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R markdown does not create a pdf file #1285

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bdeepthi opened this Issue Mar 11, 2018 · 59 comments

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bdeepthi commented Mar 11, 2018

Hi,

When I try to knit the vanilla example Rmd file to "pdf" I get the below error. I tried re-installing the packages and restarting the R session several time but it dint help.

Output created: test.pdf
Error in tools::file_path_as_absolute(output_file) :
file 'test.pdf' does not exist
Calls: ->
In addition: Warning messages:
1: running command '"pdflatex" -halt-on-error -interaction=batchmode "test.tex"' had status 1
2: In readLines(logfile) : incomplete final line found on 'test.log'
Execution halted

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condwanaland commented Mar 11, 2018

I couldn't reproduce this; would you mind adding the minimal structure of Rmd file that fails to knit (i.e., can you include the yaml metadata and any chunks you have)?

Could you please also include the output of sessionInfo()

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bdeepthi commented Mar 11, 2018

Thank you for getting back to me. The Rmd file I'm using the vanilla script you get when you choose a new R markdown.

Rmd file

---
title: "Untitled"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, error= TRUE)
```
## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Session Info details

R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.3  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2 htmltools_0.3.6
 [6] tools_3.4.3     yaml_2.1.17     Rcpp_0.12.15    stringi_1.1.6   rmarkdown_1.9  
[11] knitr_1.20      stringr_1.3.0   digest_0.6.15   evaluate_0.10.1
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condwanaland commented Mar 11, 2018

What does list.files(pattern = ".Rmd") return?

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bdeepthi commented Mar 11, 2018

It returns the list of rmd files I have in my directory. For this particular file it's "test.Rmd"

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NMarkgraf commented Mar 12, 2018

Try current repository rmarkdown! devtools::install_github("rmarkdown")!

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Zanidean commented Mar 12, 2018

Getting this same bug as well, happy to see it's not my system.

I tried the github repo and it hasn't helped.

If I press the 'Knit' button it works, but when i use rmarkdown::render() it fails with the same error message. Same default .Rmd file as well.

Error: Failed to compile Test.tex.
In addition: Warning message:
running command '"pdflatex" -halt-on-error -interaction=batchmode "Test.tex"' had status 1 

Here is my sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] rmarkdown_1.9.3 tinytex_0.4    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15     digest_0.6.15    withr_2.1.1.9000
 [4] rprojroot_1.3-2  R6_2.2.2         backports_1.1.2 
 [7] git2r_0.21.0     magrittr_1.5     evaluate_0.10.1 
[10] httr_1.3.1       stringi_1.1.6    curl_3.1        
[13] devtools_1.13.5  tools_3.4.3      stringr_1.3.0   
[16] yaml_2.1.18      compiler_3.4.3   memoise_1.1.0   
[19] htmltools_0.3.6  knitr_1.20   
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NMarkgraf commented Mar 12, 2018

Can you please show us the complete rmarkdown::render() command, I'd like to see the parameters you use.

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Zanidean commented Mar 12, 2018

rmarkdown::render(input = "Test.Rmd",
                  output_format = "pdf_document",
                  output_file = "Test.pdf")

I've tried defaulting the file name and format options as well, same result.

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NMarkgraf commented Mar 12, 2018

Rendered here with no problem. Did you update tinytex to current github release 0.3.7 as well?
devtools::install_github("tinytex") ?

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Zanidean commented Mar 12, 2018

No I didn't, but I'll try.

I don't actually even use that tinytext, but installed it thinking it might be worth trying.

In the meantime, just reverting to an older rmarkdown worked for me.

devtools::install_version("rmarkdown", version = "1.8", repos = "http://cran.us.r-project.org")
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NMarkgraf commented Mar 12, 2018

Yes it does, but please give tinytex a try, it is very cool and a lot of speed up, when you use "keep_tex: yes" ;-) -- And if it work, @yihui should publish a new rmarkdown and tinytex release ASAP ;-)

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Zanidean commented Mar 12, 2018

I'm still pretty confident that this particular problem is in RMarkdown rather than tinytex as OP doesn't seem to have it running on his end and it was resolved for me by reverting to an older version of the package.

Yes, it looks like tinytex becoming a dependency is probably the cause of this for me. This commit gets rid of a ton of latexmk and now tinytex is required for pdf.

