SAN LEANDRO (CBS SF) — Track problems near BART’s Bay Fair station that started Friday morning were finally resolved in the late afternoon following major delays across the entire transit system, officials said.

The problem was discovered around 9:30 a.m. and affected service from Bay Fair in the Dublin/Pleasanton, Warm Springs, Richmond and Daly City directions.

Passengers were stuck on a San Francisco-bound train near the Bay Fair station and others took to social media to complain they were on stopped trains.

A CBS San Francisco web editor reported it took an hour and 35 minutes to travel from Castro Valley station to Bay Fair station after passengers were twice removed from Daly City-bound trains at Castro Valley that were re-routed back to Dublin-Pleasanton station.

“This originated from the train control room,” said BART spokeswoman Alicia Trost. “These are rooms that are positioned throughout the system that basically communicated between the train control system and the track system and that room was getting overheated or something where it was causing a problem communicating with the tracks and the train control system.”

BART officials tweeted at 10:23 a.m that some limited service has been established.

“We had to manually set all the routes which actually causes the delays in the first place. What we know is that there are crews working on it,” said Trost. “It hasn’t impacted system-wide. It’s really going through Bay Fair, but that does also mean if you’re heading onto Warm Springs or heading into the Dublin area – so it’s along those lines that it’s being impacted.”

Operators appeared to be hand switching the tracks as trains passed through stations during the delays.

At about 4:15 p.m., BART tweeted that the equipment problems on the tracks near Bay Fair were cleared.

AC Transit provided mutual aid on bus #10 between San Leandro, Bayfair, and Hayward during the problems.

“Went upstairs, waited, waited, waited – saw a train like way down there, like I could see the lights and I thought ‘Okay, at least the train is coming’,” said rider Cecily Odiari. “So I waited and waited and waited it wasn’t moving. It was truly an ordeal. I probably waited for about a total of maybe 40-45 minutes something like that – it was crazy.”