latexmk seems to miss the last, required rerun of *latex

Question

I am using TeX Live 2023, TeX 3.141592653, LuaHBTeX 1.16.0, Latexmk 4.79 on Windows 10.

Short description: I have a MWE that compiles without problems by doing lualatex -> biber -> lualatex -> lualatex. When using latexmk -lualatex the last run of lualatex does not happen. If calling lualatex afterwards again, everything works out.

MWE Code:

\documentclass{scrartcl}
\usepackage{biblatex}
\addbibresource{../Literatur/literatur_test.bib}

\usepackage{hyperref}
\begin{document}

\tableofcontents

\section{Introduction}
Citation 1 \cite{Aas2021} and a label \label{test_label}

\section{Another Section}
Citation 2 \cite{Lundberg2017} and a reference \ref{test_label}

\printbibliography

\end{document}

Relevant part of the .bib file:

@Article{Aas2021,
  author       = {Kjersti Aas and Martin Jullum and Anders L{\o}land},
  date         = {2021},
  journaltitle = {Artificial Intelligence},
  title        = {Explaining individual predictions when features are dependent: More accurate approximations to Shapley values},
  doi          = {10.1016/j.artint.2021.103502},
  pages        = {103502},
  volume       = {298},
  abstract     = {Explaining complex or seemingly simple machine learning models is an important practical problem. We want to explain individual predictions from such models by learning simple, interpretable explanations. Shapley value is a game theoretic concept that can be used for this purpose. The Shapley value framework has a series of desirable theoretical properties, and can in principle handle any predictive model. Kernel SHAP is a computationally efficient approximation to Shapley values in higher dimensions. Like several other existing methods, this approach assumes that the features are independent. Since Shapley values currently suffer from inclusion of unrealistic data instances when features are correlated, the explanations may be very misleading. This is the case even if a simple linear model is used for predictions. In this paper, we extend the Kernel SHAP method to handle dependent features. We provide several examples of linear and non-linear models with various degrees of feature dependence, where our method gives more accurate approximations to the true Shapley values.},
  day          = {31},
  keywords     = {Feature attribution, Shapley values, Kernel SHAP, Dependence},
  publisher    = {Elsevier {BV}},
  year         = {2021},
}

@InProceedings{Lundberg2017,
  author    = {Lundberg, Scott and Lee, Su-In},
  booktitle = {Advances in Neural Information Processing Systems},
  date      = {2017},
  title     = {A unified approach to interpreting model predictions},
  pages     = {4765--4774},
}

Manual attempt: I cleaned up everything, there is only the .tex file in the directory. Calling lualatex on that gives (excerpt):

[...]
No file Main.toc.

LaTeX Warning: Citation 'Aas2021' on page 1 undefined on input line 11.

LaTeX Warning: Citation 'Lundberg2017' on page 1 undefined on input line 14.

LaTeX Warning: Reference `test_label' on page 1 undefined on input line 14.

LaTeX Warning: Empty bibliography on input line 16.

[1{c:/MeineProgramme/TeXLive/2023/texmf-var/fonts/map/pdftex/updmap/pdftex.map}
] (./Main.aux)

LaTeX Warning: There were undefined references.

LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

Package rerunfilecheck Warning: File `Main.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)                Main
(biblatex)                and rerun LaTeX afterwards.
[...]

Running biber gives only a warning about 8 characters of junk seen at toplevel.

Running lualatex again gives (excerpt):

[...]
LaTeX Warning: There were undefined references.

Package biblatex Warning: Please rerun LaTeX.
[...]

Running lualatex for the third time in total produces no warning and leads to the expected result in a PDF file.

latexmk attempt: I cleaned up everything, there is only the .tex file in the directory. When running latexmk -lualatex the expected behavior is, that it runs lualatex and biber as often as needed. Produced output (full):

    L:[...]\Dokument>latexmk --lualatex
Initial Win CP for (console input, console output, system): (CP437, CP437, CP1252)
I changed them all to CP1252
Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 7 Jan. 2023. Version 4.79.
No existing .aux file, so I'll make a simple one, and require run of *latex.
Latexmk: applying rule 'lualatex'...
Rule 'lualatex':  Reasons for rerun
Category 'other':
  Rerun of 'lualatex' forced or previously required

