Increase latex buf_size

[petergarbers]

Hey all,

I'm looking to convert a jupyter notebook to a PDF via Latex. The issue I'm running into is that there is a lot of data inside of the notebook and as a result, latex fails when trying to convert to PDF with the following:

nbconvert failed: PDF creating failed, captured latex output:
This is XeTeX, Version 3.14159265-2.6-0.99992 (TeX Live 2015/Debian) (preloaded format=xelatex)
 restricted \write18 enabled.
entering extended mode
(/home/jovyan/docs/WorkGroupAnalytics/notebook.tex
LaTeX2e <2016/02/01>
Babel <3.9q> and hyphenation patterns for 3 language(s) loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo))
(/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathpazo.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/latexconfig/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/xelatex/xetex-def/xetex.def
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty))))
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty
(/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty))
(/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjustbox.sty
(/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex)))
(/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjcalc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/adjustbox/trimclip.sty
(/usr/share/texlive/texmf-dist/tex/latex/collectbox/collectbox.sty)
(/usr/share/texlive/texmf-dist/tex/latex/adjustbox/tc-xetex.def))
(/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty)
(/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty))
(/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg))
(/usr/share/texlive/texmf-dist/tex/latex/tools/enumerate.sty)
(/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty
For additional information on amsmath, use the `?' option.
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def))
(/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty)
(/usr/share/texlive/texmf-dist/tex/latex/eurosym/eurosym.sty)
(/usr/share/texlive/texmf-dist/tex/latex/ucs/ucs.sty
(/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-global.def))
(/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty

Package inputenc Warning: inputenc package ignored with utf8 based engines.

) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grffile.sty
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty))))
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty))
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty))
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def)
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hxetex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hxetex.def
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def)
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/stringenc.sty)
(/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))
(/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty)
(/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty)
(/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty)
(/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty)
No file notebook.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ppl.fd)
(/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty)
*geometry* driver: auto-detecting
*geometry* detected driver: xetex
*geometry* verbose mode - [ preamble ] result:
* driver: xetex
* paper: <default>
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: 
* h-part:(L,W,R)=(72.26999pt, 469.75502pt, 72.26999pt)
* v-part:(T,H,B)=(72.26999pt, 650.43001pt, 72.26999pt)
* \paperwidth=614.295pt
* \paperheight=794.96999pt
* \textwidth=469.75502pt
* \textheight=650.43001pt
* \oddsidemargin=0.0pt
* \evensidemargin=0.0pt
* \topmargin=-37.0pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=11.0pt
* \footskip=30.0pt
* \marginparwidth=59.0pt
* \marginparsep=10.0pt
* \columnsep=10.0pt
* \skip\footins=10.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidefalse
* \@mparswitchfalse
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

(/usr/share/texlive/texmf-dist/tex/latex/ucs/ucsencs.def)
(/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty
(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty))

Package hyperref Warning: Rerun to get /PageLabels entry.

(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1ppl.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omlzplm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omszplm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/omxzplm.fd)
(/usr/share/texlive/texmf-dist/tex/latex/psnfss/ot1zplm.fd)

LaTeX Warning: No \author given.

(/usr/share/texlive/texmf-dist/tex/generic/oberdiek/se-ascii-print.def)
(/usr/share/texlive/texmf-dist/tex/latex/base/t1cmtt.fd)
(/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [1] [2] [3] [4]
[5] [6] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ppl.fd) [7]
<use  "output_18_0.png" > [8]
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<use  "output_28_0.png" > [11]
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[12]
Overfull \hbox (220.56624pt too wide) in paragraph at lines 931--931
[]\T1/cmtt/m/n/10.95 interactive(children=(IntSlider(value=10, description=\TS1
/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.95 x\TS1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.95 , 
max=30, min=-10), Output()), _dom_classes=(\TS1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10
.95 widget-interact\TS1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.95 ,))[] 

Overfull \hbox (3100.67706pt too wide) in paragraph at lines 958--958
[]\T1/cmtt/m/n/10.95 SelectionRangeSlider(index=(0, 11), layout=Layout(width=\T
S1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.95 80%\TS1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.9
5 ), options=((\TS1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.95 20150101\TS1/cmtt/m/n/10
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me.date(2015, 12, 1))), value=(datetime.date(2015, 1, 1), datetime.date(2015, 1
2, 1)))[] 

Overfull \hbox (967.4712pt too wide) in paragraph at lines 975--975
[]\T1/cmtt/m/n/10.95 HBox(children=(VBox(children=(Button(description=\TS1/cmtt
/m/n/10.95 '\T1/cmtt/m/n/10.95 correct\TS1/cmtt/m/n/10.95 '\T1/cmtt/m/n/10.95 ,
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n/10.95 , style=ButtonStyle())))))[] 
[13]! Unable to read an entire line---bufsize=200000.
Please increase buf_size in texmf.cnf.

xdvipdfmx:fatal: File ended prematurely

Output file removed.

Please increase buf_size in texmf.cnf, being what seems like the correct action:

I took a look on the filesystem and saw:

jovyan@75f27eaa1954:/$ find . -name "texmf.cnf"
./usr/share/texmf/web2c/texmf.cnf
./usr/share/texlive/texmf-dist/web2c/texmf.cnf
find: ‘./var/cache/ldconfig’: Permission denied
find: ‘./var/cache/apt/archives/partial’: Permission denied
find: ‘./var/lib/apt/lists/partial’: Permission denied
find: ‘./root’: Permission denied
find: ‘./proc/tty/driver’: Permission denied
./etc/texmf/web2c/texmf.cnf
find: ‘./etc/ssl/private’: Permission denied
find: ‘./tmp/tmpRldPwF_kernels’: Permission denied

How do I build my docker image that I can configure this to handle larger notebooks?

