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That's not a warning, it's an error. BibTeX is trying to tell you that you tried to remove an item from the stack, but there are no items on it. Think of it like being told to draw a card, but there are no more cards to draw. It's coming from the fact that you modified the add.doi function and did a...

I poked around in the code for mhchem for a while, but it's not obvious how to define => to mean what you want it to mean. (Writing \Rightarrow is always going to use the math symbol, hence the curviness; if you used \rightarrow instead of -> it would do the same thing.) One workaround is to use the...

According to the wrapfig documentation, using the uppercase version of the placement specifier allows the environment to float. That is, \begin{wrapfigure}[12]{o}{2in} ... \end{wrapfigure} would produce a non-floating environment 12 lines deep and 2 in wide, whereas \begin{wrapfigure}[12]{O}{2in} .....

This could be a number of things, but if there's a problem, it's somewhere in the \include ed or \input ted files, not in the main document. Since you didn't post those, it's hard to say. (This is why the board rules tell you to always prepare a .) My guess: change the \inputenc line in your style f...

The premise of your post (i.e., that LyX is a better tool) is flawed. You may prefer LyX and its interface, but it's not for everyone, and there are times that even the best LyX user will be relegated to writing "plain LaTeX" (as you somewhat amusingly put it---if you think LaTeX is "...

Do you actually want the glossaries as sections, or is it more that you want them as unnumbered chapters? It would be weird to have a chapter-level entity (such as a glossary) as a subsection of the previous chapter, but if that's what you want...try this: \documentclass{report} \usepackage[nonumber...

This seems to be linked to all the changes to \headsep , \topmargin , and so forth, combined with including/not including certain environments. For example, if the copyright page is included, the spacing is different on the acknowledgments page! Modifying these lengths should generally be avoided; i...

You might need \noindent before the minipage?

Sorry to reply to a "solved" post, but you might check out the endfloat package, which would satisfy your journal's request without you having to do essentially anything at all with the figures. (Now that you have solved the singlespace scoping problem.)

It will always give you this warning the first time running LaTeX; you then run BibTeX on the .aux file, then run LaTeX again (twice) to resolve the links. Think of LaTeX runs this way: the first reads which citation keys it needs from BibTeX. BibTeX then operates on the notes LaTeX left for it, tur...