gmane.comp.lang.r.mac

history & comments behaviour

Peter Dixon — 2012-05-23T20:36:59

Hi -
I want to embed comments in the history file using "#". However, if I have "Cleanup history entries" checked in the GUI preferences, the "#" is stripped from the entry so that, for example, if I type "# this is a comment" and then up-arrow, " this is a comment" is added to the console without the hash. On the other hand, if I uncheck "Cleanup history entries," then lines retrieved from the history seem to have an return at the end (which generates extra blank lines when these entries are executed). I'm thinking that this behaviour might be a bug since it did not occur with the last version I was using (R.14.0, R.app GUI 1.42 (5933)). I observed this with a fresh install of R 2.15.0, R.app GUI 1.51 (6148), but maybe there's something funny about my configuration that's tickling the latest v
 ersion?

R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  gr

Trouble installing rgdal --- libcurl.4.dylib

de Larminat, Pierre — 2012-05-18T16:34:39

Hello everyone,

I have trouble installing the rgdal package.
I run R 2.15.0 on Mac OS 10.6.8.

I followed the instructions given by Roger Bivand, who develops rgdal and ran:
--- SVP sélectionner un miroir CRAN pour cette session ---
essai de l'URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15/rgdal_0.7-8.tgz'
Content type 'application/x-gzip' length 13810017 bytes (13.2 Mb)
URL ouverte
==================================================
downloaded 13.2 Mb

It seemed to be OK, but when I try to call rgdal, I get:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgdal/libs/i386/rgdal.so':
  dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgdal/libs/i386/rgdal.so, 6): Library not loaded: /usr/lib/libcurl.4.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgdal/libs/i386/rgdal.so
  Reason: Incompatible library version: rgd

.First for R.app called twice?

R. Michael Weylandt — 2012-05-16T17:10:24

Suppose I have the following very simple ~/.Rprofile

.First <- function(){
    assign("e", exp(1), .GlobalEnv)
    lockBinding("e", .GlobalEnv)
}

If I start R from the terminal, all is fine, but if I use R.app this
throws an error about not being able to change the assigned value of a
locked binding on "e". This makes me think that R.app hits .First()
twice -- is that the intended behavior? [You can demonstrate this with
cat() statements more directly, but I figured I'd show a use case]

I don't have access to another computer right now to confirm, but the
difference between Terminal and R.app seems funny. If it seems to be a
problem with my machine, I'll hunt further.

Thanks,
Michael

R.app ''crashing'' when trying to install bioconductorpackages

Federico Calboli — 2012-05-10T16:05:25

Hi,

on a R64 R.app [R.app GUI 1.52 (6153) x86_64-apple-darwin9.8.0] the R.app stops responding and has to be force quit if I try to install any Bioconductor package.

sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.15.0



BW

F



--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

FastRWeb Questions

Carl pfisterer — 2012-05-07T17:04:53

I have gotten FastRWeb working on Mac OS X 10.5 but I have a few of questions.  Is it possible to send more than one argument to run(...)?  How would I parse a range sent as an argument (i.e. run(x=1:20))?  Finally, what is the syntax to call the R script from within a PERL script?  I have read Simon's paper at: http://urbanek.info/research/pub/urbanek-iasc08.pdf and it has helped, but I didn't see these particular items addressed.  FastRWeb looks very promising, my current implementation initializes R each time and is a bit slow, I am hopeful this will speed things up a lot. 

-Carl
[[alternative HTML version deleted]]

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac< at >r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

Crash on pasting large amounts of text.

Demitri Muna — 2012-05-02T20:59:37

Hi,

I'm getting a repeatable crash with R64:

R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
[R.app GUI 1.51 (6148) x86_64-apple-darwin9.8.0]

I have two (admittedly long) lines of values where I am creating two arrays. When I have them both in my clipboard and paste them into the console, things work without a problem. If I open a new text document in R and paste the lines, R crashes. The precision in the data is ridiculous, yes (they are output from another program as double precision), but the program probably shouldn't crash in any event. I don't know if a buffer is being exceeded or if it's another problem, but since it's trivially repeatable I thought I'd report it.

To reproduce, copy the entire text block below the divider at the bottom of this email, create a new text document, and paste.

Cheers,
Demitri

---

x = c(2300.2654319061871320,2300.7951485790772495,2301.3249872377800784,2301.8549479103917292,2302.3850306250055837,2302.9152354097309399,2303.4455622926739

Check for R updates… (doesn't visit CRAN)

Timothy Bates — 2012-04-24T14:49:51

hi,
selected Check for R updates from R.app’s Application menu

get:

This version of R is 2.14.1
There is a newer version of R on CRAN which is 2.15.0 
Do you want to visit CRAN now? Y



So, no opening of browser...should this be giving an informative error?

OS X 10.7 Lion "Gotchas"

Richard R. Liu — 2012-05-02T08:57:24

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac< at >r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

png() segfaults inside a parallel::mclapply loop?

