Re: [R] history in R.app on Mac

[Rob J Goedman]

If you click on the history icon in the toolbar in R.app you will see  
them. Or up and down arrows.
R.app implements some extra features, such as multiline command  
retrieval.

Through preference settings you can control if you want to see just a  
single ls() or multiple, etc.

Rob

On Jun 11, 2007, at 9:18 AM, Weiwei Shi wrote:

> hi,
>
> I am really confused by history function in R.app for Mac:
>
> Here is some test from command-line:
>> ls()
> character(0)
>> ls()
> character(0)
>> ls()
> character(0)
>> history()
> ls()
> ls()
> ls()
> history()
>
> That is what I expected. But from R.app, it does not show anything.
>
>_
> platform   i386-apple-darwin8.9.1
> arch   i386
> os darwin8.9.1
> system i386, darwin8.9.1
> status
> major  2
> minor  5.0
> year   2007
> month  04
> day23
> svn rev41293
> language   R
> version.string R version 2.5.0 (2007-04-23)
>
> Thanks,
>
>
>
> -- 
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
> __
> R-help@stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide http://www.R-project.org/posting- 
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] New package Ryacas

[Rob J Goedman]

Simon,

 > library(Ryacas)
Loading required package: XML
 > yacas("Integrate(x) x")
[1] "Starting Yacas!"
Accepting requests from port 9734
expression(x^2/2)
 > yacas('Integrate(x) x')
expression(x^2/2)
 > yacas('Integrate(x)x')
expression(x^2/2)
 > yacas('Integrate(x)x;')
CommandLine(1) : Expecting ) closing bracket for sub-expression, but  
got ; instead
 >

The 'Accepting ...' message shows yacas was already running. Which is  
also the case
on your system (hence the socket already in use message). You can  
ignore that.
On Mac OS and I guess several other unix/linux environments, yacas  
will remain
running.

If you leave off the ";", it should work.

As this is quite Ryacas/yacas specific, for future messages I'll  
respond directly.

Regards,
Rob


On Oct 17, 2006, at 1:39 AM, Gabor Grothendieck wrote:

> Maybe there are timing problems using that setup with sockets?  I  
> once tried
> VMware (not with Ryacas but just to try it out) and found it slow  
> as can
> be expected with an emulated environment. Since you have Windows XP  
> just
> use the Windows version of Ryacas directly.
>
> On 10/17/06, Simon Blomberg <[EMAIL PROTECTED]> wrote:
>> Hi Gabor,
>>
>> I'm running Quantian (Debian) inside a VMware virtual machine, on a
>> Windows XP host.
>>
>> I installed the latest version of yacas from the source tarball. I
>> remembered to ./configure --enable-server to allow server  
>> connections.
>> make and make install worked ok, after some fiddling. I checked  
>> that the
>> yacas server option worked, by doing yacas --server , and then
>> telnet'ing to 127.0.0.1  to check. It worked fine. I installed
>> Ryacas. I then tried it out and got the following error:
>>
>>> library(Ryacas)
>> Loading required package: XML
>>> yacas('Integrate(x)x;')
>> [1] "Starting Yacas!"
>> Error in socketConnection(host = "127.0.0.1", port = 9734, server =
>> FALSE,  :
>>   unable to open connection
>> In addition: Warning message:
>> 127.0.0.1:9734 cannot be opened
>>> Accepting requests from port 9734
>>
>> I tried again (stubborn, I guess):
>>
>>> yacas('Integrate(x)x;')
>>  [1] "Starting Yacas!"
>>  Accepting requests from port 9734
>>  YacasServer Could not bind to the socket
>>  : Address already in use
>>  /usr/local/lib/R/site-library/Ryacas/yacdir/R.ys(1) : File not found
>>  CommandLine(1) : Expecting ) closing bracket for sub-expression, but
>> got x instead
>>
>> Any ideas where I may be going wrong? I don't know anything about
>> sockets. I've cross-posted to r-sig-debian. They may be interested.
>>
>> Cheers,
>>
>> Simon.
>>
>> --
>> Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat.
>> Centre for Resource and Environmental Studies
>> The Australian National University
>> Canberra ACT 0200
>> Australia
>> T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au
>> F: +61 2 6125 0757
>> CRICOS Provider # 00120C
>>
>> The combination of some data and an aching desire for
>> an answer does not ensure that a reasonable answer
>> can be extracted from a given body of data.
>> - John Tukey.
>>
>>
>
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Re: [R] problems with R and tckl/tk on Mac OS X

[Rob J Goedman]

Hi John, Alex and Ingo,

Thanks for catching this question. I'd missed Ingo's original email.

Rcmdr does need X.11 and Tcl/Tk, although it uses the versions that  
come with Mac OS 10.4. Hence, as Alex indicates, there is no need to  
separately install these.

Ingo, if you can't get it to work using John's link, let me know  
where you get stuck.  R-Sig-Mac is an alias dedicated to Mac OS  
specific questions.

