It happened at P.S. 132 in Laurelton just before 5:30 a.m.
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The FDNY said construction materials on the roof caught fire.
The flames was brought under control quickly.
The fire department is checking the building for any water damage.
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The school custodian was the only person in the school and was not injured.
Despite the fire, school is open for the day Tuesday, though three classrooms were out of use.
The Department of Education issued the following statement: "FDNY immediately responded to a fire on the PS 132 roof this morning before school started, and no students were in the building. The building was cleared in time for the school day and classes are continuing normally."
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