Re: [Rd] R Cocoa GUI 1.12 (R 2.1.1 Framework) crashes on acf() (PR#8032)

2005-07-25 Thread stefano iacus
can you send us the crash report? I cannot reproduce it.
stefano

On 25/lug/05, at 02:34, [EMAIL PROTECTED] wrote:

> After I upgraded my installation of R for OS X (Tiger) to 1.12, it
> consistently crashes when calling the function acf() [stats lib].
>
> Roberto Osorio
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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Re: [Rd] Buglet in src/appl/splines.c (PR#8030)

2005-07-25 Thread maechler

> "BeT" == Berwin A Turlach <[EMAIL PROTECTED]>
> on Sun, 24 Jul 2005 16:24:51 +0200 (CEST) writes:

BeT> I was looking at "splinefun" and the underlying C code
BeT> and believe that there is a memory access error in the
BeT> C routine "spline_eval".

...
...

Excellent, Berwin!

Specifically the part about why the bug never really triggers
wrong behavior.
Your mail should be saved in  "The Annals of R"  ...

I'm fixing according to your proposal -- for "R-devel" or
(SVN) R/trunk/ only.

Martin Maechler, ETH Zurich

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[Rd] density() fails if x contains Inf or -Inf (PR#8033)

2005-07-25 Thread michael . beer
Full_Name: Michael Beer
Version: 2.1.0 and 2.1.1
OS: linux-gnu and mingw32
Submission from: (NULL) (134.21.49.141)


The command "density(c(0.5,0.6,Inf,0.7))" fails saying "Wrong type for argument
2 in call to massdist". This problem can be resolved by replacing "nx = nx" by
"nx = as.integer(nx)" in the call to massdist. When there are infinite values,
the value of sum(x.finite) is attributed to nx before. Thus nx is changed to
class "numeric" instead of "integer".

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Re: [Rd] Buglet in src/appl/splines.c (PR#8030)

2005-07-25 Thread Torsten Hothorn

On Mon, 25 Jul 2005 [EMAIL PROTECTED] wrote:

>
> > "BeT" == Berwin A Turlach <[EMAIL PROTECTED]>
> > on Sun, 24 Jul 2005 16:24:51 +0200 (CEST) writes:
>
> BeT> I was looking at "splinefun" and the underlying C code
> BeT> and believe that there is a memory access error in the
> BeT> C routine "spline_eval".
>
> ...
> ...
>
> Excellent, Berwin!
>
> Specifically the part about why the bug never really triggers
> wrong behavior.
> Your mail should be saved in  "The Annals of R"  ...
>

the next version of the `fortunes' package will have

R> fortune(134)

Excellent, Berwin!
Specifically the part about why the bug never really triggers wrong
behavior. Your mail should be saved in `The Annals of R' ...
   -- Martin Maechler (after Berwin A Turlach reported a buglet in
  `spline_eval')
  R-devel (July 2005)

Best,

Torsten

> I'm fixing according to your proposal -- for "R-devel" or
> (SVN) R/trunk/ only.
>
> Martin Maechler, ETH Zurich
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

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[Rd] Rmath library problems

2005-07-25 Thread Anders Brix Jensen
Hello,

Has anybody successfully called the Rmath library from C using the MS 
Visual Studio compiler (I am using Visual Studio 6.0)?

I have compiled the Rmath library using gcc, and the 'test.c' program 
(which makes a call to qnorm) works fine when compiled with gcc. However, 
I get a fatal memory error when I run it after compiling it with Visual C.
Would this memory problem be related to the compiler, or is it because I 
have not used the right compiler and/or linker options?

Two things puzzles me regarding compilation of Rmath:
1) The gcc compiler only seems to need the Rmath.dll to compile and 
execute. It needs neither Rmath.a nor Rmath.def.
2) The VC compiler needs a '.a'-file, but Rmath.a does not work (cannot 
find the symbols isnan and expm1). It compiles fine with libRmath.a 
however, but then it crashes as mentioned above.

Can anyone explain this to me?


