In Plot: character encoding issue

Panidiomorphic · July 18, 2018, 9:25am

Hello

I'm having problems with plots in rstudio server since I upgraded from Oracle Linux to RHEL7. When I execute plot(...), the characters are cryptic: usually some mathematic signs; even the numbers on the axis are cryptic. When I do the plots from inside of R, everything works fine; also when I'm saving the plot with

> png("~/cars.png")
> plot(cars)
> dev.off()

So it seems to be originating from rstudio somehow.

capabilities() and sessionInfo() give me the following output:

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua    http/ftp     sockets      libxml        fifo 
       TRUE        TRUE       FALSE        TRUE       FALSE       FALSE        TRUE        TRUE        TRUE        TRUE 
     cledit       iconv         NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE       FALSE        TRUE        TRUE        TRUE        TRUE 
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ggplot2_2.1.0 shiny_1.0.5  

loaded via a namespace (and not attached):
 [1] colorspace_1.2-6 scales_0.3.0     plyr_1.8.3       R6_2.1.1         htmltools_0.3.6  tools_3.3.3      gtable_0.1.2    
 [8] yaml_2.1.13      Rcpp_0.12.10     grid_3.3.3       digest_0.6.8     xtable_1.7-4     httpuv_1.3.5     mime_0.4        
[15] munsell_0.4.2

Can you guess where the problem is? Thanks very much.

EconomiCurtis · July 19, 2018, 1:12pm

Could you offer an example of the plot with cryptic plots?

Panidiomorphic · July 20, 2018, 7:05am

Certainly:

The "cryptic" plot:

I can't post the second plot with the "regular" image, but when I create it directly from within the same R binary, the axis are labeled with dist and speed and the respective numbers.

Panidiomorphic · July 20, 2018, 7:06am

Here is actually the "regular" plot that I mentioned in the previous post:

Panidiomorphic · July 20, 2018, 9:55am

I didn't think that this might be of importance, but maybe it is after all: I didn't install R at the "standard" location but I compiled it myself and took my own path as prefix. R is not installed otherwise on the system.

EconomiCurtis · July 20, 2018, 5:22pm

It could be worth checking if other graphics output has the same issue, e.g. pdf() output.

You could also reset your graphics device:

Panidiomorphic · July 23, 2018, 10:09am

Thanks for this tip. I have already tried resetting the device without a result.

But when I'm plotting to a PDF from within rstudio, it works like a charm. So it probably has to be something with the PNG routines. What does rstudio do differently when it invokes the plot() function as opposed to a regular plot() invocation outside of rstudio?

EconomiCurtis · July 23, 2018, 5:01pm

One more thing, could you provide str(par())?
Perhaps a custom font is being set there, but it's not working as expected.

Panidiomorphic · July 24, 2018, 10:31am

This doesn't mean so much to me, but I hope it will help:

