When knitting an Rmarkdown document to Powerpoint, I do not understand why by default the inline code (or chunks code) is rendered in the presentation in font Courier size 18pt, whereas the rest of the non-code text is in font Calibri size 28pt.
I could only change the later using a custom template, but not the code appearance. Did I miss something?
Here is a simple example:
---
title: "Untitled"
author: "Julien Roux"
date: "9/18/2019"
output:
powerpoint_presentation: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
## R Markdown
Why is `inline code` appearing smaller?
Which results in this output slide after knitting in Rstudio (version 1.2.1578):
My session info:
> sessionInfo()
R version 3.6.0 Patched (2019-05-14 r76503)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.0 htmltools_0.3.6 tools_3.6.0 yaml_2.2.0 Rcpp_1.0.2 rmarkdown_1.15 knitr_1.24
[8] xfun_0.9 digest_0.6.20 evaluate_0.14
Related
I use the kableExtra package all the time to create tables in R Markdown and save them to PDF. However today I upgraded to MacOS Catalina and now when I export to PDF, I cannot open the PDF image and get the error, "insufficient data for an image" in Adobe Reader. I don't get an error message in R Markdown and the PDF appears in my files, but I cannot open it in Adobe. If I use another application to open it (i.e., Preview) the resolution is very poor - and not typical of PDF. Has anyone else run into this problem and is there a solution? Many thanks for your help!
My code to retrieve the error is below:
mtcars %>%
kable() %>%
kable_styling() %>%
save_kable("test.pdf")
And session info is:
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] metafor_2.1-0 Matrix_1.2-18 MASS_7.3-51.5 RColorBrewer_1.1-2 tidyr_1.0.2 knitr_1.28
[7] sandwich_2.5-1 plotROC_2.2.1 ggROC_1.0 pROC_1.16.1 dplyr_0.8.4 plyr_1.8.5
[13] foreign_0.8-75 gridExtra_2.3 kableExtra_1.1.0 scales_1.1.0 ggplot2_3.2.1 psych_1.9.12.31
loaded via a namespace (and not attached):
[1] Rcpp_1.0.3 lattice_0.20-38 ps_1.3.2 zoo_1.8-7 utf8_1.1.4 assertthat_0.2.1
[7] digest_0.6.24 R6_2.4.1 evaluate_0.14 httr_1.4.1 highr_0.8 pillar_1.4.3
[13] rlang_0.4.4 lazyeval_0.2.2 rstudioapi_0.11 callr_3.4.2 magick_2.3 rmarkdown_2.1
[19] labeling_0.3 webshot_0.5.2 readr_1.3.1 stringr_1.4.0 munsell_0.5.0 compiler_3.6.2
[25] xfun_0.12 pkgconfig_2.0.3 mnormt_1.5-6 htmltools_0.4.0 tidyselect_1.0.0 tibble_2.1.3
[31] fansi_0.4.1 viridisLite_0.3.0 crayon_1.3.4 withr_2.1.2 grid_3.6.2 nlme_3.1-144
[37] jsonlite_1.6.1 gtable_0.3.0 lifecycle_0.1.0 magrittr_1.5 cli_2.0.1 stringi_1.4.6
[43] farver_2.0.3 xml2_1.2.2 vctrs_0.2.2 tools_3.6.2 glue_1.3.1 purrr_0.3.3
[49] hms_0.5.3 processx_3.4.2 parallel_3.6.2 yaml_2.2.1 colorspace_1.4-1 rvest_0.3.5
New to Rmarkdown (and markdown in general). I've inherited some code that works great for the html_document output format but not for pdf_document. It seems to get stuck on the knitr asis_output function in the .Rmd script. When I comment out chunks containing that function, it writes to pdf no problem. Here's some troubleshooting I've tried:
xfun::session_info('rmarkdown')
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1, RStudio 1.2.1335
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
Locale: en_CA.UTF-8 / en_CA.UTF-8 / en_CA.UTF-8 / C / en_CA.UTF-8 / en_CA.UTF-8
:Package version:
base64enc_0.1.3 digest_0.6.20 evaluate_0.14 glue_1.3.1 graphics_3.6.1 grDevices_3.6.1 highr_0.8
htmltools_0.4.0 jsonlite_1.6 knitr_1.25 magrittr_1.5 markdown_1.1 methods_3.6.1 mime_0.7
Rcpp_1.0.2 rlang_0.4.0 rmarkdown_1.16 stats_3.6.1 stringi_1.4.3 stringr_1.4.0 tinytex_0.17.1
