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jupyter / nbconvert

Jupyter Notebook Conversion
https://nbconvert.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Latex undefined control sequence error when nbconvert R notebook to pdf R with help() #1973

Open pnasrat opened 1 year ago

pnasrat commented 1 year ago

Steps to reproduce, using jupyter/r-notebook for ease of reproduction

  1. docker pull jupyter/r-notebook
  2. docker run -p 8888:8888 jupyter/r-notebook:latest
  3. Connect browser to jupyter lab link URL that is output by docker run
  4. Create new R notebook from launcher
  5. In a cell input ?mtcars (or help(mtcars)) and run
  6. Ensure notebook saved
  7. Launch a terminal from jupyter lab
  8. jupyter-nbconvert --to pdf Untitled.ipynb

Expected: a pdf is created latex error with xelatex (expand details below for full log

Actual:

LaTeX Warning: No \author given.

! Undefined control sequence.
l.400     \inputencoding
                        {utf8}
? 
! Emergency stop.
l.400     \inputencoding
                        {utf8}
No pages of output.
Transcript written on notebook.log.

Workaround use pdflatex

jupyter-nbconvert \
    --to pdf \
    --PDFExporter.latex_command pdflatex \
    --PDFExporter.latex_command {filename} \
Untitled.ipynb
nbconvert output ``` jupyter-nbconvert --to pdf Untitled.ipynb [NbConvertApp] Converting notebook Untitled.ipynb to pdf [NbConvertApp] Writing 21886 bytes to notebook.tex [NbConvertApp] Building PDF [NbConvertApp] Running xelatex 3 times: ['xelatex', 'notebook.tex', '-quiet'] [NbConvertApp] CRITICAL | xelatex failed: ['xelatex', 'notebook.tex', '-quiet'] b"This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2022/dev/Debian) (preloaded format=xelatex)\n restricted \\write18 enabled.\nentering extended mode\n(./notebook.tex\nLaTeX2e <2021-11-15> patch level 1\nL3 programming layer <2022-01-21>\n(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls\nDocument Class: article 2021/10/04 v1.4n Standard LaTeX document 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file notebook.aux.\n(/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty)\n*geometry* driver: auto-detecting\n*geometry* detected driver: xetex\n*geometry* verbose mode - [ preamble ] result:\n* driver: xetex\n* paper: \n* layout: \n* layoutoffset:(h,v)=(0.0pt,0.0pt)\n* modes: \n* h-part:(L,W,R)=(72.26999pt, 469.75502pt, 72.26999pt)\n* v-part:(T,H,B)=(72.26999pt, 650.43001pt, 72.26999pt)\n* \\paperwidth=614.295pt\n* \\paperheight=794.96999pt\n* \\textwidth=469.75502pt\n* \\textheight=650.43001pt\n* \\oddsidemargin=0.0pt\n* \\evensidemargin=0.0pt\n* \\topmargin=-37.0pt\n* \\headheight=12.0pt\n* \\headsep=25.0pt\n* \\topskip=11.0pt\n* \\footskip=30.0pt\n* \\marginparwidth=59.0pt\n* \\marginparsep=10.0pt\n* \\columnsep=10.0pt\n* \\skip\\footins=10.0pt plus 4.0pt minus 2.0pt\n* \\hoffset=0.0pt\n* \\voffset=0.0pt\n* \\mag=1000\n* \\@twocolumnfalse\n* \\@twosidefalse\n* \\@mparswitchfalse\n* \\@reversemarginfalse\n* (1in=72.27pt=25.4mm, 1cm=28.453pt)\n\n(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty\n(/usr/share/texlive/texmf-dist/tex/latex/refcount/refcount.sty)\n(/usr/share/texlive/texmf-dist/tex/generic/gettitlestring/gettitlestring.sty))\n\nPackage hyperref Warning: Rerun to get /PageLabels entry.\n\n(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd)\n(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd)\n(/usr/share/texlive/texmf-dist/tex/latex/jknapltx/ursfs.fd)\n\nLaTeX Warning: No \\author given.\n\n! Undefined control sequence.\nl.400 \\inputencoding\n {utf8}\n? \n! Emergency stop.\nl.400 \\inputencoding\n {utf8}\nNo pages of output.\nTranscript written on notebook.log.