> str(par())
List of 72
 $ xlog     : logi FALSE
 $ ylog     : logi FALSE
 $ adj      : num 0.5
 $ ann      : logi TRUE
 $ ask      : logi FALSE
 $ bg       : chr "white"
 $ bty      : chr "o"
 $ cex      : num 1
 $ cex.axis : num 1
 $ cex.lab  : num 1
 $ cex.main : num 1.2
 $ cex.sub  : num 1
 $ cin      : num [1:2] 0.15 0.2
 $ col      : chr "black"
 $ col.axis : chr "black"
 $ col.lab  : chr "black"
 $ col.main : chr "black"
 $ col.sub  : chr "black"
 $ cra      : num [1:2] 14.4 19.2
 $ crt      : num 0
 $ csi      : num 0.2
 $ cxy      : num [1:2] 0.441 7.004
 $ din      : num [1:2] 8.95 5.48
 $ err      : int 0
 $ family   : chr ""
 $ fg       : chr "black"
 $ fig      : num [1:4] 0 1 0 1
 $ fin      : num [1:2] 8.95 5.48
 $ font     : int 1
 $ font.axis: int 1
 $ font.lab : int 1
 $ font.main: int 2
 $ font.sub : int 1
 $ lab      : int [1:3] 5 5 7
 $ las      : int 0
 $ lend     : chr "round"
 $ lheight  : num 1
 $ ljoin    : chr "round"
 $ lmitre   : num 10
 $ lty      : chr "solid"
 $ lwd      : num 1
 $ mai      : num [1:4] 1.02 0.82 0.82 0.42
 $ mar      : num [1:4] 5.1 4.1 4.1 2.1
 $ mex      : num 1
 $ mfcol    : int [1:2] 1 1
 $ mfg      : int [1:4] 1 1 1 1
 $ mfrow    : int [1:2] 1 1
 $ mgp      : num [1:3] 3 1 0
 $ mkh      : num 0.001
 $ new      : logi FALSE
 $ oma      : num [1:4] 0 0 0 0
 $ omd      : num [1:4] 0 1 0 1
 $ omi      : num [1:4] 0 0 0 0
 $ page     : logi TRUE
 $ pch      : int 1
 $ pin      : num [1:2] 7.71 3.64
 $ plt      : num [1:4] 0.0916 0.9531 0.1862 0.8503
 $ ps       : int 12
 $ pty      : chr "m"
 $ smo      : num 1
 $ srt      : num 0
 $ tck      : num NA
 $ tcl      : num -0.5
 $ usr      : num [1:4] 3.16 25.84 -2.72 124.72
 $ xaxp     : num [1:3] 5 25 4
 $ xaxs     : chr "r"
 $ xaxt     : chr "s"
 $ xpd      : logi FALSE
 $ yaxp     : num [1:3] 0 120 6
 $ yaxs     : chr "r"
 $ yaxt     : chr "s"
 $ ylbias   : num 0.2

jay_analytics · August 2, 2018, 7:57pm

Have similar issue in RHEL7 with plot

Locale on the machine
LANG=en_US.UTF-8
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=en_US.UTF-8

Locale -a output
C
en_US
en_US.iso88591
en_US.iso885915
en_US.utf8
POSIX

sessionInfo output
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)

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

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

other attached packages:
[1] RevoUtilsMath_10.0.0

loaded via a namespace (and not attached):
[1] RevoUtils_10.0.

capabilities
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE TRUE TRUE FALSE TRUE
NLS profmem cairo ICU long.double libcurl
TRUE TRUE TRUE TRUE TRUE TRUE

EconomiCurtis · August 9, 2018, 3:32pm

Hi @jay_analytics and @Panidiomorphic,
Folks are still not sure what's causing the issue, but we've set-up an issue at the following link.
You can follow progress on this issue by commenting, or clicking subscribe under notifications on the github page.