Steve Lianoglou — 2012-05-01T16:30:38

Hi,

I can't figure this out -- I have to (slightly different) OSX boxes
running the same version of R that I grabbed from r.research.att.com a
little while ago:

R version 2.15.0 Patched (2012-04-18 r59079)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

Simply calling png() w/in a parallel loop always crashed the
subprocesses on one machine. This code, for example:

library(parallel)
mclapply(1:10, function(i) {
  png(paste("~/tmp/p", i, "png", sep="."))
  plot(1:10)
  dev.off()
}, mc.cores=8)

The error (from each subprocess) is pasted below, however swapping out
the png() call to pdf() works on both.

The machine that png() fails on is a ~ 2008 2x4-core mac pro. The one
that doesn't have a problem is a late 2010 core2duo macbook pro 13"

Both are running OSX.6.8

Anybody else have this problem?

-steve

Error from one process:

 *** caught segfault ***
address 0x108, cause 'memory not mapped'

Traceback:
 1: png(paste("~/tmp/p", i, "png", sep = "."))
 2: FUN(7L[[1L]], ...)
 3: lapply(X = S, FUN = FUN

clearing plot / over plotting of points

jochen laubrock — 2012-04-30T12:40:45

Hello,

points are not completely erased if overplotted in the background color, using points from base graphics. Instead, they leave a faint grey trace, both if running R.app and R in Terminal. Is this intended? What is the proper way to erase a plot if one does not want to create a new plot, which presumably has some overhead in an animation?

Example,  using points:

A <- matrix(rnorm(1000), 500, 2)
plot(range(A), range(A), type="n")
points(A)
points(A[1:250, 1:2], col="white", bg="white")

I'm posting to this list because I have not tested under a different OS.

Jochen

R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lattice_0.20-6 MASS_7.3-17   

loaded via a namespace (and not attached):
[1] grid_2.15.0  tools_2.15.0



PS: Points *are* erased if using image

# using im

Unexpected behavior from sprintf()

Joran Elias — 2012-04-24T20:24:35

I stumbled across this by accident from this StackOverflow question:

http://stackoverflow.com/q/10300325/324364

and a subsequent discussion in the StackOverflow R chat room:

http://chat.stackoverflow.com/transcript/message/3431991#3431991

The issue is the output from the following code:

sprintf('%05s',as.character(1:5))

It appears that when this is run in OS X in either 2.14.2 or 2.15.0, the
output is:

[1] "00001" "00002" "00003" "00004" "00005"

whereas when it is run on other platforms (I saw examples from various
Windows versions and one user on Ubuntu, all using 2.15.0 I believe) you
get:

[1] "    1" "    2" "    3" "    4" "    5"

There was some uncertainty as to which behavior is "expected". Does anyone
have any insight into which behavior is "correct" and whether this is a bug
or not?

- Joran

[[alternative HTML version deleted]]

troubles with tkrplot

Day, Roger S — 2012-04-23T18:00:48

**** Let me give this another try. Still a problem with 2.14.2 ***

Problems with tcl/tk, tkrplot etc, running R.app or R on Lion :


Running the example from tkrplot,
dozens of error messages are generated of the form
1: In plot.xy(xy, type, ...) :
 X11 protocol error: BadMatch (invalid parameter attributes)
2: In plot.xy(xy, type, ...) :
 X11 protocol error: BadMatch (invalid parameter attributes)
3: In axis(side = side, at = at, labels = labels, ...) :
 X11 protocol error: BadMatch (invalid parameter attributes)
etcetera.

My work with tcltk was dormant for a long time ... over a year.
I don't remember these messages before.  Makes me suspect Lion.
I've reinstalled R and tcltk;  no change.

X11 "about" shows "XQuartz 2.6.3 (xorg-server 1.10.3)".
I've tried installing XQuartz 2.7.1, but then R hangs on loading tcltk.
So I reset DISPLAY to ":0" or ":1", and X11 works fine but generates the error messages noted.

The tkrplot example code does work as it's supposed to - the plot updates as one resets the slid

digest.so not found

Marius Hofert — 2012-04-22T18:01:14

Dear Mac expeRts,

I'm working with R-2.15.0 on Mac OS X 10.7.3. I need to install the development
version of ggplot2. This can be done as follows (note that actually some more
things are required, see https://gist.github.com/1150934, but that doesn't play a role here):

,----
| require(devtools)
| dev_mode(TRUE)
| install_github("scales")
| install_github("ggplot2")
`----

When installing ggplot2 (executing the last line), I obtain...

,----
| ...
| * installing *source* package ‘ggplot2’ ...
| ** R
| ** data
| **  moving datasets to lazyload DB
| ** inst
| ** preparing package for lazy loading
| Error in library.dynam(lib, package, package.lib) : 
|   shared object ‘digest.so’ not found
| ERROR: lazy loading failed for package ‘ggplot2’
| * removing ‘/Users/mhofert/R-dev/ggplot2’
| * restoring previous ‘/Users/mhofert/R-dev/ggplot2’
| Error: Command failed (1)
`----

... although the R package digest is installed and locate gave:
/Library/Frameworks/R.framework/library/digest/libs/diges

configuration failed for package ‘rJava’

2012-04-20T18:59:30

I am on a Mac Lion.  sessionInfo() is below my signature.