Funny that it doesn't seem to translate to the button inside RStudio though, does anybody know why that might be?

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bdeepthi commented Mar 12, 2018

I couldnt install the dev version of the rmarkdown because of folder permission issues. But I installed it using install.packages("rmarkdown") and tried to knit it but the same issue.

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Zanidean commented Mar 12, 2018

Try installing an older version of RMarkdown if you need to knit right away. I had luck with version 1.8 but I think anything prior to 1.9.3 should solve this as it's when tinytex became required.

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NMarkgraf commented Mar 12, 2018

If you can't get both current development releases (rmarkdown 1.9.3 and tinytex 0.3.7) on your system, please your rmarkdown 1.8. Or encourage @yihui to release the current devilment releases as 1.10 and 0.4 on CRAN asap! ;-)

Yes, the older rmarkdown will do the job, but tinytex will become a needed part of rmarkdown soon.

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yihui commented Mar 12, 2018

@NMarkgraf tinytex 0.4 is on CRAN. I have been sick for a few days, so haven't tagged the 0.4 release on Github yet.

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NMarkgraf commented Mar 12, 2018

Thanks @yihui! - Get healthy first. - We need you and your work ;-)

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Zanidean commented Mar 12, 2018

I actually noticed that 0.4 was there - I think I'll just need to play around with getting it working and installed as I had some additional Status 4 errors.

Thank you for your help!

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bdeepthi commented Mar 12, 2018

I tried different ways to downgrade the version but I was unsuccessful. I will wait till @yihui released the 1.10 version and try again.

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Zanidean commented Mar 12, 2018

Do you have devtools installed?

If so, you could try this:

devtools::install_version("rmarkdown", version = "1.8", repos = "http://cran.us.r-project.org")

You might try going here and installing from source.

FWIW, I got tinytex going and rendering a pdf, but when I use xelatex it throws me the same status 1 error.

I think I'm going to wait until this can all be wrapped up into RStudio itself because I don't have time to bother with figuring out why tinytex isn't playing nicely.

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yihui commented Mar 12, 2018

@bdeepthi @Zanidean I tried for a while on Windows but I just could not reproduce the problem. I wonder if any of you are able to do a 10-min chat with me (anytime this afternoon or any day this week) and show me the problem on your computer (with screensharing). I don't think rmarkdown 1.10 will magically fix your issue if I don't figure out the reason of the failure. Thanks!

If you install.packages(c('rmarkdown', 'tinytex')) (i.e. both from CRAN), you may add a code chunk with options(tinytex.verbose = TRUE), and see if it gives you more information about the error.

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yihui commented Mar 12, 2018

BTW, if you have the log file (e.g., test.log), it might be helpful if I can take a look at it.

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Zanidean commented Mar 12, 2018

As much as I'd like to, I won't be able to screen share at work.

But I would like to help. As mentioned, pdflatex doesn't give me any issues but when I call xelatex I seem to get similar issues.

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bdeepthi commented Mar 12, 2018

I have the same 'Permission Denied' error when I use devtools to install the package. I also downloaded the tar file from the archive and used that but its the same issue.

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bdeepthi commented Mar 12, 2018

log file: (Replace the actual path with "path"

This is pdfTeX, Version 3.14159265-2.6-1.40.19 (MiKTeX 2.9.6630 64-bit) (preloaded format=pdflatex 2018.3.11) 12 MAR 2018 11:59 entering extended mode **./test.tex (test.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 75 language(s) loaded.

("path\MiKTeX 2.9\tex\latex\base\artic
le.cls"
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class

("path\MiKTeX 2.9\tex\latex\base\size1
0.clo"
File: size10.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
)
\c@part=\count79
\c@section=\count80
\c@subsection=\count81
\c@subsubsection=\count82
\c@paragraph=\count83
\c@subparagraph=\count84
\c@figure=\count85
\c@table=\count86
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
("path\MiKTeX 2.9\tex\latex\lm\lmodern
.sty"
Package: lmodern 2009/10/30 v1.6 Latin Modern Fonts
LaTeX Font Info: Overwriting symbol font operators' in version normal'
(Font) OT1/cmr/m/n --> OT1/lmr/m/n on input line 22.
