Group Manager for Greater Manchester Fire and Rescue Service, Andy Heywood said: "At the moment we are applying water to the outside of the building to stop the fire spreading.
"By allowing the fire to burn inside the building it stays hot and gives off smoke which is relatively clean.
"Unfortunately because the building and fire is right next to the railway line we have asked for the trains to be stopped and overhead line equipment isolated.
"It could be several hours before we can be confident of what will happen to the building and how the fire will develop."
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The move comes amid a boycott of the paper in Liverpool due to its controversial coverage of the 1989 Hillsborough disaster.
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