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Rain totals exceeded 5 inches in parts of the Bronx and Northern New Jersey.
The 114-year-old tunnels are in dire need of repairs, but some experts warn the railroad's plan to fix them will spell trouble for New York commuters.
Amid heavy rainfall, NYC is deploying talking drones in low-lying areas of the outer boroughs.
The Federal Aviation Administration issued a notice saying flights out of Newark faced delays of more than two hours.