Mac OS X R.app has trouble rendering certain fonts.

I ?recently experienced ?the same problem. ?Text ?that was missing from
plots in the Quartz window appeared on plots that were sent directly to a
pdf file. Interestingly, ?text that was printed using the expression
function did appear in the quartz window, for example,
ylab=expression(hat(psi))

As Marc wrote, the problem was resolved when I used Fontbook to resolve
duplicated fonts, which for me were Arial and Helvetica stored at both the
System and User level. ? Hopefully this will work for you as well.

--Susan

Susan Gruber
UC Berkeley

EDIT:

Okay, it seems that X11 renders the fonts etc...okay

Typing in:

X11()
demo(plotmath)
dev.off()

seemed to render everything including the fonts fine, so I don't think

any

of my fonts are corrupted.

But is there a way to configure R to set X11 as the default device for

graphics? Right now, it uses quartz as its default device for rendering to

the screen. I'm a bit of a newbie here, so could somebody explain how to

add to my R config file to have the default device be X11?

On Jul 1, 2010, at 1:00 PM, Marc Schwartz wrote:

On Jul 1, 2010, at 11:50 AM, Carlo Tambuatco wrote:

I noticed this running a few graphics demos the other day.
In particular the plotmath and the persp graphics demos, certain fonts

don't seem to render on the demos.

The plotmath demo displays certain math equations on a quartz window

that don't render properly, and the persp demo displays a 3D model of a
mountain with labels on the graph rendered in a certain font. (None of the
data labels render at all.)

This problem appeared recently, (like last week), and has not happened

before. I'm fairly new to using the R gui and R in general, so I don't
really know where to check if I have the proper true type fonts
available on my computer or if it is a problem within R itself. This
doesn't appear to be a problem with the functioning of R itself, just an
inability for it to render certain fonts on graphical displays. I just
want to fix it now before I use it in a major project that
requires the rendering of fonts onto the screen for presentations
etc...

You might want to review this reply by Simon to a similar post

recently:

?https://stat.ethz.ch/pipermail/r-sig-mac/2010-June/007531.html
Another resource that might be relevant:
?http://www.maclife.com/article/news/howto_clear_your_macs_font_cache
HTH,
Marc Schwartz

For most men life is a search for the proper manila envelope in which to

get themselves filed.

? - Clifton Fadiman


? ? ? [[alternative HTML version deleted]]

I like to do all my upgrades at once and then leave well enough alone for a while.

My hard drive died so I had them put 10.6.4 on my iMac when they resurrected it.

After some finagling my guys were able to get rattle to run with GTK 2.18.5 under R64 2.11.

I was able to get lattistist to run under rattle but not rggobi--though regular GGobi runs.

My guys want me to go back to 32 bit R2.10 but I am inclined to think that this will sort itself out in the next few months.

Does anyone have any insights on how long it takes to make everything play together nicely?


Eric Ditwiler
Director, Academic Operations
Harvey Mudd College
909-607-3134

On Jul 2, 2010, at 9:37 PM, David Winsemius wrote:

As far I can remember you have never offered either sessionInfor(),  
nor a sample problem in R code, nor an explicit description of what  
is being produced, nor a pdf file that can be examined. I have run  
demo(plotmath) and it appears not to exercise fonts ot any  
exceptional degree .... no theta's, tau's or gamma's. Do you care  
to exapnd on your difficulties?

-- 
David.

From sessionInfo()

R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/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] tools_2.11.1


demo(plotmath) produces a table of equations loaded with sigmas and  
pi's, alphas, omicrons, upsilons, etc...

I'm not sure what demo you're running quite frankly.

How else do you want me to "expound on my difficulties"?

I've said as straightforwardly as I can what is happening. My  
newsgroup client doesn't allow me to post images to this newsgroup,  
so it is difficult for me to show you what I mean, so if you've run  
demo(plotmath) you should know which fonts I am referring to.

On Jul 2, 2010, at 8:48 PM, Carlo Tambuatco wrote:

On Fri, Jul 2, 2010 at 4:10 PM,  <sgruber at berkeley.edu> wrote:

I  recently experienced  the same problem.  Text  that was  
missing from
plots in the Quartz window appeared on plots that were sent  
directly to a
pdf file. Interestingly,  text that was printed using the  
expression
function did appear in the quartz window, for example,
ylab=expression(hat(psi))

As Marc wrote, the problem was resolved when I used Fontbook to  
resolve
duplicated fonts, which for me were Arial and Helvetica stored at  
both the
System and User level.   Hopefully this will work for you as well.

--Susan

Susan Gruber
UC Berkeley

I did have some duplicated fonts in my font book. So I resolved the
duplicates but it did not take care of the problem. There are  
still no
letters or numbers being rendered in quartz. Only in X11. I looked  
up
the quartzFont() function, to see if it might help, but so far
nothing. Quartz is the graphics engine that renders PDF, so if it
renders in PDF it should render in Quartz and vice versa. But that  
is
not the case apparently.

I hope that somebody has any additional input as to why this  
happens.

EDIT:

Okay, it seems that X11 renders the fonts etc...okay

Typing in:

X11()
demo(plotmath)
dev.off()

seemed to render everything including the fonts fine, so I don't  
think

any

of my fonts are corrupted.

But is there a way to configure R to set X11 as the default  
device for

graphics? Right now, it uses quartz as its default device for  
rendering to

the screen. I'm a bit of a newbie here, so could somebody  
explain how to

add to my R config file to have the default device be X11?

On Jul 1, 2010, at 1:00 PM, Marc Schwartz wrote:

On Jul 1, 2010, at 11:50 AM, Carlo Tambuatco wrote:

I noticed this running a few graphics demos the other day.
In particular the plotmath and the persp graphics demos,  
certain fonts

don't seem to render on the demos.

