meeting the challenges of adapting to an evolving pastoral landscape,” Francis said, during a service concelebrated by more than 40 bishops, including Cardinal Timothy M. Dolan, the archbishop of New York. “Whatever difficulties and trials you face, I ask you, like Saint Peter, to be at peace and to respond to them as Christ did: he thanked the Father, took up his cross and looked forward!”

The formal service began at the end of a glorious fall day, with soft, golden light streaming through the cathedral’s majestic stain-glass windows. Ushers in morning suits and white gloves led the faithful to their seats amid the strains of Bach and Mozart, and they cheered loudly when NBC Today Show host Matt Lauer took the microphone to announce that Pope Francis had landed in New York. They cheered again as Francis pulled up in his white Jeep popemobile.

Just arrived from his two-day visit to Washington, Francis sprinkled holy water on the crowd, then joined a procession down the center aisle past a crowd that was mainly clergy or lay church leaders and supporters, but also New York political dignitaries including Gov. Andrew Cuomo (D), Mayor Bill de Blasio (D), U.S. Sen. Chuck Schumer (D) and Henry Kissinger.

He opened his remarks with an offering of condolence for the hundreds of Muslim pilgrims who were killed this week in a stampede in Mecca.

“I unite myself with you all,” he said, to all Muslims.

Draped in elegant green and gold vestments, Francis clearly aimed to reassure U.S. religious women after several years of troubled relations, singling them out for special praise and thanks, starting with Saint Elizabeth Ann Seton, the first U.S-born saint, who founded the first free Catholic school for girls in America.

“What would the Church be without you? Women of strength, fighters, with that spirit of courage which puts you in the front lines in the proclamation of the Gospel,” he said. “To you, religious women, sisters and mothers of this people, I wish to say ‘thank you,’ a big thank you… and to tell you that I love you very much.”

He received three sustained ovations during that single paragraph in his speech, despite pleas by church officials beforehand that no one applaud during the ceremony.

The relationship between the Vatican and U.S nuns has been tense at times in recent years, particularly after Holy See’s Congregation for the Doctrine of the Faith released a 2012 assessment of the Leadership Conference of Women Religious, accusing the group of straying from Catholic orthodoxy, particularly on issues such as women’s ordination, abortion, and same-sex marriage.

Last December, the Vatican’s investigation into the American nuns concluded on a conciliatory note. Rather than calling for any changes in their behavior of women in U.S. religious orders, it professed “profound gratitude” for their work. It was widely seen as an effort by Pope Francis to mend soured relations with the nuns that started before he became pope.

His message was eagerly welcomed by religious women at St. Patrick’s.

“It’s just so nice to hear him affirm our vocation and our fidelity, which we know is true but had been called into question,” said Marylin Gramas, 73, a nun who lives in Harlem.

“It just wasn’t fair, but we had to live through it,” she said. “Hearing him be a brother to us means a great deal to us. He’s just a great gift to us, to the church and to the world.”

Patricia Bruck, 76, another Sister of Saint Ursula nun, said she hasn’t felt so warmly toward a pope since John XXIII, who died in 1963.

“I love this pope’s incredible openness, his desire to be among the poor, his preference for the poor—that’s right up my alley,” said Bruck, who recently retired after 57 years teaching at a Catholic girls’ school in New York.

“With all the criticism we’ve had recently, his approval is very refreshing,” she said. “I feel heard. I feel appreciated.”

As he did in Washington, Francis again stressed the Catholic themes of service to the poor and the most needy, including new immigrants.

He urged the gathered clergy to grateful to be serving God, and to work hard and not become “jealous of free time, when we think that surrounding ourselves with worldly comforts will help us serve better.”

He said reliance on such comforts “diminishes our spirit of sacrifice, renunciation and hard work. It also alienates people who suffer material poverty and are forced to make greater sacrifices than ourselves.”

“We need to learn how to rest in a way that deepens our desire to serve with generosity,” he said. “Closeness to the poor, the refugee, the immigrant, the sick, the exploited, the elderly living alone, prisoners and all God’s other poor, will teach us a different way of resting, one which is more Christian and generous.”

The pope also continued praising Americans who have contributed to the Catholic Church’s growth since the founding of the country. At St. Patrick’s, in addition to Saint Elizabeth Seton, he also praised the life of Saint John Neumann, a 19th Century bishop in Philadelphia who founded the first Catholic diocesan school system.

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