------------
Run number 1 of rule 'lualatex'
------------
------------
Running 'lualatex  -recorder  "Main.tex"'
------------
This is LuaHBTeX, Version 1.16.0 (TeX Live 2023)
 restricted system commands enabled.
(./Main.tex
LaTeX2e <2022-11-01> patch level 1
 L3 programming layer <2023-02-22>
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrartcl.cls
Document Class: scrartcl 2022/10/12 v3.38 KOMA-Script document class (article)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrkbase.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrbase.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrlfile.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrlfile-hook.
sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrlogo.sty)))
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/graphics/keyval.sty)))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/tocbasic.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrsize11pt.cl
o)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/typearea.sty))
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/biblatex.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.st
y
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/infwarerr/infwarerr.sty)
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/iftex/iftex.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/logreq/logreq.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/logreq/logreq.def))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/ifthen.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/url/url.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-dm.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-unicode.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-compat.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/biblatex.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/bbx/numeric.bbx
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/bbx/standard.bbx)
) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/cbx/numeric.cbx
) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/biblatex.cfg)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/l3kernel/expl3.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/l3backend/l3backend-luatex
.def))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-case-expl3.st
y
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/l3packages/xparse/xparse.s
ty)))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/hyperref.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/kvdefinekeys/kvdefinekey
s.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hycolor/hycolor.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/letltxmacro/letltxmacro.st
y) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/auxhook/auxhook.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/nameref.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/refcount/refcount.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/gettitlestring/gettitles
tring.sty))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/pd1enc.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/intcalc/intcalc.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/puenc.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/bitset/bitset.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/bigintcalc/bigintcalc.st
y)) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/atbegshi-ltx.sty)
) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/hluatex.def
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/stringenc/stringenc.sty)
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/rerunfilecheck/rerunfilech
eck.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/uniquecounter/uniquecoun
ter.sty))) (./Main.aux)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/ts1cmr.fd)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
No file Main.bbl.
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/bookmark/bookmark.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/bookmark/bkm-pdftex.def))
No file Main.toc.

LaTeX Warning: Citation 'Aas2021' on page 1 undefined on input line 11.


LaTeX Warning: Citation 'Lundberg2017' on page 1 undefined on input line 14.


LaTeX Warning: Reference `test_label' on page 1 undefined on input line 14.


LaTeX Warning: Empty bibliography on input line 16.

[1{c:/MeineProgramme/TeXLive/2023/texmf-var/fonts/map/pdftex/updmap/pdftex.map}
] (./Main.aux)

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.


Package rerunfilecheck Warning: File `Main.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.


Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)                Main
(biblatex)                and rerun LaTeX afterwards.

)
 491 words of node memory still in use:
   3 hlist, 1 vlist, 1 rule, 2 glue, 3 kern, 1 glyph, 4 attribute, 65 glue_spec
, 4 attribute_list, 1 write nodes
   avail lists: 1:2,2:135,3:75,4:4,5:42,6:15,7:562,9:99,10:1,11:42
<c:/MeineProgramme/TeXLive/2023/texmf-dist/fonts/opentype/public/lm/lmroman10-b
old.otf><c:/MeineProgramme/TeXLive/2023/texmf-dist/fonts/opentype/public/lm/lmr
oman10-regular.otf><c:/MeineProgramme/TeXLive/2023/texmf-dist/fonts/opentype/pu
blic/lm/lmsans10-bold.otf>
Output written on Main.pdf (1 page, 10772 bytes).
Transcript written on Main.log.
Latexmk: fls file doesn't appear to have been made.
Latexmk: Getting log file 'Main.log'
Latexmk: Examining 'Main.log'
Latexmk: Missing bbl file 'Main.bbl' in following:
 No file Main.bbl.
Latexmk: Missing input file 'Main.toc' (or dependence on it) from following:
  No file Main.toc.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'Main.pdf'
Latexmk: Bibliography file(s) form .bcf file:
  ../Literatur/literatur_test.bib
Latexmk: applying rule 'biber Main'...
Rule 'biber Main':  Reasons for rerun
Category 'other':
  Rerun of 'biber Main' forced or previously required

