Rmarkdown knit pdf issues!

E.Maroney · June 22, 2018, 6:11pm

Thank you in advance for any help! I have MikTeX installed on my computer (2.9.6) and the tinytex package but Rmarkdown will not knit to a pdf (it will however for html) no matter what engine I use. I updated the packages and the other solutions seem to suggest downgrading or updating the packages so Im not sure what to do!

Output created: ttest.pdf 
Error in tools::file_path_as_absolute(output_file) : 
file 'ttest.pdf' does not exist
Calls: <Anonymous> -> <Anonymous>
In addition: Warning message:
In readLines(logfile) : incomplete final line found on 'ttest.log'
Execution halted

Session info

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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     

other attached packages:
[1] tinytex_0.5

loaded via a namespace (and not attached):
[1] compiler_3.5.0  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2 
htmltools_0.3.6
[6] tools_3.5.0     yaml_2.1.19     Rcpp_0.12.17    stringi_1.1.7   
rmarkdown_1.10 
[11] knitr_1.20      stringr_1.3.1   digest_0.6.15   evaluate_0.10.1
RMD File

---
title: "ttest"
author: "Erik Maroney"
date: "June 22, 2018"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = 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)
```

jcblum · June 22, 2018, 6:30pm

It sounds like you've been trying a bunch of things, so I'm sorry if this is ground you've already covered, but I wasn't totally sure: did you try uninstalling MikTeX, making sure you're on the latest version of tinytex, and then installing TinyTeX via tinytex::install_tinytex()?

(I know that's a lot of different references to something called tinytex/TinyTeX — tinytex is the R package that contains the function for installing TinyTeX, the custom TeXLive distribution).

E.Maroney · June 24, 2018, 6:55pm

Yeah I tried this but it says it finishes (and maybe times out) but when i check if TinyTex exists, it says false...having a lot of trouble with TinyTex

jonspring · June 24, 2018, 8:22pm

FWIW, I recently tried installing TinyTex and it seemed to hang indefinitely. After I uninstalled MikTeX (from Windows 10 in my case) and started a fresh R session, the install proceeded fine. While tinytex:::is_tinytex() was initially FALSE, it turned to true once I restarted RStudio. Similar to this person's experience...

github.com/rstudio/tinytex

the final step might be something wrong

opened 12:27PM - 05 Dec 17 UTC

closed 03:03AM - 06 Dec 17 UTC

donk3yzz

my computer OS is windows and I met this problem while installing tinytex, I run… `tinytex::install_tinytex()` twice and the results are same like below > ... running mktexlsr ... done running mktexlsr. running updmap-sys ... done running updmap-sys. regenerating fmtutil.cnf in C:/Users/Administrator/AppData/Local/Temp/RtmpQ3NVWQ/install-tl-20171205/TinyTeX/texmf-dist running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine pdftex ... done running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine pdftex. running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine xetex ... done running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine xetex. running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luatex ... done running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luatex. running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luajittex ... done running fmtutil-sys --no-error-if-no-engine=luajittex,mfluajit --no-error-if-no-format --byengine luajittex.tlmgr.pl:package log updated: C:/Users/Administrator/AppData/Local/Temp/RtmpQ3NVWQ/install-tl-20171205/TinyTeX/texmf-var/web2c/tlmgr.log Use of uninitialized value in bitwise or (|) at C:\Users\ADMINI~1\AppData\Roaming\TinyTeX\texmf-dist\scripts\texlive\tlmgr.pl line 1429. then I run `tinytex:::is_tinytex()` and it comes `FALSE`..I have no idea now

E.Maroney · June 25, 2018, 9:01pm

This is what was on my console when I tried what you did jon

Starting to install TinyTeX to C:\Users\3572974\AppData\Roaming/TinyTeX. It will take a few minutes.