github.com/rstudio/rstudio

Unexpected Math Symbol Characters in Base-R Plots using RStudio

opened 03:30PM - 09 Aug 18 UTC

closed 01:57PM - 14 Aug 18 UTC

EconomiCurtis

external

Originates from here: https://community.rstudio.com/t/in-plot-character-encodi…ng-issue/11184/2 When doing something like this ```r png("~/cars.png") plot(cars) dev.off() ``` results in an image like this: ![](https://discourse-cdn-sjc1.com/business4/uploads/tidyverse/original/2X/a/a6d8c14636f93705db37b665cf110d70210c9846.png) ------- ``` r capabilities() jpeg png tiff tcltk X11 aqua http/ftp sockets libxml fifo TRUE TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE cledit iconv NLS profmem cairo ICU long.double libcurl TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE ``` ```r sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_2.1.0 shiny_1.0.5 loaded via a namespace (and not attached): [1] colorspace_1.2-6 scales_0.3.0 plyr_1.8.3 R6_2.1.1 htmltools_0.3.6 tools_3.3.3 gtable_0.1.2 [8] yaml_2.1.13 Rcpp_0.12.10 grid_3.3.3 digest_0.6.8 xtable_1.7-4 httpuv_1.3.5 mime_0.4 [15] munsell_0.4.2 ``` Additional comments: > I didn't think that this might be of importance, but maybe it is after all: I didn't install R at the "standard" location but I compiled it myself and took my own path as prefix. R is not installed otherwise on the system. > I have already tried resetting the device without a result. > But when I'm plotting to a PDF from within rstudio, it works like a charm. So it probably has to be something with the PNG routines. What does rstudio do differently when it invokes the plot() function as opposed to a regular plot() invocation outside of rstudio? ---- Kevin U asked for the results of ` str(par())` ``` > str(par()) List of 72 $ xlog : logi FALSE $ ylog : logi FALSE $ adj : num 0.5 $ ann : logi TRUE $ ask : logi FALSE $ bg : chr "white" $ bty : chr "o" $ cex : num 1 $ cex.axis : num 1 $ cex.lab : num 1 $ cex.main : num 1.2 $ cex.sub : num 1 $ cin : num [1:2] 0.15 0.2 $ col : chr "black" $ col.axis : chr "black" $ col.lab : chr "black" $ col.main : chr "black" $ col.sub : chr "black" $ cra : num [1:2] 14.4 19.2 $ crt : num 0 $ csi : num 0.2 $ cxy : num [1:2] 0.441 7.004 $ din : num [1:2] 8.95 5.48 $ err : int 0 $ family : chr "" $ fg : chr "black" $ fig : num [1:4] 0 1 0 1 $ fin : num [1:2] 8.95 5.48 $ font : int 1 $ font.axis: int 1 $ font.lab : int 1 $ font.main: int 2 $ font.sub : int 1 $ lab : int [1:3] 5 5 7 $ las : int 0 $ lend : chr "round" $ lheight : num 1 $ ljoin : chr "round" $ lmitre : num 10 $ lty : chr "solid" $ lwd : num 1 $ mai : num [1:4] 1.02 0.82 0.82 0.42 $ mar : num [1:4] 5.1 4.1 4.1 2.1 $ mex : num 1 $ mfcol : int [1:2] 1 1 $ mfg : int [1:4] 1 1 1 1 $ mfrow : int [1:2] 1 1 $ mgp : num [1:3] 3 1 0 $ mkh : num 0.001 $ new : logi FALSE $ oma : num [1:4] 0 0 0 0 $ omd : num [1:4] 0 1 0 1 $ omi : num [1:4] 0 0 0 0 $ page : logi TRUE $ pch : int 1 $ pin : num [1:2] 7.71 3.64 $ plt : num [1:4] 0.0916 0.9531 0.1862 0.8503 $ ps : int 12 $ pty : chr "m" $ smo : num 1 $ srt : num 0 $ tck : num NA $ tcl : num -0.5 $ usr : num [1:4] 3.16 25.84 -2.72 124.72 $ xaxp : num [1:3] 5 25 4 $ xaxs : chr "r" $ xaxt : chr "s" $ xpd : logi FALSE $ yaxp : num [1:3] 0 120 6 $ yaxs : chr "r" $ yaxt : chr "s" $ ylbias : num 0.2 ``` --------- The same issue occured with another user, details at this link: https://community.rstudio.com/t/in-plot-character-encoding-issue/11184/10?u=economicurtis

jay_analytics · August 13, 2018, 4:34pm

@Panidiomorphic @EconomiCurtis
Found what could be the issue. Rhel7 is missing one package "urw-fonts-2.4-16.el7.noarch"
After installing the package I was able to get the English labels.

yum install urw-fonts

Let me know if this helps.

Panidiomorphic · August 14, 2018, 10:09am

Thanks @jay_analytics, this solved my problem! No idea how it could be rendered for the other user, but now, it works for all users!