------------
Run number 1 of rule 'biber Main'
------------
------------
Running 'biber  "Main.bcf"'
------------
INFO - This is Biber 2.19
INFO - Logfile is 'Main.blg'
INFO - Reading 'Main.bcf'
INFO - Found 2 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex file '../Literatur/literatur_test.bib' for section 0
INFO - LaTeX decoding ...
INFO - Found BibTeX data source '../Literatur/literatur_test.bib'
INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = non-ignorable'
INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 'normalization = prenormalized'
INFO - Sorting list 'nty/global//global/global' of type 'entry' with template 'nty' and locale 'en-US'
INFO - No sort tailoring available for locale 'en-US'
INFO - Writing 'Main.bbl' with encoding 'UTF-8'
INFO - Output to Main.bbl
Latexmk: Found biber source file(s) [../Literatur/literatur_test.bib Main.bcf]
Latexmk: applying rule 'lualatex'...
Rule 'lualatex':  Reasons for rerun
Changed files or newly in use/created:
  Main.aux
  Main.bbl
  Main.toc

------------
Run number 2 of rule 'lualatex'
------------
------------
Running 'lualatex  -recorder  "Main.tex"'
------------
This is LuaHBTeX, Version 1.16.0 (TeX Live 2023)
 restricted system commands enabled.
(./Main.tex
LaTeX2e <2022-11-01> patch level 1
 L3 programming layer <2023-02-22>
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrartcl.cls
Document Class: scrartcl 2022/10/12 v3.38 KOMA-Script document class (article)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrkbase.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrbase.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrlfile.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrlfile-hook.
sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrlogo.sty)))
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/graphics/keyval.sty)))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/tocbasic.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/scrsize11pt.cl
o)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/koma-script/typearea.sty))
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/biblatex.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/pdftexcmds/pdftexcmds.st
y
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/infwarerr/infwarerr.sty)
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/iftex/iftex.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/ltxcmds/ltxcmds.sty))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/etoolbox/etoolbox.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/kvoptions/kvoptions.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/kvsetkeys/kvsetkeys.sty))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/logreq/logreq.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/logreq/logreq.def))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/ifthen.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/url/url.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-dm.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-unicode.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-compat.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/biblatex.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/bbx/numeric.bbx
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/bbx/standard.bbx)
) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/cbx/numeric.cbx
) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/biblatex.cfg)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/l3kernel/expl3.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/l3backend/l3backend-luatex
.def))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/blx-case-expl3.st
y
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/l3packages/xparse/xparse.s
ty)))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/hyperref.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/kvdefinekeys/kvdefinekey
s.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/pdfescape/pdfescape.sty)
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hycolor/hycolor.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/letltxmacro/letltxmacro.st
y) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/auxhook/auxhook.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/nameref.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/refcount/refcount.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/gettitlestring/gettitles
tring.sty))
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/pd1enc.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/intcalc/intcalc.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/etexcmds/etexcmds.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/puenc.def)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/bitset/bitset.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/bigintcalc/bigintcalc.st
y)) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/atbegshi-ltx.sty)
) (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/hyperref/hluatex.def
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/stringenc/stringenc.sty)
 (c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/atveryend-ltx.sty)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/rerunfilecheck/rerunfilech
eck.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/generic/uniquecounter/uniquecoun
ter.sty))) (./Main.aux)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/base/ts1cmr.fd)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/biblatex/lbx/english.lbx)
(./Main.bbl) (./Main.out) (./Main.out)
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/bookmark/bookmark.sty
(c:/MeineProgramme/TeXLive/2023/texmf-dist/tex/latex/bookmark/bkm-pdftex.def))
(./Main.toc) [1{c:/MeineProgramme/TeXLive/2023/texmf-var/fonts/map/pdftex/updma
p/pdftex.map}] (./Main.aux)

LaTeX Warning: There were undefined references.


Package biblatex Warning: Please rerun LaTeX.

