rstudio / bookdown

Authoring Books and Technical Documents with R Markdown
https://pkgs.rstudio.com/bookdown/
GNU General Public License v3.0
3.75k stars 1.27k forks source link

r bookdown pdf format does not work #394

Closed MarioGS closed 7 years ago

MarioGS commented 7 years ago

Hi,

First of all thanks Yihui for this amazing package! I tied to find help in stackoverflow but nobody reply to me. Here is the post:

https://stackoverflow.com/questions/43816983/r-bookdown-pdf-format-does-not-work

I do not understand why I am not able to create a pdf using bookdown. I can render all html formats using bookdown without any issue. Moreover, I can create pdf with no problem using regular Rmarkdown files. However, when I run

bookdown::render_book("index.Rmd", "bookdown::pdf_document2")

it does not generate any pdf.

Any idea about how can this issue be solved?

I am runing Windows10 64bits and the lastest Rstudio and MikTeX version.

Thanks a lot in advance,

Mario

yihui commented 7 years ago

If you see a log file (should be named _main.log by default), please copy and paste its content here. Thanks!

MarioGS commented 7 years ago

Hi Yihui,

Thanks for your reply.

When I render to pdf_book using:

bookdown::render_book("index.Rmd", "bookdown::pdf_book")

the _main.log file is not generated. Nevertheless, files: _main.md, _main.rds and _main.tex are generated. If I open _main.tex and compile to pdf (not using R) the following files are generated: _main.aux, _main.dvi, _main.out, _main.rds, _main.toc and _main.log. The content of _main.log is as follows:

This is pdfTeX, Version 3.14159265-2.6-1.40.18 (MiKTeX 2.9.6300 64-bit) (preloaded format=latex 2017.5.9)  9 MAY 2017 16:11
entering extended mode
**./_main.tex
(_main.tex
LaTeX2e <2017-04-15>
Babel <3.9r> and hyphenation patterns for 75 language(s) loaded.
("C:\Program Files\MiKTeX 2.9\tex\latex\base\book.cls"
Document Class: book 2014/09/29 v1.4h Standard LaTeX document class
("C:\Program Files\MiKTeX 2.9\tex\latex\base\bk10.clo"
File: bk10.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
)
\c@part=\count79
\c@chapter=\count80
\c@section=\count81
\c@subsection=\count82
\c@subsubsection=\count83
\c@paragraph=\count84
\c@subparagraph=\count85
\c@figure=\count86
\c@table=\count87
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
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(Font)                  OT1/cmtt/m/n --> OT1/lmtt/m/n on input line 38.
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("C:\Program Files\MiKTeX 2.9\tex\latex\amsfonts\amssymb.sty"
Package: amssymb 2013/01/14 v3.01 AMS font symbols

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Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
\@emptytoks=\toks14
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LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
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))
("C:\Program Files\MiKTeX 2.9\tex\latex\amsmath\amsmath.sty"
Package: amsmath 2016/11/05 v2.16a AMS math features
\@mathmargin=\skip43

For additional information on amsmath, use the `?' option.
("C:\Program Files\MiKTeX 2.9\tex\latex\amsmath\amstext.sty"
Package: amstext 2000/06/29 v2.01 AMS text

("C:\Program Files\MiKTeX 2.9\tex\latex\amsmath\amsgen.sty"
File: amsgen.sty 1999/11/30 v2.0 generic functions
\@emptytoks=\toks15
\ex@=\dimen103
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("C:\Program Files\MiKTeX 2.9\tex\latex\amsmath\amsbsy.sty"
Package: amsbsy 1999/11/29 v1.2d Bold Symbols
\pmbraise@=\dimen104
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Package: amsopn 2016/03/08 v2.02 operator names
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\Mathstrutbox@=\box26
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LaTeX Font Info:    Redeclaring font encoding OML on input line 712.
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\macc@depth=\count93
\c@MaxMatrixCols=\count94
\dotsspace@=\muskip10
\c@parentequation=\count95
\dspbrk@lvl=\count96
\tag@help=\toks16
\row@=\count97
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\andhelp@=\toks17
\eqnshift@=\dimen106
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\tagshift@=\dimen108
\tagwidth@=\dimen109
\totwidth@=\dimen110
\lineht@=\dimen111
\@envbody=\toks18
\multlinegap=\skip44
\multlinetaggap=\skip45
\mathdisplay@stack=\toks19
LaTeX Info: Redefining \[ on input line 2817.
LaTeX Info: Redefining \] on input line 2818.
)
("C:\Program Files\MiKTeX 2.9\tex\generic\ifxetex\ifxetex.sty"
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
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Package: ifluatex 2016/05/16 v1.4 Provides the ifluatex switch (HO)
Package ifluatex Info: LuaTeX not detected.
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("C:\Program Files\MiKTeX 2.9\tex\latex\base\fixltx2e.sty"
Package: fixltx2e 2016/12/29 v2.1a fixes to LaTeX (obsolete)
Applying: [2015/01/01] Old fixltx2e package on input line 46.

