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I was wondering why pdflatex displays some references in the text as question marks the first time that the file is compiled? For instance, with bibliographies at the end of an article that are referenced in the text that is the case - the first time I compile the document, I get questionmarks instead of numbers that point to respective entries. The second time it's fine.

Does this mean that pdflatex goes through the document only once?

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Yes. That's right. While going through the document, the engine writes all related informations, such as placement of the labels, etc. into an extra file with the suffix .aux. At the second run, this file is read and used for resolving the labels.

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