Regards,
Rob


On Sep 29, 2006, at 8:04 AM, John Fox wrote:

> Dear Alex,
>
> It's possible, though not clear from the original posting, that  
> Ingo is
> trying to install the Rcmdr package. If that's the case, then he  
> might find
> the installation instructions for Mac users at
>  notes.html>
> helpful.
>
> Regards,
>  John
>
> 
> John Fox
> Department of Sociology
> McMaster University
> Hamilton, Ontario
> Canada L8S 4M4
> 905-525-9140x23604
> http://socserv.mcmaster.ca/jfox
> 
>
>> -Original Message-
>> From: [EMAIL PROTECTED]
>> [mailto:[EMAIL PROTECTED] On Behalf Of Alex Brown
>> Sent: Friday, September 29, 2006 8:48 AM
>> Cc: r-help@stat.math.ethz.ch
>> Subject: Re: [R] problems with R and tckl/tk on Mac OS X
>>
>> I assume you are running MacOS X 10.4?
>>
>> The Mac version of R does not require X11 or Tcl/TK since it
>> uses a separate GUI interface developed exclusively for the
>> Mac using native widgets and a quartz based graphing mechanism.
>>
>> Try downloading the following binary installer which includes the gui
>> interface:
>>
>> http://cran.r-project.org/bin/macosx/R-2.3.1.dmg
>>
>> -Alex Brown
>>
>> On 29 Sep 2006, at 08:04, Ingo wrote:
>>
>>
>>> Dear R-help team,
>>> I am trying to run "R" on my Intel-based Mac.  I have installed R,
>>> X11 and Tcl/TK (I thought), but the GUI doesn't run.  My system
>>> administrator doesn't support R and therefore, I'm a little
>> helpless.
>>> What can I do?
>>>
>>> Regards,
>>>
>>> Ingo
>>>
>>>
>>> __
>>> R-help@stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-
>>> guide.html and provide commented, minimal, self-contained,
>>> reproducible code.
>>>
>>
>>
>> On 29 Sep 2006, at 08:04, Ingo wrote:
>>
>>> Dear R-help team,
>>> I am trying to run "R" on my Intel-based Mac.  I have installed R,
>>> X11 and Tcl/TK (I thought), but the GUI doesn't run.  My system
>>> administrator doesn't support R and therefore, I'm a little
>> helpless.
>>> What can I do?
>>>
>>> Regards,
>>>
>>> Ingo
>>>
>>>
>>> __
>>> R-help@stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-
>>> guide.html and provide commented, minimal, self-contained,
>>> reproducible code.
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Statitics Textbook - any recommendation?

[Rob J Goedman]

I would certainly consider the Michael Crawley's: Statistics, an  
introduction using R
(maybe before turning to MASS?).

Rob


On Sep 20, 2006, at 2:09 PM, Berton Gunter wrote:

> Not withstanding Prof. Heiberger's admirable enthusiasm, I think the
> canonical answer is probably MASS (Modern Applied Statistics with  
> S) by
> Venables and Ripley. It is very comprehensive, but depending on your
> background, you may find it too telegraphic.
>
> -- Bert Gunter
> Genentech Non-Clinical Statistics
> South San Francisco, CA
>
> "The business of the statistician is to catalyze the scientific  
> learning
> process."  - George E. P. Box
>
>
>
>> -Original Message-
>> From: [EMAIL PROTECTED]
>> [mailto:[EMAIL PROTECTED] On Behalf Of Iuri Gavronski
>> Sent: Wednesday, September 20, 2006 1:22 PM
>> To: r-help@stat.math.ethz.ch
>> Subject: [R] Statitics Textbook - any recommendation?
>>
>> I would like to buy a basic statistics book (experimental design,
>> sampling, ANOVA, regression, etc.) with examples in R. Or
>> download it
>> in PDF or html format.
>> I went to the CRAN contributed documentation, but there were only R
>> textbooks, that is, textbooks where R is the focus, not the
>> statistics. And I would like to find the opposite.
>> Other text I am trying to find is multivariate data analysis (EFA,
>> cluster, mult regression, MANOVA, etc.) with examples with R.
>> Any recommendation?
>>
>> Thank you in advance,
>>
>> Iuri.
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Problems with OS X R

[Rob J Goedman]

Hi Catherine,

Not sure if you got any answers yet. This is a Mac issue, so a better  
mailing list
is R-SIG-Mac. For now we can take it offline.

Can you tell me how you installed R? What exactly does show up in the  
R Console?

Rob


On Aug 31, 2006, at 5:52 AM, Catherine Carter wrote:

> Hi everyone,
> I hope I'm not repeating someone else, but I am having trouble with
> my R installation on my MacBook with OS X Universal. I get this error
> when R starts up:
>
> 2006-08-30 10:53:50.222 R[1021] *** -[NSBundle load]: Error loading
> code /Users/clc/Library/InputManagers/Smart Crash Reports/Smart Crash
> Reports.bundle/Contents/MacOS/Smart Crash Reports for bundle /Users/
> clc/Library/InputManagers/Smart Crash Reports/Smart Crash
> Reports.bundle, error code 2 (link edit error code 0, error number  
> 0 ())
>
> and this one when I try to update packages.
>
> Error in update.packages(lib = ""/Library/Frameworks/R.framework/
> Resources/library/"",  :
>   object "Library" not found
>>
>
> I have tried deleting all the pieces I could find and re-installing,
> but that didn't seem to work.
> Any suggestions?
>
> Thanks,
> Catherine
>
> -
> Dr. Catherine Carter
> University of Maryland
> Department of Geography
> A Lefrak
> 301.405.4620u
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
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Re: [R] Importing data from clipboard on Mac OSX

[Rob J Goedman]

Hi Rense,

Not sure how robust this is, but maybe to get you started:

In R console:

 > a <- 1:10

Copy that line to or part of it to the clipboard.

 > system("osascript -e 'set y to the clipboard' -e 'tell application  
\"R.app\" to cmd y'")

If course you could use this in an R function. I would opt for using  
a file to read in the data.

