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

[Tena Sakai]

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.  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
>> 
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