LaTeX Font Info: Overwriting symbol font letters' in version normal'
(Font) OML/cmm/m/it --> OML/lmm/m/it on input line 23.
LaTeX Font Info: Overwriting symbol font symbols' in version normal'
(Font) OMS/cmsy/m/n --> OMS/lmsy/m/n on input line 24.
LaTeX Font Info: Overwriting symbol font largesymbols' in version normal'
(Font) OMX/cmex/m/n --> OMX/lmex/m/n on input line 25.
LaTeX Font Info: Overwriting symbol font operators' in version bold'
(Font) OT1/cmr/bx/n --> OT1/lmr/bx/n on input line 26.
LaTeX Font Info: Overwriting symbol font letters' in version bold'
(Font) OML/cmm/b/it --> OML/lmm/b/it on input line 27.
LaTeX Font Info: Overwriting symbol font symbols' in version bold'
(Font) OMS/cmsy/b/n --> OMS/lmsy/b/n on input line 28.
LaTeX Font Info: Overwriting symbol font largesymbols' in version bold'
(Font) OMX/cmex/m/n --> OMX/lmex/m/n on input line 29.
LaTeX Font Info: Overwriting math alphabet \mathbf' in version normal'
(Font) OT1/cmr/bx/n --> OT1/lmr/bx/n on input line 31.
LaTeX Font Info: Overwriting math alphabet \mathsf' in version normal'
(Font) OT1/cmss/m/n --> OT1/lmss/m/n on input line 32.
LaTeX Font Info: Overwriting math alphabet \mathit' in version normal'
(Font) OT1/cmr/m/it --> OT1/lmr/m/it on input line 33.
LaTeX Font Info: Overwriting math alphabet \mathtt' in version normal'
(Font) OT1/cmtt/m/n --> OT1/lmtt/m/n on input line 34.
LaTeX Font Info: Overwriting math alphabet \mathbf' in version bold'
(Font) OT1/cmr/bx/n --> OT1/lmr/bx/n on input line 35.
LaTeX Font Info: Overwriting math alphabet \mathsf' in version bold'
(Font) OT1/cmss/bx/n --> OT1/lmss/bx/n on input line 36.
LaTeX Font Info: Overwriting math alphabet \mathit' in version bold'
(Font) OT1/cmr/bx/it --> OT1/lmr/bx/it on input line 37.
LaTeX Font Info: Overwriting math alphabet \mathtt' in version bold'
(Font) OT1/cmtt/m/n --> OT1/lmtt/m/n on input line 38.
)
("path\MiKTeX 2.9\tex\latex\amsfonts\a
mssymb.sty"
Package: amssymb 2013/01/14 v3.01 AMS font symbols

("path\MiKTeX 2.9\tex\latex\amsfonts\a
msfonts.sty"
Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
@emptytoks=\toks14
\symAMSa=\mathgroup4
\symAMSb=\mathgroup5
LaTeX Font Info: Overwriting math alphabet \mathfrak' in version bold'
(Font) U/euf/m/n --> U/euf/b/n on input line 106.
))
("path\MiKTeX 2.9\tex\latex\amsmath\am
smath.sty"
Package: amsmath 2017/09/02 v2.17a AMS math features
@mathmargin=\skip43
For additional information on amsmath, use the `?' option.

("path\MiKTeX 2.9\tex\latex\amsmath\am
stext.sty"
Package: amstext 2000/06/29 v2.01 AMS text

("path\MiKTeX 2.9\tex\latex\amsmath\am
sgen.sty"
File: amsgen.sty 1999/11/30 v2.0 generic functions
@emptytoks=\toks15
\ex@=\dimen103
))
("path\MiKTeX 2.9\tex\latex\amsmath\am
sbsy.sty"
Package: amsbsy 1999/11/29 v1.2d Bold Symbols
\pmbraise@=\dimen104
)
("path\MiKTeX 2.9\tex\latex\amsmath\am
sopn.sty"
Package: amsopn 2016/03/08 v2.02 operator names
)
\inf@bad=\count87
LaTeX Info: Redefining \frac on input line 213.
\uproot@=\count88
\leftroot@=\count89
LaTeX Info: Redefining \overline on input line 375.
\classnum@=\count90
\DOTSCASE@=\count91
LaTeX Info: Redefining \ldots on input line 472.
LaTeX Info: Redefining \dots on input line 475.
LaTeX Info: Redefining \cdots on input line 596.