As this is Mac specific, maybe a better list is R-SIG-Mac.

Rob


On Aug 26, 2006, at 4:00 PM, Rense Nieuwenhuis wrote:

> Dear R users,
>
> I am trying to get data from the clipboard into R on MacOSX. I tried
> the following, but got an error message:
>
> read.delim("clipboard")
> Error in file(file, "r") : unable to open connection
> In addition: Warning message:
> unable to contact X11 display
>
> Obviously, I'm not running R using X11. I'm wondering, can I import
> data from the clipboard on MacosX?
>
> Thanks in advance,
>
> Rense Nieuwenhuis
>
>> version
> _
> platform   powerpc-apple-darwin8.6.0
> arch   powerpc
> os darwin8.6.0
> system powerpc, darwin8.6.0
> status
> major  2
> minor  3.0
> year   2006
> month  04
> day24
> svn rev37909
> language   R
> version.string Version 2.3.0 (2006-04-24)
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting- 
> guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Matrix binary for Mac OS X

[Rob J Goedman]

Just checked the list from Bristol. Matrix 0.995-11 is on there.

Regards,
Rob

On Jul 13, 2006, at 1:47 AM, A.R. Criswell wrote:

> Hello all,
>
> I can't seem to find package "Matrix" for Mac OS X. The R package
> installer, when pointed to Bristol (UK) does not have Matrix amongst
> its list.
>
> Thank you
>
> __
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Re: [R] R-GUI

[Rob J Goedman]

Hi Scott,

Can you explain a bit further what steps you took to get to where you  
are?

There is a Mac specific mailing list R-SIG-Mac, which might be good  
to ask
Mac specific questions.

Regards,
Rob


On Apr 30, 2006, at 6:09 PM, Scott Cunningham wrote:

> I'm trying to install R-GUI on my Mac OSX, but for some reason it is
> not working.  Anyone with a Mac able to answer why I would be getting
> the following error?  I am currently running Mac OS X 10.4.6, which
> it seems to not be recognizing.
>
> ***
>
> R.app GUI 1.15 for R 2.3.0
> for Mac OS X 10.4.4 and higher
>
> This package contains universal Cocoa-based R GUI for R 2.3.x for Mac
> OS X 10.4.4 (Tiger) or higher.
>
> Requirements:
> - Mac OS X 10.4.4 or higher
> - R framework 2.3.x installed in its default location /Library/
> Frameworks
>
> The application called R will be installed by default in your
> Applications folder, but you can change the location during the
> installation.
>
> This is a universal binary for both PowerPC and Intel based Macs.
>
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Re: [R] R 2.3.0 OS X Binary

[Rob J Goedman]

Hi Joran

Do you possibly have a saved workspace created after loading tcltk?

Rob

On Apr 27, 2006, at 11:15 AM, Joran Elias wrote:

> I downloaded the 2.3.0 OS X Universal binary off of the Berkeley
> mirror (found it on the R for Mac OS X link at the bottom of the
> page).  Installation went fine, but when I launch via the GUI it
> opens the console window and then (after several seconds) quits with
> no error message.
>
> I'm sorry I'm not very proficient with the Terminal, so I don't know
> if I can use R 2.3.0 with that, or if it's only the GUI startup
> that's causing the problem.
>
> I'm using a G4 Powerbook (PowerPC) laptop with OS X 10.4.6.  A
> universal binary ought to work, right?  Or is there something else
> going on?
>
> Just thought I'd let people know...
>
>
> Joran
>
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Re: [R] R for MacOSX - History and command line problems

[Rob J Goedman]

Hi Wiebke,

To figure out what is happening, would you mind sending me:

1)  The exact version of the GUI you are running (the line at the  
bottom of
'About R' , something like: R Cocoa GUI 1.14 (2283), S.M.Iacus &  
S.Urbanek.
would be fine),

2)  Your R plist file (in ~/Library/Prefrences/org.R-project.R.plist),  
and

3)  Your .Rhistory file in the working dir *after closing a session of  
R*.

R-Sig-Mac is a better place to ask specific Mac questions.

Regards,
Rob

On Mar 24, 2006, at 12:59 AM, Wiebke Timm wrote:

> Hi!
>
> I have the following issues using "R for Mac OS X 2.2.1" (from the
> ppc-.dmg) on a Mac OS X 10.4.5:
>
> 1) The command history is never saved (automatically) to .Rhistory.
> (The file stays empty.)
>
> 2) If I save a history to some file via the "Save History" button,
> and I load it afterwards via "Load History", only the first entry of
> the saved History appears in the GUI. But: If I save that (seemingly
> almost empty) history again, the file holds all the entries that
> should have been in the loaded history file before. The loaded
> history can also be viewed with history(). In addition, if I try to
> recall the entries using the up-arrow, _alle the entries_ are
> recalled at once, allthough the history()-function seems to be able
> to consider them as _different_ entries.
>
> 3) Having typed some command and entered it with the return key, if I
> then recall that command via the up-arrow, the line _with an
> additional_ carriage return is recalled. Executing it, results in the
> command and an empty line being entered. (Of course, repeatedly
> recalling the last commands leads to a growing number of returns
> being recalled and entered...) This is quite annoying :(
>
> I'd appreciate any help on this subject!
>
> Ciao!
> Wiebke
>
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Re: [R] R GUI's on a Mac?

