Cropped plot labels in knitted PDF's in Linux

knitr

#1

Has anyone experienced having their plot labels cropped in knitted PDF's in Linux? This does not happen in my Windows machine.

Here is a minimal example to replicate this problem.

---
output: 
  pdf_document:
    keep_tex: true
---

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

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

Here is the output.

enter image description here

I have submitted this as a bug report here.

sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: elementary OS 0.4.1 Loki

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] tseries_0.10-44        httr_1.3.1             tufte_0.3             
 [4] tidyr_0.8.0            jsonlite_1.5           uroot_2.0-9           
 [7] modelr_0.1.1           assertthat_0.2.0       TTR_0.23-3            
[10] selectr_0.4-1          cellranger_1.1.0       yaml_2.1.18           
[13] progress_1.2.0         pillar_1.2.2           backports_1.1.2       
[16] lattice_0.20-35        glue_1.2.0             quadprog_1.5-5        
[19] digest_0.6.15          rvest_0.3.2            colorspace_1.3-2      
[22] htmltools_0.3.6        plyr_1.8.4             psych_1.8.3.3         
[25] timeDate_3043.102      pkgconfig_2.0.1        broom_0.4.4           
[28] haven_1.1.1            purrr_0.2.4            scales_0.5.0.9000     
[31] git2r_0.21.0           tibble_1.4.2           ggplot2_2.2.1.9000    
[34] withr_2.1.2            urca_1.3-0             nnet_7.3-12           
[37] ansistrings_1.0.0.9000 lazyeval_0.2.1         cli_1.0.0.9002        
[40] quantmod_0.4-13        mnormt_1.5-5           magrittr_1.5          
[43] crayon_1.3.4           readxl_1.1.0           memoise_1.1.0         
[46] evaluate_0.10.1        nlme_3.1-131.1         forcats_0.3.0         
[49] xts_0.10-2             xml2_1.2.0             foreign_0.8-69        
[52] rsconnect_0.8.8        tools_3.4.4            prettyunits_1.0.2     
[55] hms_0.4.2              stringr_1.3.0          munsell_0.4.3         
[58] bindrcpp_0.2.2         compiler_3.4.4         rlang_0.2.0.9001      
[61] grid_3.4.4             rstudioapi_0.7         labeling_0.3          
[64] rmarkdown_1.9          gtable_0.2.0           fracdiff_1.4-2        
[67] curl_3.2               reshape2_1.4.3         R6_2.2.2              
[70] zoo_1.8-1              lubridate_1.7.4        knitr_1.20            
[73] dplyr_0.7.4            utf8_1.1.3             bindr_0.1.1           
[76] rprojroot_1.3-2        readr_1.1.1            stringi_1.1.7         
[79] parallel_3.4.4         Rcpp_0.12.16           lmtest_0.9-36 

#2

Have you tried installing the tinytex package and then producing the pdf?


#3

I just did, but nothing happened. I also have a full vanilla installation of TeXLive 2017.


#4

Please edit your code as follows:

{r pressure, out.width = "300px", fig.align='center', echo=FALSE}

Try different values of out.width.
HTH


#5

@yihui currently recommends that you uninstall your existing TeX installation while using tinytex, and IIRC other users here have had problems trying to knit documents while running both side-by-side. Might not be the cause of your problems, though!


#6

My guess is that this is irrelevant to LaTeX, but a pure R issue. And it is likely to be a font config issue. I have never used (or even heard of) elementary OS, so I don't know.


#7

Elementary OS is based on Ubuntu 16.04. I will test it on that and see if I see the same results. Also, FWIW, this may have something to do with my pandoc version, which is the default in most Linux distributions.

pandoc -v
pandoc 1.19.2.1
Compiled with pandoc-types 1.17.0.4, texmath 0.9, skylighting 0.1.1.4

#8

Have you made any changes in the .Rprofile file?
Try deleting this file. It will be a hiddem file. After deleting, start Rstudio.


#9

No, there is nothing in my .Rprofile that causes this behavior. I tried deleting it, but the same behavior remains.