Package fixltx2e Warning: fixltx2e is not required with releases after 2015
(fixltx2e)                All fixes are now in the LaTeX kernel.
(fixltx2e)                See the latexrelease package for details.

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) ("C:\Program Files\MiKTeX 2.9\tex\latex\base\fontenc.sty"
Package: fontenc 2017/04/05 v2.0i Standard LaTeX package

("C:\Program Files\MiKTeX 2.9\tex\latex\base\t1enc.def"
File: t1enc.def 2017/04/05 v2.0i Standard LaTeX file
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))
("C:\Program Files\MiKTeX 2.9\tex\latex\base\inputenc.sty"
Package: inputenc 2015/03/17 v1.2c Input encoding file
\inpenc@prehook=\toks20
\inpenc@posthook=\toks21

("C:\Program Files\MiKTeX 2.9\tex\latex\base\utf8.def"
File: utf8.def 2017/01/28 v1.1t UTF-8 support for inputenc
Now handling font encoding OML ...
... no UTF-8 mapping file for font encoding OML
Now handling font encoding T1 ...
... processing UTF-8 mapping file for font encoding T1

("C:\Program Files\MiKTeX 2.9\tex\latex\base\t1enc.dfu"
File: t1enc.dfu 2017/01/28 v1.1t UTF-8 support for inputenc
   defining Unicode char U+00A0 (decimal 160)
   defining Unicode char U+00A1 (decimal 161)
   defining Unicode char U+00A3 (decimal 163)
   defining Unicode char U+00AB (decimal 171)
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   defining Unicode char U+00BB (decimal 187)
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   defining Unicode char U+00CF (decimal 207)
   defining Unicode char U+00D0 (decimal 208)
   defining Unicode char U+00D1 (decimal 209)
   defining Unicode char U+00D2 (decimal 210)
   defining Unicode char U+00D3 (decimal 211)
   defining Unicode char U+00D4 (decimal 212)
   defining Unicode char U+00D5 (decimal 213)
   defining Unicode char U+00D6 (decimal 214)
   defining Unicode char U+00D8 (decimal 216)
   defining Unicode char U+00D9 (decimal 217)
   defining Unicode char U+00DA (decimal 218)
   defining Unicode char U+00DB (decimal 219)
   defining Unicode char U+00DC (decimal 220)
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   defining Unicode char U+00DE (decimal 222)
   defining Unicode char U+00DF (decimal 223)
   defining Unicode char U+00E0 (decimal 224)
   defining Unicode char U+00E1 (decimal 225)
   defining Unicode char U+00E2 (decimal 226)
   defining Unicode char U+00E3 (decimal 227)
   defining Unicode char U+00E4 (decimal 228)
   defining Unicode char U+00E5 (decimal 229)
   defining Unicode char U+00E6 (decimal 230)
   defining Unicode char U+00E7 (decimal 231)
   defining Unicode char U+00E8 (decimal 232)
   defining Unicode char U+00E9 (decimal 233)
   defining Unicode char U+00EA (decimal 234)
   defining Unicode char U+00EB (decimal 235)
   defining Unicode char U+00EC (decimal 236)
   defining Unicode char U+00ED (decimal 237)
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   defining Unicode char U+00EF (decimal 239)
   defining Unicode char U+00F0 (decimal 240)
   defining Unicode char U+00F1 (decimal 241)
   defining Unicode char U+00F2 (decimal 242)
   defining Unicode char U+00F3 (decimal 243)
   defining Unicode char U+00F4 (decimal 244)
   defining Unicode char U+00F5 (decimal 245)
   defining Unicode char U+00F6 (decimal 246)
   defining Unicode char U+00F8 (decimal 248)
   defining Unicode char U+00F9 (decimal 249)
   defining Unicode char U+00FA (decimal 250)
   defining Unicode char U+00FB (decimal 251)
   defining Unicode char U+00FC (decimal 252)
   defining Unicode char U+00FD (decimal 253)
   defining Unicode char U+00FE (decimal 254)
   defining Unicode char U+00FF (decimal 255)
   defining Unicode char U+0100 (decimal 256)
   defining Unicode char U+0101 (decimal 257)
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   defining Unicode char U+0114 (decimal 276)
   defining Unicode char U+0115 (decimal 277)
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   defining Unicode char U+0117 (decimal 279)
   defining Unicode char U+0118 (decimal 280)
   defining Unicode char U+0119 (decimal 281)
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   defining Unicode char U+011B (decimal 283)
   defining Unicode char U+011C (decimal 284)
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   defining Unicode char U+016C (decimal 364)
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   defining Unicode char U+200C (decimal 8204)
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   defining Unicode char U+2014 (decimal 8212)
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   defining Unicode char U+1E21 (decimal 7713)
)
Now handling font encoding OT1 ...
... processing UTF-8 mapping file for font encoding OT1