tools_3.6.1 utils_3.6.1 xfun_0.10 yaml_2.2.0
Pandoc version: 2.7.3
Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/opt/X11/bin"
tinytex::tinytex_root()
[1] "/usr/local/texlive/2019"
(tinytex::tlmgr_path())
tlmgr path add add_link_dir_dir: /usr/local/share/info/dir exists;
not making symlink. add_link_dir_dir: destination
/usr/local/share/man/man5 not writable, no links from
/usr/local/texlive/2019/texmf-dist/doc/man/man5.tlmgr: An error has
occurred. See above messages. Exiting. add of symlinks had 1
error(s), see messages above.[1] 6
So maybe the problem is a path issue? In which case I have no clue how to fix. Or should I be using an alternative to the asis_output function? Any help is much appreciated. Here's the relevant bits of my code:
In the R script:
id <- 44
rmarkdown::render('mymarkdown.Rmd',
output_format = "pdf_document",
output_file = paste("report_", id,".pdf", sep=''),
output_dir = '/Users/myname/Documents/test')
In the Rmd file:
---
title: "Monitoring Activity Summary Report"
mode: selfcontained
date: "November 2019"
output:
pdf_document: default
html_document: default
self_contained: yes
---
[some code chunks...]
[then these code chunks that get stuck only for "pdf_document"...]
``` {r setup_Samp1a, echo=FALSE}
sampling_1 <- !is.na(sampling_unique[1])```
```{r conditional block, eval = sampling_1}
asis_output("### 3.1 Sampling 1\\n") # Header that is only shown if
sampling_1 == TRUE```
The error message
! Undefined control sequence.
<argument> 3.1 Sampling 1\n
Error: Failed to compile /Users/myname/Documents/test/report_44.tex.
See https://yihui.name/tinytex/r/#debugging for debugging tips. See
report_44.log for more info.
I've built a for loop to generate a series of PDF files automatically, but it says:
output file: test_chinese.knit.md
"C:/PROGRA~2/Pandoc/pandoc" +RTS -K512m -RTS test_chinese.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output 1TEST.tex --template "C:\Users\adminstor\Documents\R\win-library\3.4\rmarkdown\rmd\latex\default-1.17.0.2.tex" --highlight-style tango --pdf-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --variable "compact-title:yes"
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (MiKTeX 2.9.6650 64-bit)
entering extended mode
! Argument of \CJK#XX has an extra }.
<inserted text>
\par
l.30 breaklinks=true}
Error: Failed to compile 1TEST.tex. See 1TEST.log for more info.
In addition: Warning messages:
1: running command '"pdflatex" -halt-on-error -interaction=batchmode "1TEST.tex"' had status 1
2: running command '"pdflatex" -halt-on-error -interaction=batchmode "1TEST.tex"' had status 1
Have to mention that: The .rmd file could run successfully without the for loop.
The for loop I built is:
for (i in 1:5){
cat(i, '\n')
rmarkdown::render("test_chinese.Rmd",
encoding = 'UTF-8',
params = list(file_number = i),
output_file = paste0(i, "TEST.pdf"),
output_format = 'pdf_document')
}
Since I'm generating a Chinese file, the TeX Template is CTeX Template with TinyTex.
Here is my sessionInfo():
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 LC_MONETARY=Chinese (Simplified)_China.936
[4] LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rvest_0.3.2 xml2_1.2.0 knitr_1.20 rmarkdown_1.10
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 magrittr_1.5 devtools_1.13.6 R6_2.2.2 stringr_1.3.1 httr_1.3.1 highr_0.6 tools_3.4.4
[9] xfun_0.3 tinytex_0.8 postr_0.0.0 git2r_0.23.0 withr_2.1.2 selectr_0.4-1 htmltools_0.3.6 yaml_2.2.0
[17] rprojroot_1.3-2 digest_0.6.15 rsconnect_0.8.8 curl_3.2 memoise_1.1.0 evaluate_0.11 stringi_1.1.7 compiler_3.4.4
[25] rticles_0.5 backports_1.1.2
Looking forward for your help!
