`make` fails on fresh clone

[pmeier]

Repro:

$ git clone https://github.com/ReScience/template
[...]
$ make
[...]
=== TeX engine is 'XeTeX'
Latexmk: References changed.
Latexmk: Missing bbl file 'article.bbl' in following:
 No file article.bbl.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'article.pdf'
Latexmk: List of undefined refs and citations:
  Citation 'Roboto:2011' on page 2 undefined on input line 74
  Citation 'Rougier:2017' on page 1 undefined on input line 12
  Citation 'Rougier:2017' on page 1 undefined on input line 26
  Citation 'Rougier:2018' on page 1 undefined on input line 13
  Citation 'Science:2018' on page 1 undefined on input line 11
  Citation 'SourceCodePro:2012' on page 2 undefined on input line 74
  Citation 'SourceSerifPro:2014' on page 2 undefined on input line 74
  Citation 'Topalidou:2015' on page 1 undefined on input line 4
Latexmk: 'pdflatex': source file 'article.bbl' doesn't exist. I'll try making it...
------------
Running 'make "article.bbl"'
------------
make[1]: Entering directory '/tmp/template'
make[1]: *** No rule to make target 'article.bbl'.  Stop.
make[1]: Leaving directory '/tmp/template'
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 8 citation(s)
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'article.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
make: *** [Makefile:30: article.pdf] Error 12

Any idea why the file is not generated? Am I missing a package?

Full output

$ make
latexmk -pdf -pdflatex="xelatex -interaction=nonstopmode" -use-make article.tex
Rc files read:
  NONE
Latexmk: This is Latexmk, John Collins, 21 September 2021, version: 4.75.
Latexmk: applying rule 'pdflatex'...
Rule 'pdflatex': File changes, etc:
   Changed files, or newly in use since previous run(s):
      'article.tex'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'xelatex -interaction=nonstopmode  -recorder  "article.tex"'
------------
This is XeTeX, Version 3.141592653-2.6-0.999993 (MiKTeX 21.8)
entering extended mode
(article.tex
LaTeX2e <2021-06-01> patch level 1
L3 programming layer <2021-08-27> (rescience.cls
Document Class: rescience 2019/04/12 Style for ReScience articles
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Document Class: article 2021/02/12 v1.4n Standard LaTeX document class
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Package hyperref Warning: Rerun to get /PageLabels entry.

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No file article.bbl.
(header.tex (/home/philip/.miktex/texmfs/install/tex/latex/microtype/mt-cmr.cfg
)
! Undefined control sequence.
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                                                  /
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LaTeX Warning: Citation 'Topalidou:2015' on page 1 undefined on input line 4.


LaTeX Warning: Citation 'Science:2018' on page 1 undefined on input line 11.


LaTeX Warning: Citation 'Rougier:2017' on page 1 undefined on input line 12.


LaTeX Warning: Citation 'Rougier:2018' on page 1 undefined on input line 13.


Overfull \hbox (50.95569pt too wide) in paragraph at lines 2--15
\TU/SourceSerifPro(0)/m/n/10 replication of existing computational research. Si
nce ReScience published its first article$[]$,

Overfull \hbox (14.59589pt too wide) in paragraph at lines 2--15
\TU/SourceSerifPro(0)/m/n/10 the meantime, we have published around 24 articles
 (mostly in computational neuroscience

Overfull \hbox (20.12456pt too wide) in paragraph at lines 2--15
\TU/SourceSerifPro(0)/m/n/10 conferences worldwide, gave some interviews$[]$, a
nd published an article introducing

LaTeX Warning: Citation 'Rougier:2017' on page 1 undefined on input line 26.


