The magistrate judge set the bond for a weapons charge but doesn't have the authority to set bond on the counts. That will be left up to a circuit judge at a later date.
Roof appeared by video and stared straight ahead stone faced as five victims' family members gave statements, some of them saying "hate won't win." Roof showed no reaction as they told him they would have mercy on him and that they forgave him.
RAW VIDEO: Roof court appearance
"I forgive you," the daughter of victim Ethel Lance said through tears. "You hurt me, you hurt a lot of people."
Felicia Sanders, the mother of the slain Tywanza Sanders, said, "We welcomed you Wednesday night in our bible study with open arms."
"Every fiber in my body hurts," Sanders said. "And I'll never be the same. Tywanza Sanders was my son. But he was my hero. But as we said at bible study, may God have mercy on you."
Alana Simmons, granddaughter of victim Daniel Simmons, said, "Although my grandfather and the other victims died at the hands of hate, this is proof everyone's plea for your soul is proof that they -- they lived and loved and their legacies will live and love. So hate won't win and I just want to thank the court for making sure that hate doesn't win."
The judge set the bond with the understanding that Roof will be held until his bond hearing on the murder charges.
In a statement by Dylann Roof's public defender, the Roof family extended "their deepest sympathy and condolences to the families of the victims."
"Words cannot express our shock, grief and disbelief as to what happened that night," the statement continued. "Our thoughts and prayers are with the families and friends of those killed this week. We have all been touched by the moving words from the victim's families offering God's forgiveness and love in the face of such horrible suffering."
The statement concluded by asking for privacy for the Roof family and referring media questions to his attorney.
Meanwhile, the Justice Department says it is investigating the slayings from all angles, including whether it could be a hate crime or domestic terrorism.
Agency spokeswoman Emily Pierce said in a statement Friday that "heartbreaking episode was undoubtedly designed to strike fear and terror into this community" and that the investigation is ongoing.
Meanwhile, a former friend who had recently reconnected with Roof recently says had become an avowed racist.
Joey Meek said he met with Roof a few weeks ago and said that while they got drunk together on vodka, Roof began complaining that "blacks were taking over the world" and that "someone needed to do something about it for the white race."
Roof, 21, is accused of fatally shooting nine people during a Bible study at The Emanuel African Methodist Episcopal Church in Charleston on Wednesday night, ripping out a piece of South Carolina's civic heart and adding to the ever-growing list of America's racial casualties.
Related: A timeline of events
Police captured Roof in Shelby, North Carolina, after a motorist spotted him at a traffic light on her way to work. His apprehension ended an intense, hours-long manhunt.
RAW VIDEO: Accused shooter in custody
Roof waived extradition and was back in Charleston on Thursday night. On Friday, South Carolina Gov. Nikki Haley told NBC's "Today" show the shooter should get the death penalty.
"We will absolutely will want him to have the death penalty," Haley said.
A relative of one of the nine people killed said a survivor of the massacre told her Roof entered the church asking to see the Rev. Clementa Pinckney.
"They showed him where he was and Clementa, being the kind-spirited person that he is, he had him sit next to him," Sylvia Johnson, a cousin of the church's slain pastor, told ABC News Thursday after speaking with one of the survivors who was in the church.
Pinckney, 41, was among the nine shot to death at Wednesday night Bible study.
The woman who survived, whose name has not been publicly released, had blood on her dress when she was speaking to Johnson on Wednesday night. Both the survivor and her granddaughter reportedly evaded the gunman by pretending they were dead.
"She said it was just like...it was just blood all over the place," Johnson told ABC News.
The survivor's son, who was in his 20s, was also at the Bible study but he was fatally shot after he tried to check on Pinckney and directly engaged the shooter.
Johnson said the survivor told her the gunman, addressing her son, said, "You all rape women and you're taking over our country."
The gunman added, "I have to do what I have to do," Johnson said, quoting the survivor.
The survivor said it wasn't until the end of Bible study when the suspect just started shooting, according to Johnson. The survivor said the suspect loaded his gun about five times.
