I've simplified it so that it's reproducible:
---
title: "Barking up the wrong tree"
author: "Patrick Connolly"
date: "`r format(Sys.time(), '%a %d/%m/%Y %H:%M')`"
output:
ioslides_presentation: default
slidy_presentation: default
beamer_presentation: default
---
```{r global_options, echo=FALSE}
knitr::opts_chunk$set(tidy=TRUE,
warning=FALSE,
message=FALSE,
cache=FALSE,
dpi = 300)
```
## 6 different Regression Trees
```{r 6 different Regression Trees, echo = FALSE, messages=FALSE, fig.width = 7,
fig.height = 5}
par(mfrow = c(2, 3))
plot(1:10)
plot(12:4)
plot(seq(0, 800))
plot(-100:-900)
plot(12:50)
plot(90:54)
```
I've tried it on a different machine which gives a slightly more
informative message:
X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 12 could
not be loaded
That seems to be associated with the Cairo plotting device which isn't
necessary with pdf devices which I normally use, nor, it would seem by
the plot pane in Rstudio. Consequently, running the plot code itself
works fine, but if is to be incorporated in HTML, we run into the Cairo
issue, Looking into that one, it appears something has been orphaned
for a couple of years. If anyone has information about that, I'd be
interested.
TIA
-------------
version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /home/pat/local/R-3.5.0/lib/libRblas.so
LAPACK: /home/pat/local/R-3.5.0/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C LC_TIME=en_NZ.UTF-8
[4] LC_COLLATE=en_NZ.UTF-8 LC_MONETARY=en_NZ.UTF-8
LC_MESSAGES=en_NZ.UTF-8
[7] LC_PAPER=en_NZ.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] utils stats grDevices graphics methods base
other attached packages:
[1] sp_1.3-1 lattice_0.20-35
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 knitr_1.20 bindr_0.1.1 magrittr_1.5
tidyselect_0.2.4 munsell_0.5.0
[7] colorspace_1.3-2 xtable_1.8-2 R6_2.2.2 rlang_0.2.1
stringr_1.3.1 plyr_1.8.4
[13] dplyr_0.7.6 tools_3.5.0 grid_3.5.0 htmltools_0.3.6
crosstalk_1.0.0 rprojroot_1.3-2
[19] yaml_2.1.19 leaflet_2.0.1 assertthat_0.2.0 digest_0.6.15
tibble_1.4.2 bindrcpp_0.2.2
[25] shiny_1.1.0 purrr_0.2.5 later_0.7.3 htmlwidgets_1.2
promises_1.0.1 evaluate_0.10.1
[31] glue_1.2.0 mime_0.5 rmarkdown_1.10 stringi_1.2.3
compiler_3.5.0 pillar_1.2.3
[37] backports_1.1.2 scales_0.5.0 httpuv_1.4.4.2 pkgconfig_2.0.1
>
On Thu, 23-Aug-2018 at 07:23AM -0700, Jeff Newmiller wrote:
|> This is not reproducible because you have not provided the plot code or
sample data. Output of sessionInfo would probably be appropriate as well.
|>
|> As to whether needing to load objects is typical... yes, rmarkdown runs
from a fresh environment to emphasize reproducibility, but your load command is
bypassing that for us.
|>
|> On August 23, 2018 2:15:19 AM PDT, Patrick Connolly <p_connolly at
slingshot.co.nz> wrote:
|> >I'm having difficulty getting plots into ioslides.
[...]
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
On 25/08/2018 6:21 AM, Patrick Connolly wrote:> --- > title: "Barking up the wrong tree" > author: "Patrick Connolly" > date: "`r format(Sys.time(), '%a %d/%m/%Y %H:%M')`" > output: > ioslides_presentation: default > slidy_presentation: default > beamer_presentation: default > --- > > ```{r global_options, echo=FALSE} > knitr::opts_chunk$set(tidy=TRUE, > warning=FALSE, > message=FALSE, > cache=FALSE, > dpi = 300)Drop the dpi setting and it will work fine. Duncan Murdoch> > ``` > ## 6 different Regression Trees > > ```{r 6 different Regression Trees, echo = FALSE, messages=FALSE, fig.width = 7, fig.height = 5} > > par(mfrow = c(2, 3)) > plot(1:10) > plot(12:4) > plot(seq(0, 800)) > plot(-100:-900) > plot(12:50) > plot(90:54) > ```
On Sat, 25-Aug-2018 at 07:53AM -0400, Duncan Murdoch wrote:
|> On 25/08/2018 6:21 AM, Patrick Connolly wrote:
|> >---
|> >title: "Barking up the wrong tree"
|> >author: "Patrick Connolly"
|> >date: "`r format(Sys.time(), '%a %d/%m/%Y %H:%M')`"
|> >output:
|> > ioslides_presentation: default
|> > slidy_presentation: default
|> > beamer_presentation: default
|> >---
|> >
|> >```{r global_options, echo=FALSE}
|> >knitr::opts_chunk$set(tidy=TRUE,
|> > warning=FALSE,
|> > message=FALSE,
|> > cache=FALSE,
|> > dpi = 300)
|>
|> Drop the dpi setting and it will work fine.
Still doesn't avoid what I think is the issue with Cairo
Error in axis(side = side, at = at, labels = labels, ...) : X11
font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 12
could not be loaded Calls: <Anonymous> ... plot.default -> localAxis
-> Axis -> Axis.default -> axis
Execution halted
For interactive plotting, Rstudio plots those 6 plots on one page so
no issue is apparent, as it will if I use a pdf device within ESS.
However, when plotting interactively in ESS, a basic font is used for
the labels which is OK for preliminary quick look. No error message
is shown, but I suspect that it is defaulting to a crude font because
the helvetica font is not available.
It appears to me that the font problem doesn't arise with Rstudio
unless the desired output is ioslides. Which brings us back to the
issue with Cairo. There are lots of hits when I search for
configuring fonts, Cairo and R but I've not found anything I can use.
I would appreciate pointers where I can find useful information.
Thank you.
|>
|> Duncan Murdoch
|>
|> >```
|> >## 6 different Regression Trees
|> >
|> >```{r 6 different Regression Trees, echo = FALSE, messages=FALSE,
fig.width = 7, fig.height = 5}
|> >
|> > par(mfrow = c(2, 3))
|> >plot(1:10)
|> >plot(12:4)
|> >plot(seq(0, 800))
|> >plot(-100:-900)
|> >plot(12:50)
|> >plot(90:54)
|> >```
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.