No text while plotting in R notebook

[DivM]

While plotting any plot in R on Jupyter notebook, all text in the plot (title, axes label etc.) is not being printed. This problem is there with both ggplot and normal plot function. Here's an example of the same:

This issue is limited to R notebooks as Python notebooks are plotting properly. The locale for R is as follows:

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

Refer to this for Stackoverflow question.

[mingwandroid]

Instead of putting links to external sites, you should copy the contents here, like this:

Here's the sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Amazon Linux Bare Metal release 2012.03

Matrix products: default
BLAS: /home/dmangla/sof/anaconda3/lib/R/lib/libRblas.so
LAPACK: /home/dmangla/sof/anaconda3/lib/R/lib/libRlapack.so

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

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

other attached packages:
[1] dplyr_0.7.4     purrr_0.2.3     readr_1.1.1     tidyr_0.7.1    
[5] tibble_1.3.4    ggplot2_2.2.1   tidyverse_1.1.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13     cellranger_1.1.0 compiler_3.4.2   plyr_1.8.4      
 [5] bindr_0.1        forcats_0.2.0    tools_3.4.2      digest_0.6.12   
 [9] uuid_0.1-2       lubridate_1.6.0  gtable_0.2.0     jsonlite_1.5    
[13] evaluate_0.10.1  nlme_3.1-131     lattice_0.20-35  pkgconfig_2.0.1 
[17] rlang_0.1.2      psych_1.7.8      IRdisplay_0.4.4  IRkernel_0.8.9  
[21] parallel_3.4.2   haven_1.1.0      bindrcpp_0.2     xml2_1.1.1      
[25] httr_1.3.1       repr_0.12.0      stringr_1.2.0    hms_0.3         
[29] grid_3.4.2       glue_1.1.1       R6_2.2.2         readxl_1.0.0    
[33] foreign_0.8-69   pbdZMQ_0.2-6     modelr_0.1.1     reshape2_1.4.2  
[37] magrittr_1.5     scales_0.5.0     rvest_0.3.2      assertthat_0.2.0
[41] mnormt_1.5-5     colorspace_1.3-2 labeling_0.3     stringi_1.1.5   
[45] lazyeval_0.2.0   munsell_0.4.3    broom_0.4.2      crayon_1.3.4    

I've tried reinstalling the packages but the problem still persists. Kindly tell if anyone knows what's the problem here and how to fix it.

Thanks to all.

[mingwandroid]

AFAICT you need to install some fonts on your Linux distro here. Boxes is what you get when fonts are missing.

Run X11Fonts() from within R and show the output.

[DivM]

This is the output:

$serif
'-*-times-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$sans
'-*-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$mono
'-*-courier-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Times
'-adobe-times-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Helvetica
'-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$CyrTimes
'-cronyx-times-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$CyrHelvetica
'-cronyx-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Arial
'-monotype-arial-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Mincho
'-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*'

[mingwandroid]

You need to install some of those fonts. This is not an Anaconda problem.

[DivM]

Can you show the correct/expected output of the above?

Thanks for the help.

[mingwandroid]

That is the correct output. I wanted you to see the name of the fonts you need to install. I don't know anything about the Amazon Linux Bare Metal release 2012.03 distribution though so I do not know how you would install those fonts on that.

[shenweiyan]

This is because the fonts are missing in anaconda, what we need is to install it:

conda install -c anaconda fonts-anaconda

[mingwandroid]

Those fonts are for qt-based apps on Linux only at present (and I added them explicitly in support of RStudio). To the best of my knowledge you need system fonts here.

[BhaskarCoursera]

DivM, were you able to fix this issue?

[rtmag]

For those of you still looking for the fix, as suggested by @shenweiyan conda install -c anaconda fonts-anaconda worked for me, thanks!

[multimeric]

I'm on Linux, and conda install -c anaconda fonts-anaconda didn't help me.

My X11Fonts() returns this (not really sure what it means, though):

$serif
'-*-times-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$sans
'-*-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$mono
'-*-courier-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Times
'-adobe-times-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Helvetica
'-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$CyrTimes
'-cronyx-times-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$CyrHelvetica
'-cronyx-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Arial
'-monotype-arial-%s-%s-*-*-%d-*-*-*-*-*-*-*'
$Mincho
'-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*'

And I get plots looking like this:

If I need to install fonts onto my system, what should they be?

[MadBugs]

I am on Ubuntu 18.04

This solved to me:
conda install -c r r-cairo

This also fixes the prob:
#It can be 'cairo', 'cairo-fonts', 'Xlib'. 'quartz'
options(bitmapType="quartz")

So it is for sure a problem of fonts missing... I used Anaconda to create the R environment. It seems that they left some critical packages behind when the env was created.

[multimeric]

Oh, thank you so much, conda install -c r r-cairo is what fixed it for me, none of the other packages helped.

[ghost]

I also faced same problem. Thanks @MadBugs for your comment. conda install -c r r-cairo worked for me too.