The survivor, who is elderly, who spoke with Johnson and her 5-year-old granddaughter are two of the three people who survived the shooting. According to Johnson, when the gunman saw the elderly woman was alive, he asked her, "Did I shoot you?"
When the elderly woman said "No," the gunman said, "Good, because I need someone to survive," and said he was going to shoot himself, the survivor told Johnson. "And you'll be the only survivor."
Charleston officials have announced a prayer vigil for Friday evening. The city's mayor described the shooting at the church as an act of "pure, pure concentrated evil."
The victims included Pinckney, a state senator who doubled as the church's minister, three other pastors, a regional library manager, a high school coach and speech therapist, a government administrator, a college enrollment counselor and a recent college graduate - six women and three men who felt called to open their church to all.
Related: Remembering the victims
President Barack Obama called the tragedy yet another example of damage wreaked in America by guns.
NAACP President and CEO Cornell William Brooks said "there is no greater coward than a criminal who enters a house of God and slaughters innocent people." Others bemoaned the loss to a church that has served as a bastion of black power for 200 years, despite efforts by white supremacists to wipe it out.
"Of all cities, in Charleston, to have a horrible hateful person go into the church and kill people there to pray and worship with each other is something that is beyond any comprehension and is not explained," said Mayor Joseph P. Riley Jr. "We are going to put our arms around that church and that church family."
Surveillance video showed the gunman entering the church Wednesday night, and Charleston County Coroner Rae Wilson said he initially didn't appear threatening.
"The suspect entered the group and was accepted by them, as they believed that he wanted to join them in this Bible study," she said. Then, "he became very aggressive and violent."
Meek called the FBI after recognizing Roof in the surveillance footage, down to the stained sweatshirt he wore while playing Xbox videogames in Meek's home the morning of the attack.
PHOTOS: 9 dead after Charleston church shooting
"I didn't THINK it was him. I KNEW it was him," Meek told The Associated Press after being interviewed by investigators.
Meek said during their reunion a few weeks ago, Roof told him that he had used birthday money from his parents to buy a .45-caliber Glock pistol and that he had "a plan." He didn't say what the plan was, but Meek said it scared him enough that he took the gun out of Roof's car and hid it in his house until the next day.
It's not clear whether Roof had any connection to the 16 white supremacist organizations operating in South Carolina, but he appears to be a "disaffected white supremacist," based on his Facebook page, said Richard Cohen, president of Southern Poverty Law Center in Montgomery, Alabama.
On his Facebook page, Roof displayed the flags of defeated white-ruled regimes, posing with a Confederate flags plate on his car and wearing a jacket with stitched-on flag patches from apartheid-era South Africa and Rhodesia, which is now black-led Zimbabwe.
His previous record includes misdemeanor drug and trespassing charges.
Video: Vigil held in Chapel Hill for church shooting victims
Spilling blood inside a black church - especially "Mother Emanuel," founded in 1816 - evoked painful memories nationwide, a reminder that black churches so often have been the targets of racist violence.
A church founder, Denmark Vesey, was hanged after trying to organize a slave revolt in 1822, and white landowners burned the church in revenge, leaving parishioners to worship underground until after the Civil War. The congregation rebuilt and grew stronger, eventually winning campaigns for voting rights and political representation.
Its lead pastor, state Sen. Clementa Pinckney - among the dead - recalled his church's history in a 2013 sermon, saying "we don't see ourselves as just a place where we come to worship, but as a beacon and as a bearer of the culture."
"What the church is all about," Pinckney said, is the "freedom to be fully what God intends us to be and have equality in the sight of God. And sometimes you got to make noise to do that. Sometimes you may have to die like Denmark Vesey to do that."
Pinckney, 41, was a married father of two and a Democrat who spent 19 years in the South Carolina legislature after he was first elected at 23, becoming the youngest member of the House.
The other victims were Cynthia Hurd, 54; Tywanza Sanders, 26; Myra Thompson, 59; Ethel Lance, 70; Susie Jackson, 87; and the reverends DePayne Middleton Doctor, 49; Sharonda Singleton, 45; and Daniel Simmons Sr., 74.
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