\Mathstrutbox@=\box26
\strutbox@=\box27
\big@size=\dimen105
LaTeX Font Info: Redeclaring font encoding OML on input line 712.
LaTeX Font Info: Redeclaring font encoding OMS on input line 713.
\macc@depth=\count92
\c@MaxMatrixCols=\count93
\dotsspace@=\muskip10
\c@parentequation=\count94
\dspbrk@lvl=\count95
\tag@help=\toks16
\row@=\count96
\column@=\count97
\maxfields@=\count98
\andhelp@=\toks17
\eqnshift@=\dimen106
\alignsep@=\dimen107
\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.
)
("path\MiKTeX 2.9\tex\generic\ifxetex
ifxetex.sty"
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
)
("path\MiKTeX 2.9\tex\generic\oberdiek
\ifluatex.sty"
Package: ifluatex 2016/05/16 v1.4 Provides the ifluatex switch (HO)
Package ifluatex Info: LuaTeX not detected.
)
("path\MiKTeX 2.9\tex\latex\base\fixlt
x2e.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.

Already applied: [0000/00/00] Old fixltx2e package on input line 53.
)
("path\MiKTeX 2.9\tex\latex\base\fonte
nc.sty"
Package: fontenc 2017/04/05 v2.0i Standard LaTeX package

("path\MiKTeX 2.9\tex\latex\base\t1enc
.def"
File: t1enc.def 2017/04/05 v2.0i Standard LaTeX file
LaTeX Font Info: Redeclaring font encoding T1 on input line 48.
))
("path\MiKTeX 2.9\tex\latex\base\input
enc.sty"
Package: inputenc 2015/03/17 v1.2c Input encoding file
\inpenc@prehook=\toks20
\inpenc@posthook=\toks21

("path\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

("path\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)
defining Unicode char U+00AD (decimal 173)
defining Unicode char U+00BB (decimal 187)
defining Unicode char U+00BF (decimal 191)
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yihui commented Mar 12, 2018

@Zanidean No worries. It will be faster to debug the issue if I can see it, but that is not required. From your reply above #1285 (comment), you actually seemed to have issues with pdflatex because the warning messaged indicated so:

running command '"pdflatex" -halt-on-error -interaction=batchmode "Test.tex"' had status 1 

but you just said "pdflatex doesn't give me any issues", and it was the first time you mentioned xelatex when you said "but when I call xelatex I seem to get similar issues" above, so I'm confused what exactly your issue was. Would you give me more consistent instructions on how to reproduce your issue?

@bdeepthi For the time being, please use all packages from CRAN, and don't install the Github versions yet. I'll let you know when you need to. The first step is as I said above:

If you install.packages(c('rmarkdown', 'tinytex')), you may add a code chunk with options(tinytex.verbose = TRUE), and see if it gives you more information about the error.

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Zanidean commented Mar 12, 2018

@yihui Sorry, I have two issues and didn't delineate between them.

The initial issue with pdflatex was also present for xelatex and lualatex. This was caused by updating rmarkdown to 1.9.3, where tinytex was required but I hadn't actually installed it. I had the package installed, but not tinytex itself. For now, I've solved this by downgrading rmarkdown to 1.8, before the dependency changed.

The second issue comes when I have both tinytex fully installed, and the latest rmarkdown. When I use pdflatex to render there is no issue, but when I use xelatex I get the same status 1 error.

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yihui commented Mar 12, 2018

@Zanidean Okay, let's focus on the second issue first. Again:

If you install.packages(c('rmarkdown', 'tinytex')), you may add a code chunk with options(tinytex.verbose = TRUE) in your R Markdown document, and see if it gives you more information about the error.

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Zanidean commented Mar 12, 2018

Hm, okay.

So with the default markdown document I didn't run into that problem at all, so I think it's in how I'm using rmarkdown.

I still get it in my specific application though, where I'm using rmarkdown::render() to generate different .pdf's depending on certain input. The error doesn't occur on pdflatex.

Here is the error with xelatex. I changed the path to 'document'.

! Missing $ inserted.
<inserted text> 
                $
l.98 ..._files/figure-latex/unnamed-chunk-3-1.pdf}

Error: Failed to compile document.tex. See document.log for more info.

In addition: Warning messages:
...