Overfull \hbox (31.25378pt too wide) in paragraph at lines 18--28
\TU/SourceSerifPro(0)/m/n/10 with the upcoming creation of the “ReScience X” jo
urnal that will be dedicated to e(x)perimental

Overfull \hbox (10.28123pt too wide) in paragraph at lines 18--28
\TU/SourceSerifPro(0)/m/n/10 replications and co-directed by E.Roesch (Universi
ty of Reading) and N.Rougier (University

Overfull \hbox (0.48459pt too wide) in paragraph at lines 32--47
[] []|\TU/RobotoCondensed(0)/b/n/10 A new submission process[][]\TU/SourceSerif
Pro(0)/m/n/10 The current submission process requires authors to fork, clone

Overfull \hbox (3.98953pt too wide) in paragraph at lines 51--66
\TU/SourceSerifPro(0)/m/n/10 plugins. Consequently, articles will be now submit
ted directly in PDF with accompanying

Overfull \hbox (6.16792pt too wide) in paragraph at lines 51--66
\TU/SourceSerifPro(0)/m/n/10 and [][]JOSE[][]. This will most probably require 
some tweaking because our publishing pipeline
[1]

LaTeX Warning: Citation 'SourceSerifPro:2014' on page 2 undefined on input line
 74.


LaTeX Warning: Citation 'Roboto:2011' on page 2 undefined on input line 74.


LaTeX Warning: Citation 'SourceCodePro:2012' on page 2 undefined on input line 
74.


Overfull \hbox (15.6779pt too wide) in paragraph at lines 88--99
\TU/SourceSerifPro(0)/m/n/10 opportunity to publish \TU/SourceSerifPro(0)/m/it/
10 editorials \TU/SourceSerifPro(0)/m/n/10 when deemed necessary and to give an
yone the opportunity

Underfull \hbox (badness 10000) in paragraph at lines 88--99

)

LaTeX Warning: Empty bibliography on input line 10.

[2] (article.aux)

LaTeX Warning: There were undefined references.


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


Package rerunfilecheck Warning: File `article.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)                article
(biblatex)                and rerun LaTeX afterwards.

 )
(see the transcript file for additional information)
Output written on article.pdf (2 pages).
Transcript written on article.log.
Latexmk: Examining 'article.log'
=== TeX engine is 'XeTeX'
Latexmk: References changed.
Latexmk: Missing bbl file 'article.bbl' in following:
 No file article.bbl.
Latexmk: References changed.
Latexmk: References changed.
Latexmk: Log file says output to 'article.pdf'
Latexmk: List of undefined refs and citations:
  Citation 'Roboto:2011' on page 2 undefined on input line 74
  Citation 'Rougier:2017' on page 1 undefined on input line 12
  Citation 'Rougier:2017' on page 1 undefined on input line 26
  Citation 'Rougier:2018' on page 1 undefined on input line 13
  Citation 'Science:2018' on page 1 undefined on input line 11
  Citation 'SourceCodePro:2012' on page 2 undefined on input line 74
  Citation 'SourceSerifPro:2014' on page 2 undefined on input line 74
  Citation 'Topalidou:2015' on page 1 undefined on input line 4
Latexmk: 'pdflatex': source file 'article.bbl' doesn't exist. I'll try making it...
------------
Running 'make "article.bbl"'
------------
make[1]: Entering directory '/tmp/template'
make[1]: *** No rule to make target 'article.bbl'.  Stop.
make[1]: Leaving directory '/tmp/template'
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 8 citation(s)
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to 'article.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
make: *** [Makefile:30: article.pdf] Error 12

[khinsen]

I can confirm that with a fresh (less than two weeks old) TeXLive installation, make fails in the way you describe. It used to work in the past, so I suspect that the TeX ecosystem has evolved a bit too much for our needs. I can't look into this right now, sorry!

[pmeier]

So what is the way forward for submitting a ReScience paper if the template is not functional anymore?

[rougier]

Sorry. I think you can try biber article and then type make again.

[khinsen]

Thanks @rougier ! That almost works. Here's a recipe that works for me:

make
biber article
touch article.tex
make
touch article.tex
make

That comes down to doing make's work by hand, but at least it's a workaround to move on with a paper.