The plotmath demo displays certain math equations on a quartz  
window

that don't render properly, and the persp demo displays a 3D  
model of a
mountain with labels on the graph rendered in a certain font.  
(None of the
data labels render at all.)

This problem appeared recently, (like last week), and has not  
happened

before. I'm fairly new to using the R gui and R in general, so I  
don't
really know where to check if I have the proper true type fonts
available on my computer or if it is a problem within R itself.  
This
doesn't appear to be a problem with the functioning of R itself,  
just an
inability for it to render certain fonts on graphical displays. I  
just
want to fix it now before I use it in a major project that
requires the rendering of fonts onto the screen for presentations
etc...

You might want to review this reply by Simon to a similar post

recently:

https://stat.ethz.ch/pipermail/r-sig-mac/2010-June/007531.html
Another resource that might be relevant:
http://www.maclife.com/article/news/howto_clear_your_macs_font_cache
HTH,
Marc Schwartz

On Jul 3, 2010, at 1:49 AM, Carlo Tambuatco wrote:

On Jul 2, 2010, at 9:37 PM, David Winsemius wrote:

As far I can remember you have never offered either sessionInfor(), 
nor a sample problem in R code, nor an explicit description of what 
is being produced, nor a pdf file that can be examined. I have run 
demo(plotmath) and it appears not to exercise fonts ot any 
exceptional degree .... no theta's, tau's or gamma's. Do you care to 
exapnd on your difficulties?

-- 
David.

From sessionInfo()

R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/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] tools_2.11.1


demo(plotmath) produces a table of equations loaded with sigmas and 
pi's, alphas, omicrons, upsilons, etc...

Yes, I did miss the lower right corner of the second page (out of 
five) where the Greek letters were demonstrated but certainly did 
notice the set relations and arrows section. What I was asking for is 
an explicit expansion on the term you used ..."messed up". Your 
description of problems does not mimic those that I (and others) were 
earlier having,  were solved by removed corrupted versions of the 
Symbol font. In that instance printing to the Quartz device produced 
small empty boxes where Greek letters should have appeared and this 
happened also when pdf or tiff were used as output devices.

I'm not sure what demo you're running quite frankly.

How else do you want me to "expound on my difficulties"?

More specifics, especially in light of your next stated limitations.

I've said as straightforwardly as I can what is happening. My 
newsgroup client doesn't allow me to post images to this newsgroup, 
so it is difficult for me to show you what I mean, so if you've run 
demo(plotmath) you should know which fonts I am referring to.

It's not actually a newsgroup but rather a plain-text mailing list.

The default output device is set with the options function:

?device

However, when I try that, I still see a Quartz plot with:

options(device="X11")
plot(1)

What I needed to do to get X11 plotting was:

dev.off() # closing the default Quartz device

Then X11 gets the output. If this is desired for every session then 
put it in .Rprofile or some other startup mechanism ... see the 
Installation and Administration manual and

http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#The-current-and-startup-working-directories 

On 07/03/2010 09:45 AM, David Winsemius wrote:

It's not actually a newsgroup but rather a plain-text mailing list.

It's also a plain text newsgroup. According to my newsgroup client.

I like to do all my upgrades at once and then leave well enough alone for a while.

My hard drive died so I had them put 10.6.4 on my iMac when they resurrected it.

After some finagling my guys were able to get rattle to run with GTK 2.18.5 under R64 2.11.

I was able to get lattistist to run under rattle but not rggobi--though regular GGobi runs.

My guys want me to go back to 32 bit R2.10 but I am inclined to think that this will sort itself out in the next few months.

Does anyone have any insights on how long it takes to make everything play together nicely?

Hi Eric,

Unfortunately it's unlikely that we're going to have a 64-bit version
of ggobi ready in the near future.  We run it by open R in 32-bit
mode: R --arch=i386.

Hadley

On Fri, Jul 2, 2010 at 4:21 PM, Eric Ditwiler <eric_ditwiler at hmc.edu> wrote:

I like to do all my upgrades at once and then leave well enough alone for a while.

My hard drive died so I had them put 10.6.4 on my iMac when they resurrected it.

After some finagling my guys were able to get rattle to run with GTK 2.18.5 under R64 2.11.

I was able to get lattistist to run under rattle but not rggobi--though regular GGobi runs.

My guys want me to go back to 32 bit R2.10 but I am inclined to think that this will sort itself out in the next few months.

Does anyone have any insights on how long it takes to make everything play together nicely?


Eric Ditwiler
Director, Academic Operations
Harvey Mudd College
909-607-3134

-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

The official CRAN binary *is* 64-bit:

http://r.research.att.com/libs/ggobi-2.1.8-darwin9-bin3.tar.gz

Hi Eric,

Unfortunately it's unlikely that we're going to have a 64-bit version
of ggobi ready in the near future.  We run it by open R in 32-bit
mode: R --arch=i386.

Hadley

On Fri, Jul 2, 2010 at 4:21 PM, Eric Ditwiler <eric_ditwiler at hmc.edu> wrote:

I like to do all my upgrades at once and then leave well enough alone for a while.

My hard drive died so I had them put 10.6.4 on my iMac when they resurrected it.

After some finagling my guys were able to get rattle to run with GTK 2.18.5 under R64 2.11.

I was able to get lattistist to run under rattle but not rggobi--though regular GGobi runs.

My guys want me to go back to 32 bit R2.10 but I am inclined to think that this will sort itself out in the next few months.

Does anyone have any insights on how long it takes to make everything play together nicely?


Eric Ditwiler
Director, Academic Operations
Harvey Mudd College
909-607-3134

-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/