("C:\Program Files\MiKTeX 2.9\tex\latex\base\ot1enc.dfu"
File: ot1enc.dfu 2017/01/28 v1.1t UTF-8 support for inputenc
   defining Unicode char U+00A0 (decimal 160)
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   defining Unicode char U+021A (decimal 538)
   defining Unicode char U+021B (decimal 539)
   defining Unicode char U+2013 (decimal 8211)
   defining Unicode char U+2014 (decimal 8212)
   defining Unicode char U+2018 (decimal 8216)
   defining Unicode char U+2019 (decimal 8217)
   defining Unicode char U+201C (decimal 8220)
   defining Unicode char U+201D (decimal 8221)
)
Now handling font encoding OMS ...
... processing UTF-8 mapping file for font encoding OMS

("C:\Program Files\MiKTeX 2.9\tex\latex\base\omsenc.dfu"
File: omsenc.dfu 2017/01/28 v1.1t UTF-8 support for inputenc
   defining Unicode char U+00A7 (decimal 167)
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)
Now handling font encoding OMX ...
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   defining Unicode char U+00A9 (decimal 169)
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))
(C:\Users\Mario\AppData\Roaming\MiKTeX\2.9\tex\latex\upquote\upquote.sty
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tim

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\@outlinefile=\write3
\openout3 = `_main.out'.

Package hyperref Warning: Rerun to get /PageLabels entry.

[1

] [2

]
\tf@toc=\write4
\openout4 = `_main.toc'.

 [3] [4

] [5] [6

]
Chapter 1.
[7]
Package atveryend Info: Empty hook `BeforeClearDocument' on input line 190.
 [8]
Package atveryend Info: Empty hook `AfterLastShipout' on input line 190.
 (_main.aux)
Package atveryend Info: Empty hook `AtVeryEndDocument' on input line 190.
Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 190.

Package rerunfilecheck Warning: File `_main.out' has changed.
(rerunfilecheck)                Rerun to get outlines right
(rerunfilecheck)                or use package `bookmark'.

Package rerunfilecheck Info: Checksums for `_main.out':
(rerunfilecheck)             Before: <no file>
(rerunfilecheck)             After:  49C82A155556C419ED974CF02BECDC0A;126.

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

Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 190.
 ) 
Here is how much of TeX's memory you used:
 11764 strings out of 493329
 168430 string characters out of 3139151
 276733 words of memory out of 3000000
 15195 multiletter control sequences out of 15000+200000
 29705 words of font info for 23 fonts, out of 3000000 for 9000
 1141 hyphenation exceptions out of 8191
 32i,4n,38p,232b,371s stack positions out of 5000i,500n,10000p,200000b,50000s

Output written on _main.dvi (8 pages, 12916 bytes).

If I render to pdf_document2 using:

bookdown::render_book("index.Rmd", "bookdown::pdf_document2")

I have the same result.

I created a reproducible example:

1) The content of _bookdown.yml is:

new_session: yes

rmd_files: [
  "index.rmd",
  "reporting.Rmd", 
  ]

before_chapter_script: "_common.R"

2) The content of common.R is:

set.seed(1014)
options(digits = 3)

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  cache = TRUE,
  out.width = "70%",
  fig.align = 'center',
  fig.width = 6,
  fig.asp = 0.618,  # 1 / phi
  fig.show = "hold"
)

options(dplyr.print_min = 6, dplyr.print_max = 6)

3) The content of index.Rmd is:

---
knit: "bookdown::render_book"
title: "Bla bla bla"
author: ["Mario Gonzalez Sales"]
site: bookdown::bookdown_site
documentclass: book

---

#   {-}

This report has been created by [Modeling Great Solutions](http://modelinggreatsolutions.com).

4) The content of Reporting.Rmd is:

# Reporting

The creation of the analysis datasets will be described in a dedicated data management report. It
will provide a detailed and traceable description of how the analysis datasets were derived from
the source data.
The population PK analyses described in this analysis plan will be included in an overall report.
The overall analysis report will contain a thorough description of the data used in the analysis,
including any data exclusions and handling of missing data; the key components of the model
development, including the basic models, covariate analyses and model evaluation; and full
descriptions and discussions of the final models.
Both final reports will be delivered in pdf-format and will include all relevant signatures
(author(s), reviewer(s), auditor and client representative). 