PATH=C:\Users\3572974\AppData\Local\Temp\RtmpEfvNpq\install-tl-20180625\tlpkg\tlperl\bin;C:\Program Files\R\R-3.5.0\bin\x64;C:\Program Files\R\R-3.5.0\bin\x64;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Python36\Scripts\;C:\Program Files\R\R-3.4.1\library\Rtools\bin;C:\Program Files\R\R-3.4.1\library\Rtools\mingw_32\bin;C:\Python36\;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\CA\SC\CAWIN\;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\CA\DSM\bin;C:\Program Files (x86)\CA\SC\CBB\;C:\PROGRA~2\CA\SC\CAM\bin;C:\Program Files (x86)\CA\SC\Csam\SockAdapter\bin;C:\Program Files (x86)\CA\SC\Csam\SockAdapter\bin64;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Users\3572974\AppData\Local\Microsoft\WindowsApps;C:\Users\3572974\AppData\Local\atom\bin;C:\Users\3572974\AppData\Local\Programs\MiKTeX 2.9\miktex\bin\x64\
"C:\Users\3572974\AppData\Local\Temp\RtmpEfvNpq\install-tl-20180625\install-tl" -profile=../texlive.profile
Automated TeX Live installation using profile: ../texlive.profile
cannot contact mirror.ctan.org, returning a backbone server!

E.Maroney · June 25, 2018, 9:01pm

Loading http://dante.ctan.org/tex-archive/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users\3572974\AppData\Local\Temp\RtmpEfvNpq\install-tl-20180625\install-tl: TLPDB::from_file could not download http://dante.ctan.org/tex-archive/systems/texlive/tlnet/tlpkg/texlive.tlpdb;
C:\Users\3572974\AppData\Local\Temp\RtmpEfvNpq\install-tl-20180625\install-tl: maybe the repository setting should be changed.
TinyTeX installed to C:\Users\3572974\AppData\Roaming/TinyTeX
Restart your R session and check if tinytex:::is_tinytex() is TRUE.

Restarting R session...

> tinytex:::is_tinytex()
[1] FALSE
> tinytex:::is_tinytex()
[1] FALSE

EconomiCurtis · June 27, 2018, 8:29am

On the "cannot contact mirror.ctan.org, returning a backbone server!" message, discussions of returning a backbone server! suggest it may be a network issue
https://tex.stackexchange.com/questions/409037/using-tlmgr-inside-a-linux-nspawn-container
http://tex-live.tug.narkive.com/8crUDRJb/fwd

Timesaver · July 10, 2018, 8:34am

If you have miktex then taking the following steps may solve the conversion to pdf issue:

Start miktex console.
Click on “Restart as Administrator”.
Click on “settings”.
Then choose “Always install missing packages on the fly”
Close the console.
Restart Rstudio.

Knit to pdf your rmarkdown file.
I hope this solves your issue. (I am assuming you are using Windows operating system).

E.Maroney · August 13, 2018, 5:10pm

> tinytex::install_tinytex()
trying URL 'http://mirror.ctan.org/systems/texlive/tlnet/install-tl.zip'
Content type 'application/zip' length 19775481 bytes (18.9 MB)
downloaded 18.9 MB

trying URL 'https://github.com/yihui/tinytex/raw/master/tools/pkgs-custom.txt'
Content type 'text/plain; charset=utf-8' length 275 bytes
downloaded 275 bytes

E.Maroney · August 13, 2018, 5:10pm

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

Starting to install TinyTeX to C:\Users\3572974\AppData\Roaming/TinyTeX. It will take a few minutes.
PATH=C:\Users\3572974\AppData\Local\Temp\Rtmp4QYb8o\install-tl-20180813\tlpkg\tlperl\bin;C:\Program Files\R\R-3.5.0\bin\x64;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Python36\Scripts\;C:\Program Files\R\R-3.4.1\library\Rtools\bin;C:\Program Files\R\R-3.4.1\library\Rtools\mingw_32\bin;C:\Python36\;C:\ProgramData\Oracle\Java\javapath;C:\Program Files (x86)\CA\SC\CAWIN\;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\CA\DSM\bin;C:\Program Files (x86)\CA\SC\CBB\;C:\PROGRA~2\CA\SC\CAM\bin;C:\Program Files (x86)\CA\SC\Csam\SockAdapter\bin;C:\Program Files (x86)\CA\SC\Csam\SockAdapter\bin64;C:\Users\3572974\AppData\Local\Microsoft\WindowsApps;C:\Users\3572974\AppData\Local\atom\bin
"C:\Users\3572974\AppData\Local\Temp\Rtmp4QYb8o\install-tl-20180813\install-tl" -profile=../texlive.profile
Automated TeX Live installation using profile: ../texlive.profile

Warning messages:
1: In shell("install-tl-windows.bat -profile=../texlive.profile", invisible = FALSE) :
  'install-tl-windows.bat -profile=../texlive.profile' execution failed with error code 99
2: In file.remove("TinyTeX/install-tl.log") :
  cannot remove file 'TinyTeX/install-tl.log', reason 'No such file or directory'
Restart your R session and check if tinytex:::is_tinytex() is TRUE.

caustin · June 30, 2019, 4:33pm

I also had to ensure that the path to MikTex was part of the PATH environment variable. Doing so and also making the change @Timesaver noted got me squared away...