Thanks,

Anders



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Re: [Rd] Rmath library problems

2005-07-25 Thread Prof Brian Ripley
On Mon, 25 Jul 2005, Anders Brix Jensen wrote:

> Has anybody successfully called the Rmath library from C using the MS
> Visual Studio compiler (I am using Visual Studio 6.0)?
>
> I have compiled the Rmath library using gcc, and the 'test.c' program
> (which makes a call to qnorm) works fine when compiled with gcc. However,
> I get a fatal memory error when I run it after compiling it with Visual C.

What is `it'?  No interpretation I can make quite corresponds to the later 
comments.

> Would this memory problem be related to the compiler, or is it because I
> have not used the right compiler and/or linker options?

Probably the last.

> Two things puzzles me regarding compilation of Rmath:
> 1) The gcc compiler only seems to need the Rmath.dll to compile and
> execute. It needs neither Rmath.a nor Rmath.def.

> 2) The VC compiler needs a '.a'-file, but Rmath.a does not work (cannot
> find the symbols isnan and expm1). It compiles fine with libRmath.a
> however, but then it crashes as mentioned above.

These are actually statements about the linkers when linking against 
Rmath.dll, and not about compiling Rmath.  You should be linking a main 
function compiled under VC++ against a VC++ import library (which you can 
make from Rmath.def by lib /def:Rmath.def /out:Rmath.lib).  Then

cl /MT /Ox  /I..\..\include test.c Rmath.lib

works for me without any errors.

You can find all the background and hints in README.packages.

-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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Re: [Rd] R Cocoa GUI 1.12 (R 2.1.1 Framework) crashes on acf() (PR#8032)

2005-07-25 Thread stefano iacus
Hi Robert,
I'm following this to r-sig-mac and r-devel.
Btw, you said "any"  but do you have any chuck of R code to test as  
well?
example(acf) works for me.
stefano


On 25/lug/05, at 09:47, Roberto Osorio wrote:

> On 7/25/05 12:04 AM, "stefano iacus" <[EMAIL PROTECTED]> wrote:
>
>
>> can you send us the crash report? I cannot reproduce it.
>> stefano
>>
>> On 25/lug/05, at 02:34, [EMAIL PROTECTED] wrote:
>>
>>
>>> After I upgraded my installation of R for OS X (Tiger) to 1.12, it
>>> consistently crashes when calling the function acf() [stats lib].
>>>
>>> Roberto Osorio
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>>>
>>
>>
>
> Here it is. Thanks for looking at it.
>
> Roberto
>
> ---
>
> Date/Time:  2005-07-25 00:43:32.718 -0700
> OS Version: 10.4.2 (Build 8C46)
> Report Version: 3
>
> Command: R
> Path:/Applications/R.app/Contents/MacOS/R
> Parent:  WindowServer [60]
>
> Version: 1.12 (1622)
>
> PID:4330
> Thread: 0
>
> Exception:  EXC_BAD_ACCESS (0x0001)
> Codes:  KERN_INVALID_ADDRESS (0x0001) at 0xfdc07000
>
> Thread 0 Crashed:
> 0   libBLAS.dylib  0x923fca6c ATL_thread_init + 64
> 1   libBLAS.dylib  0x923f137c ATL_dptgemm + 200
> 2   libBLAS.dylib  0x91e7f548  
> atl_f77wrap_dgemm__ + 104
> 3   libBLAS.dylib  0x91e7e72c dgemm_ + 704
> 4   libR.dylib 0x00214b8c matprod + 548
> (array.c:412)
> 5   libR.dylib 0x00215418 do_matprod + 944
> (array.c:632)
> 6   libR.dylib 0x00263b24 Rf_eval + 1536
> (eval.c:405)
> 7   libR.dylib 0x00265b1c do_set + 224  
> (eval.c:1309)
> 8   libR.dylib 0x00263970 Rf_eval + 1100
> (eval.c:382)
> 9   libR.dylib 0x002652a4 do_begin + 136
> (eval.c:1058)
> 10  libR.dylib 0x00263970 Rf_eval + 1100
> (eval.c:382)
> 11  libR.dylib 0x00263970 Rf_eval + 1100
> (eval.c:382)
> 12  libR.dylib 0x002652a4 do_begin + 136
> (eval.c:1058)
> 13  libR.dylib 0x00263970 Rf_eval + 1100
> (eval.c:382)
> 14  libR.dylib 0x00263fc0 Rf_applyClosure +  
> 952
> (eval.c:576)
> 15  libR.dylib 0x00263b9c Rf_eval + 1656
> (eval.c:417)
> 16  libR.dylib 0x00265b1c do_set + 224  
> (eval.c:1309)
> 17  libR.dylib 0x00263970 Rf_eval + 1100
> (eval.c:382)
> 18  libR.dylib 0x002652a4 do_begin + 136
> (eval.c:1058)
> 19  libR.dylib 0x00263970 Rf_eval + 1100
> (eval.c:382)
> 20  libR.dylib 0x00263fc0 Rf_applyClosure +  
> 952
> (eval.c:576)
> 21  libR.dylib 0x00263b9c Rf_eval + 1656
> (eval.c:417)
> 22  org.R-project.R0x00014ff0  
> RGUI_ReplIteration + 500
> (crt.c:300)
> 23  org.R-project.R0x00014de0 RGUI_ReplConsole  
> + 148
> (crt.c:300)
> 24  org.R-project.R0x00014d34  
> run_REngineRmainloop + 156
> (crt.c:300)
> 25  org.R-project.R0xe1b4 -[REngine  
> runREPL] + 76
> (crt.c:300)
> 26  com.apple.Foundation   0x9287fcfc __NSFireTimer + 116
> 27  com.apple.CoreFoundation   0x9075edb0  
> __CFRunLoopDoTimer + 184
> 28  com.apple.CoreFoundation   0x9074b728 __CFRunLoopRun +  
> 1680
> 29  com.apple.CoreFoundation   0x9074acdc  
> CFRunLoopRunSpecific + 268
> 30  com.apple.HIToolbox0x93123be0  
> RunCurrentEventLoopInMode
> + 264
> 31  com.apple.HIToolbox0x93123274  
> ReceiveNextEventCommon +
> 380
> 32  com.apple.HIToolbox0x931230e0
> BlockUntilNextEventMatchingListInMode + 96
> 33  com.apple.AppKit   0x9361e1a4 _DPSNextEvent + 384
> 34  com.apple.AppKit   0x9361de68 -[NSApplication
> nextEventMatchingMask:untilDate:inMode:dequeue:] + 116
> 35  com.apple.AppKit   0x9361a3cc -[NSApplication  
> run] + 472
> 36  com.apple.AppKit   0x9370ac1c NSApplicationMain  
> + 452
> 37  org.R-project.R0x2dd0 _start + 392  
> (crt.c:267)
> 38  dyld   0x8fe01048 _dyld_start + 60
>
> Thread 1:
> 0   libSystem.B.dylib  0x9001efec select + 12
> 1   org.R-project.R0x435c -[RController  
> readThread:]
> + 524 (crt.c:300)
> 2   com.apple.Foundation   0x9287cf34  
> forkThreadForFunction +
> 108
> 3   libSystem.B.dylib  0x9002c3d4 _pthread_body + 96
>
> Thread 2:
> 0   libSystem.B.dylib  0x9004ca38  
> syscall_thread_switch + 8
> 1   com.apple.Foundation   0x92895330 +[NSThread
> sleepUntilDate:] + 152
> 2   com.apple.AppK

[Rd] Solaris Installation assstance

2005-07-25 Thread Givens, Jimmie D.
If anyone has suggestion as to the resolve for the problem described
below, your assistance is needed and will be greatly appreciated.

After repeated attempts to install R on a Sun Micro System Sunfire 480
with Solaris 2.8 OS (Unix), I have not been successful in completing the
installation of R v2.1.1 nor the earlier versions? At the close of 
the "make" command error codes 255 and 1 occur.