\n" Traceback (most recent call last): File "/opt/conda/bin/jupyter-nbconvert", line 10, in sys.exit(main()) File "/opt/conda/lib/python3.10/site-packages/jupyter_core/application.py", line 277, in launch_instance return super().launch_instance(argv=argv, **kwargs) File "/opt/conda/lib/python3.10/site-packages/traitlets/config/application.py", line 1043, in launch_instance app.start() File "/opt/conda/lib/python3.10/site-packages/nbconvert/nbconvertapp.py", line 414, in start self.convert_notebooks() File "/opt/conda/lib/python3.10/site-packages/nbconvert/nbconvertapp.py", line 603, in convert_notebooks self.convert_single_notebook(notebook_filename) File "/opt/conda/lib/python3.10/site-packages/nbconvert/nbconvertapp.py", line 557, in convert_single_notebook output, resources = self.export_single_notebook( File "/opt/conda/lib/python3.10/site-packages/nbconvert/nbconvertapp.py", line 483, in export_single_notebook output, resources = self.exporter.from_filename( File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/templateexporter.py", line 383, in from_filename return super().from_filename(filename, resources, **kw) # type:ignore File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/exporter.py", line 200, in from_filename return self.from_file(f, resources=resources, **kw) File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/templateexporter.py", line 389, in from_file return super().from_file(file_stream, resources, **kw) # type:ignore File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/exporter.py", line 219, in from_file return self.from_notebook_node( File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/pdf.py", line 199, in from_notebook_node self.run_latex(tex_file) File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/pdf.py", line 168, in run_latex return self.run_command( File "/opt/conda/lib/python3.10/site-packages/nbconvert/exporters/pdf.py", line 158, in run_command raise raise_on_failure(msg) nbconvert.exporters.pdf.LatexFailed: PDF creating failed, captured latex output: Failed to run "['xelatex', 'notebook.tex', '-quiet']" command: This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2022/dev/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (./notebook.tex LaTeX2e <2021-11-15> patch level 1 L3 programming layer <2022-01-21> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2021/10/04 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/tcolorbox/tcolorbox.sty (/usr/share/texlive/texmf-dist/tex/latex/pgf/basiclayer/pgf.sty (/usr/share/texlive/texmf-dist/tex/latex/pgf/utilities/pgfrcs.sty (/usr/share/texlive/texmf-dist/tex/generic/pgf/utilities/pgfutil-common.tex (/usr/share/texlive/texmf-dist/tex/generic/pgf/utilities/pgfutil-common-lists.t ex)) (/usr/share/texlive/texmf-dist/tex/generic/pgf/utilities/pgfutil-latex.def ) (/usr/share/texlive/texmf-dist/tex/generic/pgf/utilities/pgfrcs.code.tex (/usr/share/texlive/texmf-dist/tex/generic/pgf/pgf.revision.tex))) (/usr/share/texlive/texmf-dist/tex/latex/pgf/basiclayer/pgfcore.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/xetex.def))) (/usr/share/texlive/texmf-dist/tex/latex/pgf/systemlayer/pgfsys.sty (/usr/share/texlive/texmf-dist/tex/generic/pgf/systemlayer/pgfsys.code.tex (/usr/share/texlive/texmf-dist/tex/generic/pgf/utilities/pgfkeys.code.tex 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tuncbkose commented 1 year ago

The workaround with pdflatex noted above doesn't work for me. Similarly, doing

$ jupyter-nbconvert --to latex test.ipynb
$ pdflatex test.tex

doesn't work, but pdflatex complains about the next line (compared to xetex) for some reason.

Also, I am not sure if this is really a nbconvert problem. When the notebook cell is executed, the output already contains the text/latex data that seems to be the source of this problem.