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Template for article submission
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`make` fails on fresh clone #25

Open pmeier opened 3 years ago

pmeier commented 3 years ago

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 ```bash $ 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 (/home/philip/.miktex/texmfs/install/tex/latex/base/article.cls Document Class: article 2021/02/12 v1.4n Standard LaTeX document class (/home/philip/.miktex/texmfs/install/tex/latex/base/size10.clo)) (/home/philip/.miktex/texmfs/install/tex/generic/babel/babel.sty (/home/philip/.miktex/texmfs/install/tex/generic/babel/babel.def (/home/philip/.miktex/texmfs/install/tex/generic/babel/xebabel.def (/home/philip/.miktex/texmfs/install/tex/generic/babel/txtbabel.def))) 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sty)) Package hyperref Warning: Rerun to get /PageLabels entry. (/home/philip/.miktex/texmfs/install/tex/latex/biblatex/lbx/american.lbx (/home/philip/.miktex/texmfs/install/tex/latex/biblatex/lbx/english.lbx) (/home/philip/.miktex/texmfs/install/tex/latex/biblatex/lbx/english.lbx)) (/home/philip/.miktex/texmfs/install/tex/latex/biblatex/blx-case-expl3.sty) No file article.bbl. (header.tex (/home/philip/.miktex/texmfs/install/tex/latex/microtype/mt-cmr.cfg ) ! Undefined control sequence. ...chive.softwareheritage.org/\codeSWH / l.69 ...WH/}{\detokenize\expandafter{\codeSWH}}.}} ! Undefined control sequence. \detokenize \expandafter {\codeSWH } l.69 ...WH/}{\detokenize\expandafter{\codeSWH}}.}} ) (content.tex 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 commented 3 years ago

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 commented 3 years ago

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

rougier commented 3 years ago

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

khinsen commented 3 years ago

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.