Make: Fatal error: command failed for target 'libbz2.a' 
   Working directory /usr/local/R-2.1.1/src/extra/bzip2

Make: Fatal error: command failed for target 'R'
   Working directory /usr/local/R-2.1.1/src/extra/bzip2

Make: Fatal error: command failed for target 'R'
   Working directory /usr/local/R-2.1.1/src/extra/bzip2

Make: Fatal error: command failed for target 'R'
   Working directory /usr/local/R-2.1.1/src/extra

Make: Fatal error: command failed for target 'R"
   Working directory /usr/local/R-2.1.1/src



Jimmie Givens
Centers for Disease Control
3311 Toledo Road, Rm 3223
Hyattsville, Maryland 20782

Phone:  301.458.4236
Fax:   404.929.2801


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Re: [Rd] Solaris Installation assstance

2005-07-25 Thread Prof Brian Ripley
We need to see what happened prior to that message: plaes give the 
previous 20 lines of output.

We do know R 2.1.1 works on Solaris 2.8 out of the box: the see the 
comments in the R-admin manual.  For example, what compilers are you 
using? What make?

On Mon, 25 Jul 2005, Givens, Jimmie D. wrote:

> If anyone has suggestion as to the resolve for the problem described
> below, your assistance is needed and will be greatly appreciated.
>
> After repeated attempts to install R on a Sun Micro System Sunfire 480
> with Solaris 2.8 OS (Unix), I have not been successful in completing the
> installation of R v2.1.1 nor the earlier versions? At the close of
> the "make" command error codes 255 and 1 occur.
>
> Make: Fatal error: command failed for target 'libbz2.a'
>   Working directory /usr/local/R-2.1.1/src/extra/bzip2
>
> Make: Fatal error: command failed for target 'R'
>   Working directory /usr/local/R-2.1.1/src/extra/bzip2
>
> Make: Fatal error: command failed for target 'R'
>   Working directory /usr/local/R-2.1.1/src/extra/bzip2
>
> Make: Fatal error: command failed for target 'R'
>   Working directory /usr/local/R-2.1.1/src/extra
>
> Make: Fatal error: command failed for target 'R"
>   Working directory /usr/local/R-2.1.1/src
>
>
>
> Jimmie Givens
> Centers for Disease Control
> 3311 Toledo Road, Rm 3223
> Hyattsville, Maryland 20782
>
> Phone:  301.458.4236
> Fax:   404.929.2801
>
>
>   [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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[Rd] Vector of S4 Objects

2005-07-25 Thread Paul Roebuck
Can someone show me how to create a vector of S4 objects
or point me to an example?

Reading Green Book 7.1.5 to me implied I could simply add
"vector" to my object's representation. But it also implied
that would have no change to the implementation of my class,
but I did find a .Data slot defined afterwards (as though
I had used "structure" instead). But I possibly just
misunderstood that section.

Given the following example class:

require(methods)
setClass("Foo",
 representation(id = "character",
x = "integer",
y = "integer"))
Foo <- function(id = "", x, y) {
new("Foo",
id = id,
x = as.integer(x),
y = as.integer(y))
}

Would prefer to internalize such that "Foo" contained
a vector of its representation but something like this
would be a compromise if that's easier to implement.

foo.vec <- vector("Foo", 2)
foo.vec[1] <- Foo("first",1,2)
foo.vec[2] <- Foo("second",3,4)


TIA

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[Rd] error in text.default (PR#8034)

2005-07-25 Thread zac
Full_Name: roger newton
Version: 2.1.1
OS: SuSe linux 9.2
Submission from: (NULL) (80.176.228.157)


> data(trees)
> plot(trees)
Error in text.default(x, y, txt, cex = cex, font = font) : 
X11 font at size 16 could not be loaded


Attempting to plot dataframe trees fails with error message as shown. 

Get similar message (but font size 22) when run demo(graphics).

Got same error with rpm of R from CRAN linux/SuSe/9.2 (with and without latest
patch) and with downloaded and compiled source code from CRAN (with and without
latest patch).

