nbconvert ipynb to pdf returns io error

[jkarimi91]

Jays-MacBook-Pro:cormen jkarimi91$ jupyter nbconvert --to pdf graphs-sssp/dijkstra.ipynb
[NbConvertApp] Converting notebook graphs-sssp/dijkstra.ipynb to pdf
[NbConvertApp] Writing 14398 bytes to notebook.tex
[NbConvertApp] Building PDF
[NbConvertApp] Running pdflatex 3 times: [u'pdflatex', u'notebook.tex']
[NbConvertApp] CRITICAL | pdflatex failed: [u'pdflatex', u'notebook.tex']
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./notebook.tex
LaTeX2e <2015/01/01>
Babel <3.9l> and hyphenation patterns for 79 languages loaded.
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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Package hyperref Message: Driver (autodetected): hpdftex.

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No file notebook.aux.
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[Loading MPS to PDF converter (version 2006.09.02).]
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*geometry* driver: auto-detecting
*geometry* detected driver: pdftex

Package geometry Warning: The marginal notes overrun the paper.
     Add 3.73001pt and more to the right margin.

*geometry* verbose mode - [ preamble ] result:
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* (1in=72.27pt=25.4mm, 1cm=28.453pt)

(/usr/local/texlive/2015/texmf-dist/tex/latex/ucs/ucsencs.def)
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LaTeX Warning: No \author given.

! Missing $ inserted.
<inserted text>
                $
l.255 \$}{Dijkstra \$ O((V + E) V) \$}}
                                       \label{dijkstra-ov-e-v}
?
! Emergency stop.
<inserted text>
                $
l.255 \$}{Dijkstra \$ O((V + E) V) \$}}
                                       \label{dijkstra-ov-e-v}
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on notebook.log.

[NbConvertApp] Running bibtex 1 time: [u'bibtex', u'notebook']
[NbConvertApp] WARNING | bibtex had problems, most likely because there were no citations
[NbConvertApp] Running pdflatex 3 times: [u'pdflatex', u'notebook.tex']
[NbConvertApp] CRITICAL | pdflatex failed: [u'pdflatex', u'notebook.tex']
This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./notebook.tex
LaTeX2e <2015/01/01>
Babel <3.9l> and hyphenation patterns for 79 languages loaded.
(/usr/local/texlive/2015/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
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Package hyperref Message: Driver (autodetected): hpdftex.

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[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/local/texlive/2015/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
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*geometry* driver: auto-detecting
*geometry* detected driver: pdftex

Package geometry Warning: The marginal notes overrun the paper.
     Add 3.73001pt and more to the right margin.

*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: <default>
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes:
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* (1in=72.27pt=25.4mm, 1cm=28.453pt)

(/usr/local/texlive/2015/texmf-dist/tex/latex/ucs/ucsencs.def)
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(./notebook.out) (./notebook.out)
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LaTeX Warning: No \author given.

! Missing $ inserted.
<inserted text>
                $
l.255 \$}{Dijkstra \$ O((V + E) V) \$}}
                                       \label{dijkstra-ov-e-v}
?
! Emergency stop.
<inserted text>
                $
l.255 \$}{Dijkstra \$ O((V + E) V) \$}}
                                       \label{dijkstra-ov-e-v}
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on notebook.log.

Traceback (most recent call last):
  File "//anaconda/bin/jupyter-nbconvert", line 6, in <module>
    main()
  File "//anaconda/lib/python2.7/site-packages/jupyter_core/application.py", line 267, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "//anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 596, in launch_instance
    app.start()
  File "//anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 289, in start
    self.convert_notebooks()
  File "//anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 412, in convert_notebooks
    self.convert_single_notebook(notebook_filename)
  File "//anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 383, in convert_single_notebook
    output, resources = self.export_single_notebook(notebook_filename, resources)
  File "//anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 335, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
  File "//anaconda/lib/python2.7/site-packages/nbconvert/exporters/exporter.py", line 165, in from_filename
    return self.from_notebook_node(nbformat.read(f, as_version=4), resources=resources, **kw)
  File "//anaconda/lib/python2.7/site-packages/nbconvert/exporters/pdf.py", line 152, in from_notebook_node
    raise IOError("PDF creating failed")
IOError: PDF creating failed

[dunnl]

This appears to be the same as issue #326. I think nbconvert would attempt to open a file graphs-sssp/notebook.tex for writing inside a temporary directory, which will fail because the subdirectory graphs-sssp/ does not exist there.

Try running cd graphs-sssp and then jupyter nbconvert --to pdf dijkstra.ipynb

[jkarimi91]

@dunnl I tried your suggestion but I received the same IO error as before

[dunnl]

I read your post too quickly. It looks like the error is with the generated LaTeX. (Missing $ inserted. followed by Fatal error occurred, no output PDF file produced!). Look closely at your LaTeX source in your notebook for a missing $. It might be helpful to compile the notebook --to latex and opening that file in a LaTeX editor.

I'm a bit surprised that nbconvert has gotten as far as trying to compile the LaTeX given the issue I mentioned above. If you past your current issue, please let us know whether compiling --to pdf works when calling from another directory as you first tried.

[jkarimi91]

I could not find any missing $, in fact, I could find no typos at all; the ipynb renders perfectly in the browser.

So I took your suggestion and converted the ipynb to latex (the original ipynb contained github flavored markdown with inline mathjax) and inspected the tex file in a tex editor. It looks like nbconvert is not properly parsing the inline mathjax:

ipynb: * good for sparse graphs i.e. $ E = o(V^2 / \lg V) $
tex(actual): \item good for sparse graphs i.e. \$ E = o(V\^{}2 / \lg V) \$
tex(expected): \item good for sparse graphs i.e. $ E = o(V^{2} / \lg V) $

I did some investigating and came across this stack overflow post; it turns out that pandoc will not recognize the inline mathjax if either:
1) the opening $ is followed by a space or
2) the closing $ is preceded by a space

After removing the problematic spaces, I was able to resolve the --to latex issue, which in turn, resolved the --to pdf issue.
Per your request, I also verified that nbconvert --to pdf works from outside directory.

Do you think this space sensitivity is a design decision made by pandoc or a bug that should be reported to them?

[takluyver]

I would guess it's a deliberate decision, so that it doesn't treat it as an equation when you write something like prices range from $5 to $8. But I don't know that for certain, so if you want to ask, don't let me stop you.

[dunnl]

I believe @takluyver is correct. Pandoc supports a Markdown extension tex_math_dollars, (enabled by default, as it happens) which is presumably the basis of LaTeX support in Jupyter notebooks. From the Pandoc user manual

the closing $ must have a non-space character immediately to its left

[mpacer]

I'm going to close this as addressed since it's part of the core pandoc docs.