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You should use \input rather than \include for cases such as this where it is not a whole part of a document which might be compiled alone (e.g. a chapter or section or something). See this question for details. Note, in particular, that you cannot use \include in the preamble. \documentclass{standalone} \input{preamble} \begin{document} ...


While creating my minimal working example, I realized my mistake. LaTeX displays the table of contents using the .toc file that is built on the first pass through the document. Therefore, the first pass will not include the chapters that were not processed from before. To fix this issue, run the LaTeX command used to process the .tex file again. This will ...


Actually, this isn't a latexmk problem. If you look at the .log file or at the actual screen output, you'll see that it is pdflatex that had a problem. If you run pdflatex from the command line with the -output-directory=build option, you will get exactly the same errors. The primary error is that pdflatex can't create the file chapters/test.aux. The ...


I know the question is pretty old but since this post was the first on tex.sx I found this might be of help. As proposed by Martin, a solution to the problem could be to use the import package as explained in How to use the import package?.

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