1: running command '"xelatex" -halt-on-error -interaction=batchmode "document.tex"' had status 1 
2: running command '"xelatex" -halt-on-error -interaction=batchmode "document.tex"' had status 1 

When I change the output_file argument to something static like "test.pdf" it works, but when I use a variable assigned in the loop, it doesn't seem to work.

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Zanidean commented Mar 12, 2018

It looks like this has to do with spaces in the variable file name I was using.

These examples take place inside loops.

Here is the example of what I was doing that wasn't working:

  filename <- paste0("Reports/Documents/", program, ".pdf")
  rmarkdown::render(input = "Reports/Generator/Batch Template.Rmd",
         output_format = "pdf_document",
         output_file = filename)

And this is what made it work.

  filename <- paste0("Reports/Documents/", program, ".pdf") %>% 
    gsub(" ", "", .)
  print(filename)
  rmarkdown::render(input = "Reports/Generator/Batch Template.Rmd",
         output_format = "pdf_document",
         output_file = filename)

And again, only with xelatex and lualatex.

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Zanidean commented Mar 16, 2018

Did you also run tinytex::install_tinytex()?

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yihui commented Mar 16, 2018

@Zanidean Please note that rmarkdown 1.9 does not require the tinytex R package. Only the current dev version of rmarkdown requires it. Please also be aware of the fact that the tinytex R package does not require TinyTeX -- the custom LaTeX distribution I made: https://yihui.name/tinytex/r/ You can use any LaTeX distribution with tinytex (the R package). The only problem is that tinytex won't automatically install missing LaTeX packages for you if you don't use TinyTeX (TinyTeX refers to the custom LaTeX distribution; tinytex refers to the R package).

@ma1966 I have been desperately looking for someone who can reproduce this issue, since I cannot reproduce it by myself: https://community.rstudio.com/t/6155 So far I have heard both successes and failures, but haven't found a person who can screenshare with me, so I can debug it right on the problematic machine (@Zanidean cannot share due to work restrictions; @bdeepthi has not responded yet). You are the third person who has reported the issue, and I wonder if you are able to share your desktop screen with me.

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ma1966 commented Mar 16, 2018

I uninstalled MikTex. Then I installed tinytex::install_tinytex() and got an error:


> tinytex::install_tinytex()
trying URL 'http://mirror.ctan.org/systems/texlive/tlnet/install-tl.zip'
Content type 'application/zip' length 19439353 bytes (18.5 MB)
downloaded 7.9 MB

trying URL 'https://github.com/yihui/tinytex/raw/master/tools/pkgs-custom.txt'
Content type 'text/plain; charset=utf-8' length 267 bytes
downloaded 267 bytes

trying URL 'https://github.com/yihui/tinytex/raw/master/tools/texlive.profile'
Content type 'text/plain; charset=utf-8' length 295 bytes
downloaded 295 bytes

Error in setwd(dir) : character argument expected
In addition: Warning messages:
1: In download.file("http://mirror.ctan.org/systems/texlive/tlnet/install-tl.zip",  :
  downloaded length 8257536 != reported length 19439353
2: In unzip("install-tl.zip") : error 1 in extracting from zip file
Restart your R session and check if tinytex:::is_tinytex() is TRUE.

Then I restart rstudio and tinytex:::is_tinytex() was FALSE.

Yes I can share my screen. Are you available today?

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yihui commented Mar 16, 2018

@ma1966 Downloading the installer was not complete for some reason. You may try tinytex::install_tinytex() again, but please do me a favor not to do it before we chat, so that you can still reproduce the issue when I'm ready to investigate the issue on your computer. Thanks!

Edit: Oh I just saw you had uninstalled MiKTeX. Well, then please try tinytex::install_tinytex() again, and see if a different LaTeX distribution can fix your issue.

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ma1966 commented Mar 16, 2018

I uninstalled MikTex as recommended in your post and thought install_tinytex would install TeX live. I will wait for the chat. Thanks again.

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thiagocmattar commented Mar 17, 2018

Hello everyone, I got this issue too.

I'm using MikTeX with rmarkdown. This issue is caused by the lack of some packages required to compile the pdf and rmarkdown apparently is not able to require the downloads.

So I opened a sweve file and wrote the same document and when I compiled, MikTeX asked to download some packages.

After that rmarkdown is working fine.

