I'm using revtex4-1 and I get these warnings: BibTeX jnrlst (dependency: not reversed) set 1 and BibTeX I didn't find a database entry for "nielsen".
MWE:
\documentclass[aps,twocolumn,nofootinbib,floatfix]{revtex4-1}
\usepackage[utf8]{inputenc}
\begin{document}
What is Lorem Ipsum?
Lorem Ipsum is simply dummy text of the printing and typesetting industry \cite{nielsen}. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum.
\begin{thebibliography}{25}
\bibitem{nielsen} M. A. Nielsen and I. L. Chuang, Quantum Computation and Quantum Information: 10th Anniversary Edition, 10th ed. (Cambridge University Press, New York, NY, USA, 2011).
\end{thebibliography}
\end{document}
Note that this answer is not applicable to my situation as I'm not using any .bib file.
Any idea how to get rid of those warnings?

.auxand.bblfiles? Can you reproduce the issue when you run the shown example in an empty directory? – moewe Nov 05 '18 at 20:31.texfile. I'm using Overleaf. You can view and edit the MWE here. – Nov 05 '18 at 20:33.bibfile, it is possible that this is just the remnant of an earlier run. – moewe Nov 05 '18 at 20:33latexmkto make sure that the document is processed by all the right tools in the correct order. I tested the exact example you posted with my local install oflatexmkand on the non-login version of Overleaf (v1): https://v1.overleaf.com/read/yzxqtkdbzqdb. As you can see the warnings do not occur. If they occur for you with the exact example posted the only explanation I can offer are left-over auxiliary files. If you cleared those and the error persists I'm out of ideas. – moewe Nov 05 '18 at 20:40