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latexmk does not compile document in single run

Software versions:

23:02:42 master [~/Projects/latex-makefile]λ make --version
GNU Make 4.1
Built for x86_64-pc-linux-gnu
Copyright (C) 1988-2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
23:02:46 master [~/Projects/latex-makefile]λ latexmk --version

Latexmk, John Collins, 1 January 2015. Version 4.41
23:02:53 master [~/Projects/latex-makefile]λ rsvg-convert --version
rsvg-convert version 2.40.16
23:02:59 master [~/Projects/latex-makefile]λ biber --version
biber version: 2.5
23:03:08 master [~/Projects/latex-makefile]λ pdflatex --version
pdfTeX 3.14159265-2.6-1.40.17 (TeX Live 2016/Debian)
kpathsea version 6.2.2
Copyright 2016 Han The Thanh (pdfTeX) et al.
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Han The Thanh (pdfTeX) et al.
Compiled with libpng 1.6.24; using libpng 1.6.25
Compiled with zlib 1.2.8; using zlib 1.2.8
Compiled with poppler version 0.44.0

Supplying -f to latexmk solves this issue temporarily.

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