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jmschallock commented Mar 17, 2018

Hi everyone, just wanted to chime in to say I was struggling with this issue today too, and going back to rmarkdown 1.8 seems to have fixed it for me.

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yihui commented Mar 17, 2018

@thiagocmattar Interesting. I wonder if there is a chance that you still remember which missing packages MiKTeX installed?

@jmschallock Do you have a minimal reproducible example? Any spaces in your filenames?

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JasonCEC commented Mar 17, 2018

I am having this issue as well, MikTeX with rmarkdown (version 1.9) on Windows 8.1.
If I output a .tex file and compile it in MikTeX it works fine,
but fails with render(..)

My packages are:

  • \usepackage{multicol}
  • \usepackage{fancyhdr}

Edit: going back to rmarkdown version 1.8 did not fix the problem for me

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JasonCEC commented Mar 17, 2018

Edit 2:

I got the PDF rendering again by uninstalling MikTex 2.9.? and updating to the most recent version;
now with (rmarkdown 1.8 still installed) I can user render(...) and it all works.

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jmschallock commented Mar 18, 2018

@yihui I'm afraid I wasn't very diligent with documenting what I did, but I updated R and RStudio to the latest versions and reverted to rmarkdown 1.8. No spaces in any of my filenames.

(Also just want to say thank you for all your work building and supporting such awesome packages! You're kind of my hero :)

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yihui commented Mar 19, 2018

Hi everyone, I think I have finally figured out the root causes (one of which was rstudio/rstudio#2446) of the issues reported in this thread, and below are two possible solutions (with the latest version of rmarkdown on CRAN, i.e. v1.9):

If you have to use MiKTeX

You can install the devel version of the R package tinytex:

devtools::install_github('yihui/tinytex')

If you haven't installed MiKTeX, remember to check the option Yes in Install missing packages when installing it:

screen shot 2018-03-19 at 9 49 22 am

If you have already installed MiKTeX, go to the Start menu, find the menu "MiKTeX Console", and choose the option Always install missing packages on-the-fly:

screen shot 2018-03-19 at 10 05 06 am

If you don't have to use MiKTeX

Things will be a little easier. Uninstall MiKTeX if you have installed it (or temporarily rename its installation folder if you don't want to get rid of it completely), then in R:

install.packages('tinytex')
tinytex::install_tinytex()

This will install TinyTeX (a custom version of TeX Live), which can also build LaTeX documents to PDF on Windows. For more info, see https://yihui.name/tinytex/. Restart RStudio/R when the installation is done (it may take 3-5 minutes).

Please let me know if you still have trouble. Thanks!

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yihui commented Mar 26, 2018

Hi @bdeepthi @Zanidean @JasonCEC @jmschallock @thiagocmattar @ma1966, can any of you confirm if the CRAN version of rmarkdown work with the dev version of tinytex when rendering PDF?

install.packages('rmarkdown')
devtools::install_github('yihui/tinytex')

Since I haven't heard back from any of you, I feel nervous about making a new release of tinytex to CRAN. R package authors are allowed to make at most six releases of a package in six months, and I have already used four chances since last December, so I have to be very cautious now. Thanks!

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Zanidean commented Mar 26, 2018

@yihui

Working for me.

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boshek commented Mar 28, 2018

@yihui

For what it's worth it works for me as well.