[Rob J Goedman]

Hi,

On Mar 14, 2006, at 3:05 AM, Martin Maechler wrote:

> I think for Berton's question, the only necessary step is
>
>  JFox>>> 1) Install X11.app from Apple Install disks (this is a
>  JFox>>> must if you want to use any tcltk-based package with R.app).

The initial step is to make sure that the tcl/tk link is installed  
while installing
R.app on Mac OS. This is possible during the 4th step of installing  
R.app
(select the Customize button that shows up in the lower left corner  
of the
installer window). I typically suggest folks load Fortran as well at  
that point,
same customize screen.

Regards,
Rob

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Re: [R] tcl/tk - Problem unter MacOS X / X11

[Rob J Goedman]

Achim,

For the RGUI part:

Have you installed the required packages for Rcmdr (e.g. abind, car,  
effects, lmtest, multcomp, mvtnorm, relimp, sandwich, strucchange,  
and zoo)?

Rob

On Feb 23, 2006, at 3:01 AM, Achim Kayser wrote:

> Hallo !
>
> Ich habe versucht Rcmdr unter MacOSX 10.4.5 zu installieren. RGui  
> zeigt
> an, dass tcl/tk laufen. Bei Aufruf von Rcmdr friert R jedoch  
> komplett ein.
> JGR zeigt im Paketmanager dagegen an, dass tcl/tk nicht gestartet  
> werden
> konnte und spuckt folgende Meldung aus:
>
>
>> library(tcltk)
> Loading Tcl/Tk interface ... Error in fun(...) : no display name  
> and no
> $DISPLAY environment variable
> Error: .onLoad failed in 'loadNamespace' for 'tcltk'
> Error: package/namespace load failed for 'tcltk'
>>
>
> Ideen ?
>
> Achim
>
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Re: [R] last command history???

[Rob J Goedman]

Thanks David,

I'll have a look at this tomorrow.

A quick check on 10.4/R2.2.1/R Cocoa GUI 1.14 (2217) didn't
reproduce the behavior you described. Can you send me your
plist (~/Library/Preferences/org.R-project.R.plist)?

As this is Mac specific, R-Sig-Mac is a better alias.

Rob


On Feb 8, 2006, at 10:47 AM, David Ruau wrote:

> Hi,
>
> I am using R 2.2.0 on Mac OS X 10.3.9. But I test the issue also  
> with R
> 2.2.1 on OS X 10.4 (Tiger)
> I have a question regarding the functioning of the history from the
> command line.
> When I press the 'up-arrow' I call back the last command (everything
> ok), let's say that I go back until the level n-5, but when I get down
> to return to the empty line, I cannot reach the empty line... The  
> empty
> line 'level' show me the content of the line n-4.
> example, let's say I did this sequence of command:
>> x <- c(1:10)
>> mean(x)
> [1] 5.5
>> sd(x)
> [1] 3.027650
>> x
>   [1]  1  2  3  4  5  6  7  8  9 10
>>
> # If I return to the command 'x <- c(1:10)' and then get down the
> bottom line is :
>> mean(x)
>
> Well it doesn't work like that under Windows and I guess under Linux.
> What is the setting that I should change?
> Or where is the error I made...
>
> David
>
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Re: [R] Previously compilation procedure on Mac OS X no longer works

[Rob J Goedman]

Isaac,

On Mac OS 10. 4.4 with Xcode 2.2 installed, after setting:

sudo gcc_select 3.3, I get:

Robs-Laptop:~ rob$ gcc_select
Current default compiler:
gcc version 3.3 20030304 (Apple Computer, Inc. build 1819)

Robs-Laptop:~ rob$ cd Downloads/
Robs-Laptop:~/Downloads rob$ R CMD INSTALL sigPathway_1.1-0.tar.gz

gzip: sigPathway_1.1-0.tar.gz: decompression OK, trailing garbage  
ignored
* Installing *source* package 'sigPathway' ...
** libs
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c sigPathway.c - 
o sigPathway.o
gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib - 
o sigPathway.so sigPathway.o  -framework vecLib -lcc_dynamic -F/ 
Library/Frameworks/R.framework/.. -framework R
ld: warning multiple definitions of symbol _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition  
of _xerbla_
/Library/Frameworks/R.framework/../R.framework/R(print.lo) definition  
of _xerbla_
ld: warning multiple definitions of symbol _signgam
/Library/Frameworks/R.framework/../R.framework/R(lgamma.lo)  
definition of _signgam
/usr/lib/libSystem.dylib(gamma9.o) definition of _signgam
** R
** data
** help
 >>> Building/Updating help pages for package 'sigPathway'
  Formats: text html latex example
   GenesetsU133a texthtmllatex
   MuscleDatatexthtmllatex
   calcTNullFast texthtmllatex
   calcTStatFast texthtmllatex   example
   calculate.GSEAtexthtmllatex
   calculatePathwayStatisticstexthtmllatex   example
   getPathwayStatistics  texthtmllatex
   rankPathways  texthtmllatex
   runSigPathway texthtmllatex   example
   selectGeneSetstexthtmllatex
** building package indices ...
* DONE (sigPathway)

and

 > library(sigPathway)
 > example(runSigPathway)

rnSgPt> data(MuscleData)

rnSgPt> sf <- apply(MuscleData, 2, mean, tr = 0.025)

... lots more output, seems to work.

R-Sig-Mac might be a better list to ask specific Mac questions.