Is problem with R or fonts on my PC? Windows 2000 version of R on another
machine works OK

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[Rd] beginner finds a bug - crash induced. (PR#8035)

2005-07-25 Thread sholland
Full_Name: Stephen Holland M.D.
Version: 2.1.1
OS: Mac OS X
Submission from: (NULL) (67.184.33.112)


I did a bunch of stuff, then did in sequence:

> state <- c("tas", "sa",  "qld", "nsw", "nsw", "nt",  "wa",  "wa",
+   "qld", "vic", "nsw", "vic", "qld", "qld", "sa",  "tas",
+   "sa",  "nt",  "wa",  "vic", "qld", "nsw", "nsw", "wa",
+   "sa",  "act", "nsw", "vic", "vic", "act")
> factor(state)
 [1] tas sa  qld nsw nsw nt  wa  wa  qld vic nsw vic qld qld sa  tas sa  nt  wa

[20] vic qld nsw nsw wa  sa  act nsw vic vic act
Levels: act nsw nt qld sa tas vic wa
> table(state)
state
act nsw  nt qld  sa tas vic  wa 
  2   6   2   5   4   2   5   4 
> barplot(table(state))

And then boom goes the dynamite.

Doing these steps again did not reproduce the error.

Steve Holland  [EMAIL PROTECTED]

Crash report follows:

Date/Time:  2005-07-25 21:19:23 -0500
OS Version: 10.3.9 (Build 7W98)
Report Version: 2

Command: R
Path:/Applications/R.app/Contents/MacOS/R
Version: 1.12 (1622)
PID: 639
Thread:  0

Exception:  EXC_BAD_ACCESS (0x0001)
Codes:  KERN_PROTECTION_FAILURE (0x0002) at 0x

Thread 0 Crashed:
0   libR.dylib  0x010665c8 Rf_eval + 0xa4 (eval.c:300)
1   libR.dylib  0x0103b218 R_run_onexits + 0xd4 (context.c:142)
2   libR.dylib  0x01063eb4 jump_to_top_ex + 0x260 (errors.c:682)
3   com.apple.AppKit0x92fda908 -[NSToolbarButton sendAction:to:] +
0x4c
4   com.apple.AppKit0x92fda8a8 -[NSToolbarButton sendAction] + 0x50
5   com.apple.AppKit0x92f5a70c -[NSToolbarItemViewer mouseDown:] +
0x674
6   com.apple.AppKit0x92eb2a24 -[NSWindow sendEvent:] + 0x10e4
7   com.apple.AppKit0x92ea50d0 -[NSApplication sendEvent:] + 0xebc
8   com.apple.AppKit0x92ead500 -[NSApplication run] + 0x240
9   com.apple.AppKit0x92f69bec NSApplicationMain + 0x1d0
10  org.R-project.R 0x2dd0 _start + 0x188 (crt.c:267)
11  dyld0x8fe1a278 _dyld_start + 0x64

Thread 1:
0   libSystem.B.dylib   0x9000b42c select + 0xc
1   org.R-project.R 0x435c -[RController readThread:] + 0x20c
2   com.apple.Foundation0x90a6a510 forkThreadForFunction + 0x6c
3   libSystem.B.dylib   0x90024910 _pthread_body + 0x28

Thread 2:
0   libSystem.B.dylib   0x900127b8 syscall_thread_switch + 0x8
1   com.apple.Foundation0x90a0 +[NSThread sleepUntilDate:] + 0x98
2   com.apple.AppKit0x92e7a880 -[NSUIHeartBeat _heartBeatThread:] +
0x494
3   com.apple.Foundation0x90a6a510 forkThreadForFunction + 0x6c
4   libSystem.B.dylib   0x90024910 _pthread_body + 0x28

