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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.
The suspension lasted until about 2 p.m. on Monday, according to the commuter rail operator.
Most flights were grounded Friday morning and the MTA reported its notification system was down.