Rob


> On Fri, 27 Jan 2006, Isaac Kohane wrote:
>
>> Hi,
>>
>>  I was a happy user of Peter Parks' package (see http://www.chip.org/
>> ~ppark/Supplements/PNAS05/) and could compile it without error under
>> Mac OS X 10.4. I then had a disk crash and had to re-install the
>> developer tools and now I get hideous messages such as  the one
>> below. I have tried installing an earlier version of Mac OS X
>> developer tools. No joy, Could anyone put me out of my misery and
>> compile  this code and post the binaries for mac os X so that I can
>> just get back to work? Please? Or is there a surefire way to get the
>> compilation process working again?
>
> One source of information is:
>
> http://wiki.urbanek.info/index.cgi?HomePage
>
> and the R-sig-Mac list
>
>>
>> Thanks in advance.
>>
>>
>> -Zak
>>
>>
>>
>> ld: warning -L: directory name (/usr/local/lib) does not exist
>> ld: can't locate file for: -lcc_dynamic
>> make: *** [sigPathway.so] Error 1
>> ERROR: compilation failed for package 'sigPathway'
>> ** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/
>> library/sigPathway'
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting- 
>> guide.html
>>
>
> -- 
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian  
> School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: [EMAIL PROTECTED]
>
> __
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Re: [R] Tiger Mac stalls running Rcmdr program

[Rob J Goedman]

Hi Maha,

Can you provide me with a bit more info? No need to copy the R Help  
Mailing List for now.

Can you let me know:

1) When you start X11, does the X11 window popup (which I usually  
close immediately)?
2) Can you load library(car) from the R console?
3) Does the Rcmdr window pops up?
4) Any further output on the R console?

Rob


On Nov 25, 2005, at 1:25 AM, Maha Golestaneh wrote:

> I am a Macintosh computer (MAC OS X Version 10.4.3) user.  I would  
> like to
> run R for structural equation modeling and meta-analysis but am having
> difficulty using the Rcmdr interface.
>
> According to the R commander installation notes for Tiger Macs – I  
> need to
> 1) Install X11.app from Apple Install disks – which I have done
> 2) Install R.app – which I have done
> 3) Install binary package rgl from CRAN – which I have done
> 4) Install binary Rcmdr from CRAN – which I have done
>
> I then need to start R and X11 and type library (Rcmdr) in the R  
> console and
> return...
>
> My computer now is stalling (a colored CD spins) meaning possibly  
> it can’t
> run the Rcmdr (R commander) program.  Please help me install this
> successfully. Thank you.
>
> Maha
>
> Maha Golestaneh
> PhD Candidate, Graduate School of Business
> The Woolsack, Pavilion 2, Room 2.20
> University of Cape Town, Woolsack Drive
> Rondebosch, Cape Town South Africa
> [EMAIL PROTECTED]
> [EMAIL PROTECTED]
> H 011-27-21-685-4050 x222
> M 011-27-72-713-0649
>
>
>   [[alternative HTML version deleted]]
>
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Re: [R] R.app window size

[Rob J Goedman]

Jason,

?quartz lists the options, e.g.

quartz(width=6, height=7, pointsize=24)

All from the console.

A better alias for these questions is R-Sig-Mac (r-sig- 
[EMAIL PROTECTED]).

Rob


On Oct 10, 2005, at 7:25 AM, Jason Horn wrote:

> Hi all,
>
> This is a question for any of you who use R.app (OS X).  Is there any
> way to resize the quartz plot window from within R?  I know that you
> can resize the window by dragging the corner of the window, and fro
> the preferences panel.  But is there a way to specify the window size
> from the console?  I want to specify the size of the plot window from
> inside an R function.
>
> Also a related question:  I notice that text does not resize
> proportionately - it stays the same size when you resize the window.
> Can this be controlled from the console as well?  Is there a way to
> make text resize proportionately with window size?
>
> Thanks,
>
> - Jason
>
>
> Jason Horn
> Boston University Department of Biology
> 5 Cumington Street  Boston, MA 02215
>
> [EMAIL PROTECTED]
> office: 617 353 6987
> cell: 401 588 2766
>
>
>
> [[alternative HTML version deleted]]
>
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Re: [R] Installing local packages in R for MacOSX 10.4.2

[Rob J Goedman]

Hi Marije,

When you select the Package Installer, select Local Source Package and
press Install (which is now enabled). This will get you to a Finder  
window
where you can select the source file to install.

Hope this helps,
Rob

PS There is a R-SIG-Mac alias for questions specific to R on Mac OS.


On Sep 23, 2005, at 7:24 AM, Booman, M wrote:

> Dear all,
>
> I have been using R for Windows before but recently switched to  
> Mac. Now I
> am confused about how to install local packages using R 2.1.1. on  
> the Mac.
> I found the menu Packages and Data, and have used it succesfully to  
> install
> CRAN and Bioconductor packages (all binaries) by selecting these
> repositories from the pull-down menu and clicking the Get List button.
> However there is one package from OmegaHat I want to install  
> (Rcurl). Since
> this is not a listed repository in the Install Packages pull-down  
> menu, I
> tried the Other Repository function and entered the URL for the  
> OmegaHat
> page. This doesn't work as R tries to add /PACKAGES to the URL and  
> this is
> apparently not how the OmegaHat site is set up (I tried the same with
> bioconductor's URL and that did work). SO I downloaded the .tar.gz  
> file. I
> remember from my R for Windows there was an option Install Package  
> From
> Local File. But in this version of R for MAC I can't find this. In  
> the R FAQ
> for MAC OSX it says I should choose, in the Install Packages menu, the
> option Local Package from the pull-down menu. But then the Get List  
> button
> is greyed out, and no packages appear in the list. I have tried  
> putting the
> .tar.gz file in several places: in the working directory (/user/ 
> admin in
> this case), in the R-Framework/Resources/Library directory, but  
> never is the
> file listed in the Install Packages menu. I must be doing something  
> wrong
> but don't know what. This is the text from the R FAQ for OSX, which I
> followed:
> "You can also download any other package from the Internet yourself  
> and
> decide to install it from source. In such case select one of the local
> entries in the top left list." (The top left list being the pull- 
> down menu I
> described and the local entries being Local Binary package, Local  
> Source
> Package, and Local Package Directory).
>
>
> Could somebody please help me out?
>
> Best wishes,
> Marije
>
>
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor  
> de geadresseerde(n). Anderen dan de geadresseerde mogen geen  
> gebruik maken van dit bericht, het openbaar maken of op enige wijze  
> verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk  
> gesteld worden voor een incomplete aankomst of vertraging van dit  
> verzonden bericht.
>
> The contents of this message are confidential and only intended for  
> the eyes of the addressee(s). Others than the addressee(s) are not  
> allowed to use this message, to make it public or to distribute or  
> multiply this message in any way. The UMCG cannot be held  
> responsible for incomplete reception or delay of this transferred  
> message.
>
> [[alternative HTML version deleted]]
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Re: [R] Problems with R on OS X

[Rob J Goedman]

Hi Heinz,

Can you send me your version of: '~/Library/Preferences/org.R- 
project.R.plist'?

Most Mac OS questions are posted/answered on R-SIG-Mac.

Thanks,
Rob


On Jul 11, 2005, at 2:42 AM, Heinz Schild wrote:

> I used R on OS X 10.3x quite some time with no serious problems.  
> Sometimes R stopped when I tried to execute a bigger program. After  
> updating to OS X to version 10.4 R worked but I still had the  
> problem with bigger programs. Therefore I re-installed R on top of  
> the existing R version. The installation finished properly but  
> suddenly R did not work. Then I reinstalled OS X 10.4 because I  
> thought some left over registry information from R may caused the  
> problem. R still crashed. I hoped the problem would be overcome  
> with the new R version 1.12. Unfortunately this is not the case.  
> The error report (see appendix) says that Thread 0 crashed.
> What can I do?
> Heinz Schild
>
>
> 
>
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Re: [R] saving in Tiger (Mac users)

[Rob J Goedman]

Fabrice,

Which version of R/R.app are you using? If you're not using the  
latest version (R-2.1.0a.dmg),

can you upgrade and try it again?

Rob

On Jun 1, 2005, at 12:38 PM, Fabrice De Clerck wrote:


Hello-

I am relatively new to the R community and have been playing with  
the program for about a month. Last week I switched my operating  
system to Tiger (Mac OS 10.4). Since then (I think) I have been  
unable to save scripts and get a message as follows in the R console:


2005-06-01 15:27:10.152 R[203] *** -[NSBigMutableString  
writeToFile:options:error:]: selector not recognized [self =  
0x6843d30]
2005-06-01 15:27:10.174 R[203] *** NSTimer discarding exception  
'*** -[NSBigMutableString writeToFile:options:error:]: selector not  
recognized [self = 0x6843d30]' that raised during firing of timer  
with target 11cc230 and selector 'runRELP:'


Does anyone know what I might be doing wrong? or how to fix this  
error?


Thanks!
Fabrice

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Re: [R] Tiger problems

[Rob J Goedman]

Thomas,

This is explained on Simon's R Wiki page ( http://wiki.urbanek.info,  
look under TigeR

and troubleshooting tips).

It'll occur in both R.app and when running R from the terminal.

Rob

On May 31, 2005, at 4:37 PM, Thomas Davidoff wrote:


I get the following when I try to run R from the terminal (I think ok
from the gui, but not what I want to do):

dyld: Symbol not found: __cg_jpeg_resync_to_restart
   Referenced from: /System/Library/Frameworks/
ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/
Versions/A/ImageIO
   Expected in: /sw/lib/libJPEG.dylib

Trace/BPT trap

Any suggestions?  I have installed the latest both from CRAN mirrors
and from Mac.

Thomas Davidoff
Assistant Professor
Haas School of Business
UC Berkeley
Berkeley, CA 94720
phone: (510) 643-1425
fax:(510) 643-7357
[EMAIL PROTECTED]
http://faculty.haas.berkeley.edu/davidoff


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Re: [R] R unable to run on Mac OS 10.4 Tiger

[Rob J Goedman]

Hi Guillaume,

There is a R-SIG-Mac alias where many of these questions are being  
addressed.


The most likely reason is that you have a .RData file around that its  
trying to load.

It might be missing a library or trying to connect to X11.

Can you check for that 1st in a terminal window (ls -lia). Finder  
does not show .xxx files.

If you reply to me, we can take it from there or switch to R-Sig-Mac.

Rob


On May 24, 2005, at 9:05 AM, Guillaume Chapron wrote:


Hello,
I'm running a PB G4 with Mac OS 10.4.1. I have downloaded the  
latest version R-2.1.0a.dmg. It appears that R does not work. It  
launches itself, but the window never gets ready, there is written  
"Loading R..." and a small progress wheel keeps turning indefinitely.