Thanks a lot in advance!

Mario

yihui commented 7 years ago

I'm afraid this issue is going to be very difficult to debug unless we use tools like ScreenHero (so that I can investigate the issue directly on your computer).

MarioGS commented 7 years ago

Hi Yihui,

That is perfectly fine with me :)

When would it work for you?

Thanks,

Mario

MarioGS commented 7 years ago

Hi Yihui,

That is perfectly fine with me :)

When would it work for you?

Thanks,

Mario Gonzalez Sales Pharm.D, M.Sc.Stats, Ph.D in Pharmacometrics Mobile: (+34) 722279993 Email: mario_g_s@hotmail.es Call Send SMS Add to Skype You'll need Skype CreditFree via Skype Call Send SMS Call from mobile Add to Skype You'll need Skype CreditFree via Skype Call Send SMS Call from mobile Add to Skype You'll need Skype CreditFree via Skype


De: Yihui Xie notifications@github.com Enviado: miércoles, 10 de mayo de 2017 08:33 a.m. Para: rstudio/bookdown CC: MarioGS; Author Asunto: Re: [rstudio/bookdown] r bookdown pdf format does not work (#394)

I'm afraid this issue is going to be very difficult to debug unless we use tools like ScreenHero (so that I can investigate the issue directly on your computer).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/rstudio/bookdown/issues/394#issuecomment-300388933, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AJcXeTJLbtwTtJDDK9Z7UyOKHnTPBJJhks5r4VpUgaJpZM4NTN6r.

yihui commented 7 years ago

What is your timezone? (Mine is US Central Time) Please also let me know your email address so I can add you to my ScreenHero contact or send you an invite. My schedule is flexible. Pretty much any time any day works for me.

MarioGS commented 7 years ago

Hi Yihui,

I am in Washington DC. I guess it has to be Easter. I have already added you on ScreenHero. If you are available now, it would work for me. I have already finished my mandatory work for today.

yihui commented 7 years ago

Could you run (system2('pdflatex', '-v', stdout = F)) in R and let me know the output? I guess it may be 1 on your computer. And does (system2('pdflatex', '-v')) return 0?

yihui commented 7 years ago

I mean (system2('pdflatex', '-v')) should return 0, and (system2('pdflatex', '-v', stdout = F)) should return 1.

Anyway, could you restart R, install this fix devtools::install_github('rstudio/rmarkdown#1041'), and retry to compile the book to PDF?

MarioGS commented 7 years ago

Yes! The return of the first command is 1. The return of the second one is that pdflatex.exe did not succed

(system2('pdflatex', '-v', stdout = F)) [1] 1 Warning message: running command '"pdflatex" -v' had status 1 (system2('pdflatex', '-v'))

Sorry, but C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\pdflatex.exe did not succeed.

The log file hopefully contains the information to get MiKTeX going again:

C:/Users/Mario/AppData/Local/MiKTeX/2.9/miktex/log/pdflatex.log

You may want to visit the MiKTeX project page, if you need help. [1] 1 Warning message: running command '"pdflatex" -v' had status 1

yihui commented 7 years ago

How about (system2('pdflatex', '--version'))?

MarioGS commented 7 years ago

Yeeees! It works! :) I restart the R session and re-install rmardown and compile to pdf and it is working :)

The output for running:

(system2('pdflatex', '--version')) MiKTeX-pdfTeX (MiKTeX 2.9.6300 64-bit)

using bzip2 version 1.0.6, 6-Sept-2010 compiled with curl version 7.53.1; using libcurl/7.53.1 WinSSL compiled with expat version 2.2; using expat_2.2.0 compiled with jpeg version 9.2 compiled with liblzma version 50020032; using 50020032 compiled with libpng version 1.6.29; using 1.6.29 compiled with libressl version LibreSSL 2.4.5; using LibreSSL 2.4.5 compiled with MiKTeX Application Framework version 1.6300; using 1.6300 compiled with MiKTeX Core version 1.6300; using 1.6300 compiled with MiKTeX Archive Extractor version 1.6300; using 1.6300 compiled with MiKTeX Package Manager version 1.6300; using 1.6300 compiled with poppler version 0.53.0 compiled with uriparser version 0.8.4 compiled with zlib version 1.2.11; using 1.2.11 [1] 0

Thanks a lot!!

