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

Fri Jan 21 10:23:46 CET 2011

Hi,

Oddly when I had this issue I couldn't see any obvious problems on FontBook.app - I only had one Arial, and nothing seemed to be amiss. As I said in a previous message, the problem cleared up on its own, without me knowingly doing anything (i.e. I don't need to use the family = sans trick any more).

Cheers

Phil

> 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
>>>
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>>
>
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