Could someone help or suggest something?
THANKS !!
Guillaume

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Re: [R] installing R and Rcmdr onMacOS 10.3.9

[Rob J Goedman]

Hi John,

It does work on my Mac. I'm helping Karla to get it running on hers.

Rob


On May 23, 2005, at 11:32 AM, John Fox wrote:


Dear Karla,

It's likely that you don't have Tcl/Tk installed on your Mac.

I know that it's possible to get the Rcmdr working on a Mac, but  
that doing
so requires some additional steps. I'm not a Mac user, so I'm  
afraid that I
can't be of much direct help. If someone who's using the Rcmdr on a  
Mac is
willing to prepare notes about how to get it installed and working,  
I'd

gladly post them on my web site.

Regards,
 John


John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox




-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Karla Van  
Meter

Sent: Monday, May 23, 2005 11:43 AM
To: R-help@stat.math.ethz.ch
Subject: [R] installing R and Rcmdr onMacOS 10.3.9

I have been trying to install the new, patched R 2.1.0a along
with the Rcmdr on my mac. I got the basic R package
installed, but in Project Manager, the tcltk package will not  
install.


  When I downloaded the Rcmdr binary package from the
Berkeley site, it did not show up on the package installer
list until a second attempt, but it still does not show up on
the package manager list.

On the package manager list, the tcltk package is listed as
''not installed'. When I click on it to install, it won't. I tried  
the

library(tcltk) command, which failed.

The following is the output from the last command:



library(Rcmdr)


Loading required package: tcltk
Loading Tcl/Tk interface ... Error in dyn.load(x, as.logical(local),
as.logical(now)) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/tcltk/libs/
tcltk.so':
   dlcompat: dyld: /Applications/R.app/Contents/MacOS/R can't open
library: /usr/X11R6/lib/libX11.6.dylib  (No such file or
directory, errno = 2)
Error: .onLoad failed in 'loadNamespace' for 'tcltk'
Error: package 'tcltk' could not be loaded  > library(tcltk)
Loading Tcl/Tk interface ... Error in dyn.load(x, as.logical(local),
as.logical(now)) :
unable to load shared library
'/Library/Frameworks/R.framework/Resources/library/tcltk/libs/
tcltk.so':
   dlcompat: dyld: /Applications/R.app/Contents/MacOS/R can't open
library: /usr/X11R6/lib/libX11.6.dylib  (No such file or
directory, errno = 2)
Error: .onLoad failed in 'loadNamespace' for 'tcltk'
Error: package/namespace load failed for 'tcltk'






I am NOT a developer, but an application-oriented grad student.

I'd appreciate any help that will make Rcmdr work.

Thanks,

Karla Van Meter
tel: 707.765.0420
net: [EMAIL PROTECTED]

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Re: [R] R version 1.9.1

[Rob J Goedman]

Chris,

Try duplicating R.app (select the R.app in Applications and do  
Command-D).
Double click both versions and you have 2 completely separated  
versions of R.

You can drag/place the multiple icons in the dock.

Some issues will show up, e.g. it will use the history from the  
version that was closed

last, both copies will share preferences, etc.

I would be interested why you use this setup (I can think of a few  
reasons), but
would like to understand yours. If you can send these to me directly  
or to the R-SIG-Mac,

that would be appreciated.

Rob

On May 21, 2005, at 3:39 PM, Christopher Wills wrote:

Can anybody help? I have been running multiple programs  
simultaneously in Raqua windows, on Mac OS 10.3 on a G5 dual  
processor Mac, using R version 1.9.1. I rebooted my computer  
recently, and thought that I would upgrade to the latest R at the  
same time. Alas, I find that the newest R does not (so far as I can  
tell) allow multiple Raqua windows. I would like to go back to  
1.9.1, but I have erased the original compressed binary file and it  
has vanished from the official web sites. Does anyone have a binary  
of this version that they can send me? (I have Fetch, if it should  
prove too large.) Alternatively, is there a way to run multiple  
Raqua windows in the newest R?

Many thanks!
Chris Wills
Christopher Wills
Professor of Biological Sciences
University of California, San Diego
La Jolla CA 92093-0116
Phone: 858-534-4113
Fax: 858-534-7108

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Re: [R] R on Macintosh OSX Tiger

[Rob J Goedman]

Dan,
When installing Tiger, libxml.2.2.dylib version 9.0.0 should have been
installed.
Just a guess from my side, but did you update X11 while upgrading to  
Tiger
(you have to select that when the upgrade process shows customize at
the bottom). Did you install the new Xcode version from the u/g cd?

Rob
On May 6, 2005, at 12:39 PM, Dan Kelley wrote:

Hi.  I'm not having any luck installing the binary for the new
Macintosh OS called "Tiger".
I get error messages as below.
Can anyone offer me some advice?  (PS: I checked the bug list first
but a search on "Tiger" turned up nothing so I hope it's OK to post
here.)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
 unable to load shared library '/Library/Frameworks/
R.framework/Resources/library/grDevices/libs/grDevices.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/
libs/grDevices.so, 6): Library not loaded: /usr/lib/libxml2.2.dylib
   Referenced from: /System/Library/Frameworks/AppKit.framework/
Versions/C/AppKit
   Reason: Incompatible library version: AppKit requires version
9.0.0 or later, but libxml2.2.dylib provides version 8.0.0
Loading required package: grDevices
Error in dyn.load(x, as.logical(local), as.logical(now)) :
 unable to load shared library '/Library/Frameworks/
R.framework/Resources/library/grDevices/libs/grDevices.so':
   dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/
libs/grDevices.so, 6): corrupt binary, library ordinal too big
In addition: Warning message:
package grDevices in options("defaultPackages") was not found
Error: package 'grDevices' could not be loaded
Dan E. Kelley, Associate Professorphone:(902)494-1694
Oceanography Department, Dalhousie University   fax:(902)494-2885
Halifax, Nova Scotia mailto:[EMAIL PROTECTED]
Canada B3H 4J1   http://www.phys.ocean.dal.ca/~kelley/Kelley_Dan.html
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Re: [R] Installing sna package on MacOSX