Session Info
Session info ----------------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.4 (2018-03-15)
 system   x86_64, mingw32             
 ui       RStudio (1.1.442)           
 language (EN)                        
 collate  English_Canada.1252         
 tz       America/Los_Angeles         
 date     2018-03-28                  

Packages --------------------------------------------------------------------------------------------------------------------------------------------------------
 package   * version    date       source                        
 backports   1.1.2      2017-12-13 CRAN (R 3.4.3)                
 base      * 3.4.4      2018-03-15 local                         
 compiler    3.4.4      2018-03-15 local                         
 datasets  * 3.4.4      2018-03-15 local                         
 devtools  * 1.13.5     2018-02-18 CRAN (R 3.4.3)                
 digest      0.6.15     2018-01-28 CRAN (R 3.4.3)                
 evaluate    0.10.1     2017-06-24 CRAN (R 3.4.3)                
 graphics  * 3.4.4      2018-03-15 local                         
 grDevices * 3.4.4      2018-03-15 local                         
 htmltools   0.3.6      2017-04-28 CRAN (R 3.4.3)                
 knitr       1.20       2018-02-20 CRAN (R 3.4.3)                
 lobstr    * 0.0.0.9000 2018-03-14 Github (r-lib/lobstr@75254f1) 
 magrittr    1.5        2014-11-22 CRAN (R 3.4.3)                
 memoise     1.1.0      2017-04-21 CRAN (R 3.4.0)                
 methods   * 3.4.4      2018-03-15 local                         
 R6          2.2.2      2017-06-17 CRAN (R 3.4.3)                
 Rcpp        0.12.16    2018-03-13 CRAN (R 3.4.4)                
 rlang       0.2.0      2018-02-20 CRAN (R 3.4.3)                
 rmarkdown * 1.9        2018-03-01 CRAN (R 3.4.4)                
 rprojroot   1.3-2      2018-01-03 CRAN (R 3.4.3)                
 stats     * 3.4.4      2018-03-15 local                         
 stringi     1.1.7      2018-03-12 CRAN (R 3.4.4)                
 stringr     1.3.0      2018-02-19 CRAN (R 3.4.3)                
 testthat  * 2.0.0      2017-12-13 CRAN (R 3.4.3)                
 tinytex   * 0.4.2      2018-03-28 Github (yihui/tinytex@c7d62e1)
 tools       3.4.4      2018-03-15 local                         
 usethis   * 1.3.0      2018-02-24 CRAN (R 3.4.3)                
 utils     * 3.4.4      2018-03-15 local                         
 withr       2.1.2      2018-03-15 CRAN (R 3.4.4)                
 yaml        2.1.18     2018-03-08 CRAN (R 3.4.3) 03-08 CRAN (R 3.4.3)    
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yihui commented Mar 28, 2018

Excellent! Thanks @Zanidean and @boshek!

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yihui commented Apr 16, 2018

FYI I have submitted the new version of tinytex (0.5) to CRAN: https://cran.r-project.org/package=tinytex Hopefully in about two days, update.packages() will solve all problems.

@yihui yihui added this to the v1.10 milestone Apr 18, 2018

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mbedward commented May 25, 2018

Joining in late but just in case this is helpful to anyone. On my windows 10 system tinytex::install was failing some way into the process. It turned out to be caused by wget not being installed. After installing it everything worked. Perhaps the batch file could check for wget and issue a message if not found?

My thanks and respect for all the fabulous work.

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yihui commented May 25, 2018

@bdeepthi Please see yihui/tinytex#49 (the short answer is you will have to wait for at least two days before you can tinytex::install_tinytex()).

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ga122493 commented Jun 13, 2018

@mbedward Sorry this is a silly question, how did you install wget -- was this for R/R Studio?

@yihui The fix works for regular pdf knitting. However, for pdf beamer, I uninstalled MikTex and installed tinytex on my window machine -- the problem is still there... The error is

Output created: Lecture3_slides_060418.pdf
Error in tools::file_path_as_absolute(output_file) :
file 'Lecture3_slides_060418.pdf' does not exist
Calls: < Anonymous > -> < Anonymous >
Execution halted

Looking through the log file and this has an error message, not sure if it helps...

(c:/Users/tyankama/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/oberdiek/infw
arerr.sty
Package: infwarerr 2016/05/16 v1.4 Providing info/warning/error messages (HO))

I also experience this on a Mac computer, which I already posted an issue here #1360

Any suggestions? Thank you!!

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mbedward commented Jun 13, 2018

@ga122493 I installed wget on my system (Windows 10), using the version from gnuwin32 on sourceforge. But I think yihui/tinytex#49 suggests that the need for wget was due to a problem in the tinytex install script and it should no longer be required.

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yihui commented Jun 13, 2018

@mbedward You are right. Just forget about wget. It is irrelevant now.

@ga122493 The message you posted from the LaTeX log file was not an error message. Error messages in LaTeX typically start with !. I have seen your #1360. Please hold on, and give me a little more time to breathe :)

To all: I'm going to lock this issue, since the original problem has been solved. The solution was install.packages('tinytex'). If anyone runs into new issues, please file new issues separately. Thanks!

@rstudio rstudio locked as resolved and limited conversation to collaborators Jun 13, 2018

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