[R-SIG-Mac] plot() does not give labels under quartz

[Simon Urbanek]

On Jan 21, 2011, at 1:27 AM, Tena Sakai wrote:

> Hi Jari,
> 
>> it will probably also bug you elsewhere than in R graphics.
> 
> Yes, an excellent point.  I might as well fix it for good.
> I gave a quick look at FontBook.app, but I didn't get intuitive
> feel as to how to fix my problem.  

Check Arial - that is likely the font that gives you the problem. Make sure it's visible and you have only one of that name.

Cheers,
S



> I will spend more time on
> FontBook.app in a day or two.
> 
> Thank you.
> 
> Regards,
> 
> Tena Sakai
> tsakai at gallo.ucsf.edu
> 
> 
> On 1/20/11 12:59 AM, "Jari Oksanen" <jari.oksanen at oulu.fi> wrote:
> 
>> On Wed, 2011-01-19 at 23:26 -0800, Tena Sakai wrote:
>>> Hi,
>>> 
>>> I googled "os x corrupt font cache" and came up with a few hits.
>>> The top hit was:
>>>   http://www.macworld.com/article/139383/2009/03/fontcacheclear.html
>>> and it suggested issuing three lines below from unix prompt:
>>>   atsutil databases -removeUser
>>>   atsutil server -shutdown
>>>   atsutil server -ping
>>> Unfortunately, it didn't cure the problem.  The above link states:
>>> "Prior to OS X 10.5, all font caches ..."  The date of article is
>>> Mar 13, 2009.  As I stated before, mine is 10.6.6.
>>> 
>>> Another hit was:
>>>   http://hints.macworld.com/article.php?story=20071026081555971
>>> it specifically says, "10.5 Only."  It is different from
>>> the previous one, but slightly messy:
>>>   sudo rm -rf `lsof | grep com.apple.ATS/annex.aux \
>>>     | grep Finder | cut -c 66-139`
>>> 
>>> I didn't try this one because with different rev constants like
>>> 66-139 scare me.  Plus I am happy with X11() and/or adding
>>> Family="sans" in the plot(foo ~ moo). Either is good enough
>>> fix/work-around for me.
>> 
>> Tena,
>> 
>> If it is corrupted font cache, it will probably also bug you elsewhere
>> than in R graphics. I have once solved this problem in my wife's iMac
>> when she was unable to print Word documents from her job. After googling
>> around, I finally used FontBook.app  which is a standard graphical MacOS
>> application installed with your OS in the Applications folder. It was
>> able to find and remove duplicated fonts and check the integrity of the
>> font files. Took some time, but worked.
>> 
>> Cheers, Jari Oksanen
>> 
>>> On 1/19/11 3:22 AM, "Prof Brian Ripley" <ripley at stats.ox.ac.uk> wrote:
>>> 
>>>> Missing labels has been reported several times, and AFAIK has always
>>>> indicated a corrupt font cache (or other problems in the font book).
>>>> There are various ways to repair that, so I'll leave you to Google for
>>>> one.
>>>> 
>>>> On Wed, 19 Jan 2011, Phillip Jardine wrote:
>>>> 
>> 
>> 
>> 
>>> 
>>>>> Tena,
>>>>> 
>>>>> I had the same problem myself a few months ago, when I upgraded to
>>>>> OS X 10.6.5 (from OS X 10.4) I don't know why this happened, but by
>>>>> trial and error I found that putting family = "sans" into the plot
>>>>> command brought back the labels.
>>>>> 
>>>>> Bizarrely though things recently started working normally again,
>>>>> with no updates/upgrades on my part. Strange, eh?
>>>>> 
>>>>> Anyway, try the family = "sans" thing, it might help.
>>>>> 
>>>>> Best wishes,
>>>>> 
>>>>> Phil
>>>>> --
>>>>> Phil Jardine
>>>>> Geosystems Research Group
>>>>> School of Geography, Earth, and Environmental Sciences
>>>>> University of Birmingham
>>>>> Edgbaston
>>>>> Birmingham
>>>>> B15 2TT
>>>>> 
>>>>> pej083 at bham.ac.uk
>>>>> Tel. 0121 414 6146
>>>>> http://www.gees.bham.ac.uk/staff/pgpej083.shtml
>>>>> ________________________________________
>>>>> From: r-sig-mac-bounces at r-project.org [r-sig-mac-bounces at r-project.org] On
>>>>> Behalf Of Tena Sakai [tsakai at gallo.ucsf.edu]
>>>>> Sent: 19 January 2011 04:29
>>>>> To: r-sig-mac at r-project.org
>>>>> Subject: [R-SIG-Mac] plot() does not give labels under quarts.
>>>>> 
>>>>> Greetings,
>>>>> 
>>>>> I have noticed a bit odd behavior of plot() on OS X 10.6.5.
>>>>> The R I downloaded from cran is R-2.12.1.pkg.  Below is
>>>>> what I did:
>>>>> 
>>>>>       R version 2.12.1 (2010-12-16)
>>>>>              .
>>>>>              .
>>>>>       [R.app GUI 1.35 (5665) x86_64-apple-darwin9.8.0]
>>>>> 
>>>>>> foo <- c( 4, 6, 9 ,12 )
>>>>>> moo <- c( 34, 37, 41, 49 )
>>>>>> plot( foo ~ moo )
>>>>> 
>>>>> This gives me a plot with no labels.  No "moo", "foo", or numbers under
>>>>> tics.  But,
>>>>> 
>>>>>> X11()
>>>>>> plot( foo ~ moo )
>>>>> 
>>>>> This gives me xlabel ("moo"), ylabel ("foo"), and numbers under tics.
>>>>> In the first case, by default, I am using quartz, while the second,
>>>>> obviously, I am using X11.
>>>>> 
>>>>> Does anybody know why this happens under quartz and not under X11?
>>>>> 
>>>>> Thank you.
>>>>> 
>>>>> Tena Sakai
>>>>> tsakai at gallo.ucsf.edu
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
>