[p2ya]

I have got the same error: ersion 3.14159265-2.6-0.99992 (TeX Live 2015/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (/home/jovyan/work/... any resolution on this ?

[takluyver]

That doesn't look like the same error, absent further information. The error message from Latex is usually near the end of the output. In the log @petergarbers posted, the error is:

[13]! Unable to read an entire line---bufsize=200000.
Please increase buf_size in texmf.cnf.

[p2ya]

Here is the full error log, I really appreciate to have your feedback to resolve the issue:

NbConvertApp] Converting notebook ReportTest.ipynb to pdf /opt/conda/lib/python3.6/site-packages/nbconvert/filters/datatypefilter.py:41: UserWarning: Your element with mimetype(s) dict_keys(['text/html', 'text/vnd.plotly.v1+html']) is not able to be represented. mimetypes=output.keys()) /opt/conda/lib/python3.6/site-packages/nbconvert/filters/datatypefilter.py:41: UserWarning: Your element with mimetype(s) dict_keys(['text/html', 'text/vnd.plotly.v1+html']) is not able to be represented. mimetypes=output.keys()) [NbConvertApp] Writing 68979 bytes to notebook.tex [NbConvertApp] Building PDF [NbConvertApp] Running xelatex 3 times: ['xelatex', 'notebook.tex'] [NbConvertApp] CRITICAL | xelatex failed: ['xelatex', 'notebook.tex'] This is XeTeX, Version 3.14159265-2.6-0.99992 (TeX Live 2015/Debian) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (/home/jovyan/work/pdfTest/33-Alfred/notebook.tex LaTeX2e <2016/02/01> Babel <3.9q> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/mathpazo.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/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/xelatex/xetex-def/xetex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty)) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjustbox.sty (/usr/share/texlive/texmf-dist/tex/latex/xkeyval/xkeyval.sty (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkeyval.tex (/usr/share/texlive/texmf-dist/tex/generic/xkeyval/xkvutils.tex))) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/adjcalc.sty) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/trimclip.sty (/usr/share/texlive/texmf-dist/tex/latex/collectbox/collectbox.sty) (/usr/share/texlive/texmf-dist/tex/latex/adjustbox/tc-xetex.def)) (/usr/share/texlive/texmf-dist/tex/latex/ifoddpage/ifoddpage.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty)) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/tools/enumerate.sty) (/usr/share/texlive/texmf-dist/tex/latex/geometry/geometry.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amssymb.sty (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/amsfonts.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/textcomp.sty (/usr/share/texlive/texmf-dist/tex/latex/base/ts1enc.def)) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/eurosym/eurosym.sty) (/usr/share/texlive/texmf-dist/tex/latex/ucs/ucs.sty (/usr/share/texlive/texmf-dist/tex/latex/ucs/data/uni-global.def)) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty

Package inputenc Warning: inputenc package ignored with utf8 based engines.

) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grffile.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty)))) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty))

Package hyperref Message: Driver (autodetected): hxetex.

(/usr/share/texlive/texmf-dist/tex/latex/hyperref/hxetex.def (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/stringenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/booktabs/booktabs.sty) (/usr/share/texlive/texmf-dist/tex/latex/enumitem/enumitem.sty) (/usr/share/texlive/texmf-dist/tex/generic/ulem/ulem.sty) No file notebook.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ppl.fd) (/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty) geometry driver: auto-detecting geometry detected driver: xetex geometry verbose mode - [ preamble ] result:

• driver: xetex
• paper:
• layout:
• layoutoffset:(h,v)=(0.0pt,0.0pt)
• modes:
• h-part:(L,W,R)=(72.26999pt, 469.75502pt, 72.26999pt)
• v-part:(T,H,B)=(72.26999pt, 650.43001pt, 72.26999pt)
• \paperwidth=614.295pt
• \paperheight=794.96999pt
• \textwidth=469.75502pt
• \textheight=650.43001pt
• \oddsidemargin=0.0pt
• \evensidemargin=0.0pt
• \topmargin=-37.0pt
• \headheight=12.0pt
• \headsep=25.0pt
• \topskip=11.0pt
• \footskip=30.0pt
• \marginparwidth=59.0pt
• \marginparsep=10.0pt
• \columnsep=10.0pt
• \skip\footins=10.0pt plus 4.0pt minus 2.0pt
• \hoffset=0.0pt
• \voffset=0.0pt
• \mag=1000
• \@twocolumnfalse
• \@twosidefalse
• \@mparswitchfalse
• \@reversemarginfalse
• (1in=72.27pt=25.4mm, 1cm=28.453pt)

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\protect l.1160 \fontfamily{\sffamily}\selectfont \textcolor{blue}{Energy - 4.56 sta... ? ! Emergency stop. \protect l.1160 \fontfamily{\sffamily}\selectfont \textcolor{blue}{Energy - 4.56 sta... Output written on notebook.pdf (15 pages). Transcript written on notebook.log. [NbConvertApp] PDF successfully created [NbConvertApp] Writing 216108 bytes to ReportTest.pdf

[takluyver]

I've no idea. It says ! Emergency stop., but then a few lines later it says:

Output written on notebook.pdf (15 pages).
Transcript written on notebook.log.

[NbConvertApp] PDF successfully created