I have a final questions. Is it possible to remove the word "CHAPTER" from each of the chapters and from the header of the page? That way, bookdown would be perfect to generate also reports and not only books. I mean, can this text be customized and modified by the user?

yihui commented 7 years ago

Yes, it is possible. If you mean remove CHAPTER from the PDF output, I think you need to redefine the \chaptername variable like \renewcommand\chaptername{} and include this in your preamble via the includes option: https://bookdown.org/yihui/bookdown/yaml-options.html For other output formats, see https://bookdown.org/yihui/bookdown/internationalization.html

MarioGS commented 7 years ago

So... I really do not know what happened but I tried to render to pdf_document2 using:

bookdown::render_book("index.Rmd", bookdown::pdf_document2(keep_tex = TRUE)) and it looks like I messed up everything again. I get the same error as before and no matter if I render to pdf_book or pdf_document2 I get the same error:

Output created: _book/_main.pdf Error in tools::file_path_as_absolute(output_file) : file '_book/_main.pdf' does not exist In addition: Warning messages: 1: running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\latexmk.exe" -v' had status 1 2: running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\latexmk.exe" -v' had status 1 3: The LaTeX package latexmk was not correctly installed. 4: running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\latexmk.exe" -v' had status 1 5: running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\latexmk.exe" -v' had status 1 6: running command '"xelatex" -halt-on-error -interaction=batchmode "_main.tex"' had status 1 7: running command '"bibtex" "_main.aux"' had status 1 8: running command '"bibtex" "_main.aux"' had status 1 9: running command '"xelatex" -halt-on-error -interaction=batchmode "_main.tex"' had status 1 10: running command '"xelatex" -halt-on-error -interaction=batchmode "_main.tex"' had status 1

I have tried to restart the session and run again but it does not work.

yihui commented 7 years ago

Could you provide devtools::session_info('rmarkdown')?

MarioGS commented 7 years ago

devtools::session_info('rmarkdown') Session info -------------------------------------------------------------------------------------------- setting value
version R version 3.3.2 (2016-10-31) system x86_64, mingw32
ui RStudio (1.0.143)
language (EN)
collate Spanish_Spain.1252
tz Europe/Paris
date 2017-05-10

Packages ------------------------------------------------------------------------------------------------ package * version date source
backports 1.0.5 2017-01-18 CRAN (R 3.3.2)
base64enc 0.1-3 2015-07-28 CRAN (R 3.3.2)
bitops 1.0-6 2013-08-17 CRAN (R 3.3.2)
caTools 1.17.1 2014-09-10 CRAN (R 3.3.2)
digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
evaluate 0.10 2016-10-11 CRAN (R 3.3.2)
highr 0.6 2016-05-09 CRAN (R 3.3.2)
htmltools 0.3.6 2017-04-28 CRAN (R 3.3.3)
jsonlite 1.4 2017-04-08 CRAN (R 3.3.3)
knitr 1.15.1 2016-11-22 CRAN (R 3.3.2)
magrittr 1.5 2014-11-22 CRAN (R 3.3.3)
markdown 0.8 2017-04-20 CRAN (R 3.3.3)
mime 0.5 2016-07-07 CRAN (R 3.3.2)
Rcpp 0.12.10 2017-03-19 CRAN (R 3.3.2)
rmarkdown 1.5.9000 2017-05-10 Github (yihui/rmarkdown@739ba9c) rprojroot 1.2 2017-01-16 CRAN (R 3.3.2)
stringi 1.1.5 2017-04-07 CRAN (R 3.3.3)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.3)
yaml 2.1.14 2016-11-12 CRAN (R 3.3.2)

Do you want to have another look remotely. I promise no more barking :P

zjanna commented 6 years ago

Dear Yihui, I have the same problem. I cannot create pdf using book down. I got these errors: Output created: _book/bookdown-ksiazka.pdf Error in tools::file_path_as_absolute(output_file) : file '_book/bookdown-ksiazka.pdf' does not exist In addition: 4: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-ksiazka.tex"' had status 1 5: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-ksiazka.tex"' had status 1 6: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-ksiazka.tex"' had status 1 7: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-ksiazka.tex"' had status 1 8: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-ksiazka.tex"' had status 1 9: running command '"xelatex" -halt-on-error -interaction=batchmode "bookdown-ksiazka.tex"' had status 1

Do you have some idea? Html works ok. Thanks, Joanna

yihui commented 6 years ago

@zjanna No, but perhaps you can help me test TinyTeX: https://yihui.name/en/2017/12/test-tinytex/

zjanna commented 6 years ago

I installed this and still doesn't work. Do you have some idea?

yihui commented 6 years ago

@zjanna Too little information.

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