Thanks everyone.
Trying to make a selectInput's range of choices depend on the value of a first selectInput.
Flexboard header looks like:
---
title: "blabla"
output:
flexdashboard::flex_dashboard:
orientation: rows
social: menu
source_code: embed
theme: cerulean
runtime: shiny
---
The code below, which compiles but doesn't work, is within the .sidebar chunk. I am attempting to use input$book to interactively change the range of the "chapter" selectInput. Unfortunately, updateSelectInput() seems to do nothing.
# Inputs {.sidebar data-width=150}
```{r}
selectInput("book", label = "libro", choices = c("dq1605", "dq1615"), selected="dq1605")
selectInput("chapter", label = "capítulo",choices = 0:54, selected=0)
observeEvent(input$book, {
y <- input$book
if (is.null(y)) y <- "dq1605"
chs <- if(y=="dq1605") 0:54 else 0:74
updateSelectInput(session,"chapter",choices = chs)
})
```
I have invested several hrs trying to make this work (I have used the simpler observeEvent({}) as well), but to no avail. Any suggestions?
> sessionInfo()
R version 3.4.3 (2017-11-30)
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
loaded via a namespace (and not attached):
[1] compiler_3.4.3 backports_1.1.2 magrittr_1.5 rsconnect_0.8.5
[5] rprojroot_1.3-2 htmltools_0.3.6 tools_3.4.3 flexdashboard_0.5.1
[9] yaml_2.1.16 Rcpp_0.12.15 stringi_1.1.6 rmarkdown_1.9
[13] knitr_1.20 jsonlite_1.5 stringr_1.2.0 digest_0.6.15
[17] evaluate_0.10.1
It works for me actually.
All I changed is the 'selected = max(chs)' to make it easier to see if it worked.
Can't see any of your packages being older than mine either.
---
title: "blabla"
output:
flexdashboard::flex_dashboard:
orientation: rows
social: menu
source_code: embed
theme: cerulean
runtime: shiny
---
# Inputs {.sidebar data-width=150}
```{r}
selectInput("book", label = "libro", choices = c("dq1605", "dq1615"), selected="dq1605")
selectInput("chapter", label = "capítulo",choices = 0:54, selected=0)
observeEvent(input$book, {
y <- input$book
if (is.null(y)) y <- "dq1605"
chs <- if(y=="dq1605") 0:54 else 0:74
updateSelectInput(session, "chapter", choices = chs, selected = max(chs))
})
```
Using beamer in RMarkdown for presentations, I can't figure out why the TOC is empty. I have tried using a MacBook and Windows.
---
title: "test"
author: "my name"
date: "12/6/2016"
output:
beamer_presentation:
keep_tex: true
toc: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
# Slide 1
Slide content
# Slide 2
Slide content
Outputs the pdf presentation with a title slide, an empty page (where the TOC should be), and then the two slides.
On Windows platform:
> R.version
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 3.1
year 2016
month 06
day 21
svn rev 70800
language R
version.string R version 3.3.1 (2016-06-21)
nickname Bug in Your Hair
RStudio:0.99.896
Rmarkdown: 1.2
knitr: 1.15.1
Somewhat related question here: Table of content in beamer generated with R markdown/knitr
Using the keep_tex: true argument in the YAML, I see from the tex file that the level 1 headers (i.e. # Section) are not being properly converted to sections in the tex file. For example, from the tex file:
\begin{frame}{Slide 1}
Slide content
\end{frame}
It seems that RMarkdown is not making the tex file correctly.
As pointed out here, the TOC will list the sections (as defined by single #'s), and the slide level must be a level below the sections (defined below in the YAML as slide_level: 2 and in the presentation by ##'s). I don't completely understand why you can't have sections at the slide level, but at least this works.
---
title: "test"
author: "my name"
date: "12/6/2016"
output:
beamer_presentation:
keep_tex: true
toc: true
slide_level:2
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
# Section 1
## Slide 1
Slide content
# Section 2
# Slide 2
Slide content