[Rob J Goedman]

Hi Alex,
The binary, from the Mac OS website, works on my system (R-2.1.0):
library(sna)
help(package=sna)
example(bbnam)
I've not tried to install the source version. Let me know if this works 
for you.

Rob
On Apr 28, 2005, at 1:03 PM, Alex Bach wrote:
Hi folks,
I am trying to install the sna package on a MacOS X 10.3.9 and 10.3.4. 
In neither case I have been able to get the R CMD Install command to 
succeed from the Terminal window.
With 10.3.9 I get an error with the Make command, and with 10.3.4 I 
get an error on the Description(???)

Has anyone out there been able to install it successfully on a Mac?
Thanks
Alex
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Re: [R] Installation problem MacOS X

[Rob J Goedman]

Hector,
By application, you mean R or the R + GUI (R.app)?
Please check if you have an existing .RData file in the directory where 
you start R.
If it's R.app and X11 was used when .RData was saved, X11 needs to run 
when the restore takes
place.

Mac OS issues might be better raised on R-SIG-Mac 
([EMAIL PROTECTED]).

Regards,
Rob
On Mar 18, 2005, at 3:16 AM, Hector L. Ayala-del-Rio wrote:
R gurus
   I have tried to install the R 2.0.1 binary for OS X and although 
the installation was successful I can get the application going.  When 
I double click the icon R tries to load (R window shows briefly) and 
it quits immediately.  This behavior was described in this list before 
and nobody found the answer to the problem. If you try to load the x11 
version by typing "R" at the command line it loads up with no problem. 
 This means that the app is partially working and there are no 
permissions issue.  The most interesting thing is if I log to a 
different account (Dummy) and I double click the application it loads 
with no problem.  This makes me think that there has to be some type 
of user specific file or directory that is causing the gui to quit.  
Any suggestions on what file(s) could be affecting R?

Thanks
Hector
**
Héctor L. Ayala-del-Río, Ph.D.
Assistant Professor
Department of Biology
University of Puerto Rico at Humacao
CUH postal station
100 road 908
Humacao, PR 00791
Ph: 787-850- x 9001
Fax: 787-850-9439
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Re: [R] extract rows in dataframe with duplicated column values

[Rob J Goedman]

Tiago,

Assuming the column in x is sorted:

t = which(duplicated(x[, 1]))
x[sort(union(t-1, t)),]

or, if not sorted:

t = which(duplicated(sort(x[, 1])))
x[sort(union(t-1, t)),]

Rob

On Mar 17, 2005, at 6:11 PM, Tiago R Magalhaes wrote:

> Hi
>
> I want to extract all the rows in a data frame that have duplicates
> for a given column.
> I would expect this question to come up pretty often but I have
> researched the archives and surprisingly couldn't find anything.
> The best I can come up with is:
>
> x <- data.frame(a=c(1,2,2,3,3,3), b=10)
> xdup1 <- duplicated(x[,1])
> xdup2 <- duplicated(x[,1][nrow(x):1])[nrow(x):1]
> xAllDups <- x[(xdup1+xdup2)!=0,]
>
> This seems to work, but it's so convoluted that I'm sure there's a
> better method.
> Thanks for any help and enlightenment
>   [[alternative HTML version deleted]]
>
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Re: [R] an R script editor for Mac

[Rob J Goedman]

Hi,
There is also SubEthaEdit, quite an elegant editor with R/S syntax 
highlighting
as 1 of the many available modes.

With AppleScript its easy to sent the edit window, a file, a selection 
etc. to R for
execution.

http://www.codingmonkeys.de/subethaedit/
Rob
On Jan 24, 2005, at 8:41 AM, Paul Roebuck wrote:
Jacques VESLOT wrote:
Could someone please make me know if there is a nice script editor 
available
under Mac, similar to Crimson, that offers R syntax highlighting (and 
pairs
of parentheses underlining) ?
Did you look into BareBone's TextWrangler, 'BBEdit Lite' replacement?
It's now available as free (as in beer) download for 10.3.5+.

I created a quick version of the Codeless Language Module for R
but it's lacking at the moment.
--
SIGSIG -- signature too long (core dumped)
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Re: [R] lattice error

[Rob J Goedman]

I started to notice this when I moved to 1.8.0 and e.g. load MASS.

Rob

On Sunday, October 19, 2003, at 02:31 PM, Martin Wegmann wrote:

Hello,

I tried to open lattice, but I get the following error:

library(lattice)
Error in loadNamespace(i, c(lib.loc, .libPaths()), keep.source) :
package `grid' does not have a name space
Error in library(lattice) : package/namespace load failed

I retyped it after loading grid but the same message appeared.

could it be that it is caused by a recently done update.packages() ?

any idea what might cause this problem?

using

R.version.string
[1] "R version 1.7.1, 2003-06-16"

thanks in advance, Martin

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