Thread 3:
0   libSystem.B.dylib   0x90007878 mach_msg_trap + 0x8
1   libSystem.B.dylib   0x900073f8 mach_msg + 0x38
2   com.apple.CoreFoundation0x901c16e0 __CFRunLoopRun + 0x350
3   com.apple.CoreFoundation0x901c5e6c CFRunLoopRunSpecific + 0x148
4   com.apple.Foundation0x90a2d1b8 -[NSRunLoop runMode:beforeDate:] +
0xac
5   com.apple.Foundation0x90a45dbc -[NSRunLoop run] + 0x4c
6   com.apple.Foundation0x90a98054
+[NSURLConnection(NSURLConnectionInternal) _resourceLoadLoop:] + 0x20c
7   com.apple.Foundation0x90a6a510 forkThreadForFunction + 0x6c
8   libSystem.B.dylib   0x90024910 _pthread_body + 0x28

Thread 4:
0   libSystem.B.dylib   0x90007878 mach_msg_trap + 0x8
1   libSystem.B.dylib   0x900073f8 mach_msg + 0x38
2   com.apple.CoreFoundation0x901c16e0 __CFRunLoopRun + 0x350
3   com.apple.CoreFoundation0x901c5e6c CFRunLoopRunSpecific + 0x148
4   com.apple.Foundation0x90a2d1b8 -[NSRunLoop runMode:beforeDate:] +
0xac
5   com.apple.Foundation0x90a45dbc -[NSRunLoop run] + 0x4c
6   com.apple.Foundation0x90a98594 +[NSURLCache _diskCacheSyncLoop:] +
0xa8
7   com.apple.Foundation0x90a6a510 forkThreadForFunction + 0x6c
8   libSystem.B.dylib   0x90024910 _pthread_body + 0x28

Thread 5:
0   libSystem.B.dylib   0x90007878 mach_msg_trap + 0x8
1   libSystem.B.dylib   0x900073f8 mach_msg + 0x38
2   com.apple.CoreFoundation0x901c16e0 __CFRunLoopRun + 0x350
3   com.apple.CoreFoundation0x901c5e6c CFRunLoopRunSpecific + 0x148
4   com.apple.Foundation0x90a2d1b8 -[NSRunLoop runMode:beforeDate:] +
0xac
5   com.apple.Foundation0x90a45dbc -[NSRunLoop run] + 0x4c
6   com.apple.WebKit0x916eb584 +[WebFileDatabase _syncLoop:] + 0xa8
7   com.apple.Foundation0x90a6a510 forkThreadForFunction + 0x6c
8   libSystem.B.dylib   0x90024910 _pthread_body + 0x28

PPC Thread State:
  srr0: 0x010665c8 srr1: 0x0200f030vrsave: 0x
cr: 0x44044248  xer: 0x0004   lr: 0x0106652c  ctr: 0x01066524
r0: 0x0001   r1: 0xbfffe790   r2: 0x011eb350   r3: 0x
r4: 0x0445f718   r5: 0x01847fb0   r6: 0x   r7: 0x636b0

Re: [Rd] error in text.default (PR#8034)

2005-07-25 Thread ripley
This is not an error in R but in your X11 fonts setup.  It is R reporting 
your configuration problem to you.

What dpi is your screen?  If more than 75dpi (very likely these days), do 
you have 100dpi fonts installed and in your path?  We have seen that 
configuration mistake cause this on SuSe before.

On Tue, 26 Jul 2005 [EMAIL PROTECTED] wrote:

> Full_Name: roger newton
> Version: 2.1.1
> OS: SuSe linux 9.2
> Submission from: (NULL) (80.176.228.157)
>
>
>> data(trees)
>> plot(trees)
> Error in text.default(x, y, txt, cex = cex, font = font) :
>X11 font at size 16 could not be loaded
>
>
> Attempting to plot dataframe trees fails with error message as shown.
>
> Get similar message (but font size 22) when run demo(graphics).
>
> Got same error with rpm of R from CRAN linux/SuSe/9.2 (with and without latest
> patch) and with downloaded and compiled source code from CRAN (with and 
> without
> latest patch).
>
> Is problem with R or fonts on my PC? Windows 2000 version of R on another
> machine works OK


-- 
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595

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