I'm trying to get latexmk to compile a .tex file with external \include{...} references to a specific build directory so I don't pollute my directory tree with .aux files, etc.

However, it appears latexmk doesn't do as I'd expect when it compiles the included files. For example, consider a file file1.tex which has something like


When I run

latexmk -pdf -pdflatex="pdflatex -interaction=nonstopmode -file-line-error" file1.tex

everything works fine, but

latexmk -pdf -pdflatex="pdflatex -interaction=nonstopmode -file-line-error" -outdir=build file1.tex

gives me the error

Latexmk: Missing input file: 'chapters/test.aux' from line
  'No file chapters/test.aux.'

If I don't have the \include statement, using \input instead, everything compiles nicely to the build directory as you would expect.

For reference, I'm working on Mac OSX w/ MacTeX, as I understand there are a few differences in the implementation of latexmk between MacTeX and MikeTeX... any help would be much appreciated, as I've been beating my head against this for a while now.

  • 1
    you should never use the .tex extension when using \include just use \include{chapters/test} Oct 12, 2014 at 0:45
  • Ah yeah, you're right. FWIW, that just slipped in as I was typing the question, my actual source file just uses \include{chapters/test} as you suggest! I updated the question accordingly :) Oct 12, 2014 at 1:32
  • 3
    OK in that case I'll retype the comment I started to type before spotting the .tex:-) 999 times out of 1000 if people configure tex to write files in non standard places they have problems, you need to configure tex, bibtex, makeindex, everything, to find the files and it's never worth it:-) Oct 12, 2014 at 1:35

3 Answers 3


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 solution is simply to create a chapters subdirectory of your build directory.

(The messages you saw from latexmk are its summary of what it is currently programmed to treat as common significant warnings and errors. But it's an incomplete summary. In general, if you find an error and don't understand what to do about it, it's worth going through the .log file; that provides much more information than latexmk's summary.)

  • 4
    This sure sounds like a bug in pdflatex (not creating directories when they don't exist).
    – BenC
    May 4, 2015 at 2:41
  • 1
    To programmatically mirror the directory structure, you can add a line like system ("find . -type d ! -path './.git*' ! -path './$out_dir*' -exec mkdir -p $out_dir/{} \\;"); (which is just the approximately appropriate shell command wrapped in Perl's system call) after the definition of $out_dir = <...> in your local .latexmkrc file. Probably not a good idea for a global .latexmkrc, though - otherwise beware of that quick latexmk test.tex in your home directory. I agree that this is just a workaround, and a proper solution would require pdflatex to handle that situation gracefully.
    – akobel
    May 24, 2016 at 21:26

As @john-collins wrote above, this is not an issue in latexmk but in your tex interpreter like pdflatex.

Another solution to your problem is redefining the \include command to create the output dir before actually executing \include.

My implementation in lualatex:

        function makeparentdirs(path_with_filename)
            local mkdirp = require('mkdirp_lua/mkdirp')

            % -- delete lowest directory which collides with file name
            if lfs.attributes(path_with_filename).mode == 'directory' then

        \directlua{makeparentdirs(\luastring{\auxdirname} .. '/' .. \luastring{#1})}%

This solution is not nice though, because:

  • depending on both platform and command line switches, the directory for aux files may differ. You have to manually define it by running \newcommand*{\auxdirname}{auxdir} or similar before.
  • it depends on a separate lua library from https://github.com/xpol/mkdirp.lua

This solution works fine with tikz' external library, which also requires the folders in outdir/auxdir to be created when using custom (not auto-numerated) directories.


There are two possibilities:

  1. I also got these errors, when using the \doincludeonly from https://en.wikibooks.org/wiki/TeX/includeonly On this case, these errors can be safely ignored.

    But, if you would like, you can make latex stop generate these errors, if you generate a full version of the document, before using the \doincludeonly commands.

    Then, on the next times, it will not throw the errors until you clear your latex cache of the files.

  2. Can also happen due to this bug How to report the --output-directory bug on pdflatex/latexmk on Tex Live? which does not create the output directory by himself. So, you are stuck with manually creating the directories.

    You can use this I can't write on file 'foo.aux' to create the directories structure by yourself.

    You can also see this Why latex does not tell me which command is undefined? to learn more about other bugs.

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