)
 506 words of node memory still in use:
   3 hlist, 1 vlist, 1 rule, 2 glue, 3 kern, 1 glyph, 4 attribute, 68 glue_spec
, 4 attribute_list, 1 write nodes
   avail lists: 1:2,2:333,3:229,4:4,5:111,6:36,7:2309,8:28,9:195,10:2,11:198
<c:/MeineProgramme/TeXLive/2023/texmf-dist/fonts/opentype/public/lm/lmmono10-re
gular.otf><c:/MeineProgramme/TeXLive/2023/texmf-dist/fonts/opentype/public/lm/l
mromancaps10-regular.otf><c:/MeineProgramme/TeXLive/2023/texmf-dist/fonts/opent
ype/public/lm/lmroman10-italic.otf><c:/MeineProgramme/TeXLive/2023/texmf-dist/f
onts/opentype/public/lm/lmroman10-regular.otf><c:/MeineProgramme/TeXLive/2023/t
exmf-dist/fonts/opentype/public/lm/lmsans10-bold.otf>
Output written on Main.pdf (1 page, 21098 bytes).
Transcript written on Main.log.
Latexmk: fls file doesn't appear to have been made.
Latexmk: Getting log file 'Main.log'
Latexmk: Examining 'Main.log'
Latexmk: Found input bbl file 'Main.bbl'
Latexmk: Log file says output to 'Main.pdf'
Latexmk: Bibliography file(s) form .bcf file:
  ../Literatur/literatur_test.bib
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  lualatex: gave an error
----------------------
This message may duplicate earlier message.
Latexmk: Failure in processing file 'Main.tex':
   *LaTeX didn't generate the expected log file 'Main.log'
----------------------

Latexmk: If appropriate, the -f option can be used to get latexmk
  to try to force complete processing.
Reverting Windows console CPs to (in,out) = (437,437)
C:\MeineProgramme\texlive\2023\bin\windows\runscript.tlu:921: command failed with exit code 12:
perl.exe c:\MeineProgramme\TeXLive\2023\texmf-dist\scripts\latexmk\latexmk.pl --lualatex

The output shows errors, but the produced PDF seems to be fine. When running lualatex again now, it runs without problems or errors.

Is it a problem of lualatex to request a third run at the end or is it correct to run three times and latexmk falsely does not fulfill this request of lualatex?

Edit after update of latexmk:

After updating to latexmk 4.80 everything worked without errors. There is only the warning

Latexmk: I am working around an offset relative to my system time by
   -38 secs for file times in directory ''.
   This **probably** indicates that 
   (a) I (latexmk) am running on one computer, while the filesystem is
       hosted on a different computer/
   (b) There is a substantial time offset between system times on the two
       computers.
   (c) Therefore at least one of the computers has a misconfigured operating
       system such that its system time is not correctly synchronized with a
       time server.
   These issues are likely to cause problems with other software, and any
   such operating-system misconfigurations should be corrected.  By default
   current operating systems are configured to correctly synchronize system
   time when they are connected to the Internet

This is probably the case because I am working with an file server that seems to have the time set differently.

Answer 1

Puzzles in output: Near the end of the output listing, latexmk says that it didn't complete processing because there were errors. That's enough to explain why too few runs of lualatex were made.

However, the reported error was that the expected log file wasn't made. That seems contradictory, since two runs of lualatex were successful, and necessarily generated a log file. There's also a warning the the fls file was not made, even though a successful run of lualatex with the -recorder option would have generated the file. Moreover the OP had no problem running lualatex and biber separately.

So the error report from latexmk implies that there is some anomaly, but it must be of a strange kind. (And the error message could be more helpful.)

Resolution: It turns out that this problem had already been reported, and latexmk updated to v. 4.80. Simply updating TeXLive was enough to get latexmk to compile the document correctly. It also provided a message, quoted at the end of the edited question, about a mismatch of the system clocks on the computer running latexmk and the computer hosting the source files of the document. As explained in the message, that mismatch should be corrected.

That leaves the oddity of why that problem with the system clocks should have caused trouble with the previous version of latexmk.

What went wrong: After a run of *latex, latexmk gets dependency information from the .fls and .log files. Under certain misconfigurations or under certain error conditions, the files may fail to be generated, or generated in the wrong directory, or with the wrong name. In that case files with the expected names may exist but be relics from a previous run. Latexmk has to detect this situation, otherwise it gets out-of-date dependency information, which messes up its functioning.

Now the modification time of an relic file will be earlier than that of the new run of *latex. So latexmk asks whether or not the modification times were earlier than the run time, and if they are earlier it concludes that the files are relics of an earlier run and weren't generated on the latest run. Hence the error message. (The logic of how latexmk deals with this wasn't fully correct, so latexmk ran lualatex twice instead of stopping after the first run.)

With a mismatch of system clocks, the generated files can look as if they were generated before the run of lualatex started. The current version of latexmk does a measurement of the mismatch when needed, so it can work correctly.