I attempted to install GGally and its dependencies. This led to the following error:

ERROR: configuration failed for package ‘rJava’

and the following piece of advice:

Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.

So I ran "R CMD javareconf" as root. This seemed to work fine:

BEGIN QUOTE

/Volumes/spin/SoftwareDownload/R> whoami
root
/Volumes/spin/SoftwareDownload/R> R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.6.0_31
Java home path   :
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path: 
JNI linker flags : -framework JavaVM
JNI cpp flags    : -I$(JAVA_HOME)/include

Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

END QUOTE

I closed and reopened R and again attempted

ins

Can R 2.15.0 run on mac with ppc (leopard 10.5.8)

YANG Zhenzeng — 2012-04-20T07:20:39

I installed R 2.15.0 on my old mac (powerbook g4, ppc, leopard 10.5.8), but
when I input an incorrect command, plott() for example, it freezes and must
be forced to quit.

so can it run on a mac with ppc?

YANG Zhen-zeng (Ph.D.)
Economics School, Tianjin University of Finance and Economics.

[[alternative HTML version deleted]]

block selection

holly beale — 2012-04-18T20:48:58

Hi all --

I don't seem to be able to copy blocks of text from R.app anymore. In
the past, I was able to hold down the alt/option key while I selected
a column of text with the mouse. Now the selection reverts to a single
line when I release the mouse.

I'm using R version 2.15.0 (2012-03-30) GUI build 1.51 on OSX 10.6.8.

Thanks in advance for any input, suggestions or confirmation. And
thanks as always to the folks who keep improving R.app.

Holly

xmlTreeParse

John Maindonald — 2012-04-18T01:51:42

I am looking for clues on getting xmlTreeParse(), from the XML package,
working under Lion.  The help page has the note:
'Make sure that the necessary 3rd party libraries are available.'

I take it that these are the libraries that are noted at:
http://www.explain.com.au/oss/libxml2xslt.html

The page does not have any details for anything past Leopard.  Any
comments on what is needed for Lion will be helpful.  I'd been hoping
to run the code for the function wikiStat() that is given at:
http://expansed.com/2011/08/visualising-wikipedia-search-statistics-with-r/

I will be grateful for any clues.

John Maindonald             email: john.maindonald< at >anu.edu.au
phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm

Vignette package 'parallel'?

Marius Hofert — 2012-04-15T07:34:57

Hi,

I couldn't find the vignette for the package 'parallel' (Mac OS X 10.7.3; R
2.15.0). I then tried to (re)install the package (I know I comes with R
natively). I obtained:

,----
| > require(parallel)
| Loading required package: parallel
| > vignette(package="parallel")
| no vignettes found
| > install.packages("parallel", type="source")
| Installing package(s) into ‘/Library/Frameworks/R.framework/library’
| (as ‘lib’ is unspecified)
| Warning: unable to access index for repository http://cran.ch.r-project.org/src/contrib
| Warning: unable to access index for repository http://www.bioconductor.org/src/contrib
| Warning message:
| package ‘parallel’ is not available (for R version 2.15.0) 
| > 
`----

What's wrong? 

Cheers,

Marius

PS: Dirk Eddelbuettel sent me the vignette off-list, I just would like to know
how I could get it via 'vignette(package="parallel")'. 

_______________________________________________
R-SIG-Mac mailing list
R-SIG-Mac< at >r-project.org
https://stat.ethz.ch/mailman/lis

Building binary packages for distribution

Prof Brian Ripley — 2012-04-13T15:36:53

I have hitherto used a Leopard system to build Mac binary packages for 
distribution, but that system has died and we only have Lion systems 
left (and the replacement hardware only runs Lion).  I'm only concerned 
with building i386/x86_64 packages.

We saw problems with packages built on Snow Leopard which would not run 
on Leopard, and the trick was to use -mmacosx-version-min=10.5 for 
compiling and linking.

Does anyone know for certain if that suffices?  And does setting the 
environment variable MACOSX_DEPLOYMENT_TARGET to 10.5 do the same thing? 
  (My man pages suggest so, but I don't trust Apple's documentation to 
be current.)

Brian Ripley

Antw: Re: X11 hangs while plotting from R

Peter Kupfer — 2012-04-12T06:27:19

There all,
well, I have the same problem and X11 show no response at all. I have to quit X11 and R to solve this problem! 
So if I start a second X11 window its not possible for me to plot in or to access this second window
All the best
Peter





This was R started in what way? Console? Terminal? An xterm shell running
under X11?

Command-Tab switches between applications
Command-`   switches between windows within an application

The following applies to R started in a Terminal window.


You have two applications, Terminal, and X11 (though for me it's a Quartz
window, not an X11 window). After dev.new(), X11 has two windows, Terminal
has one window.

When you use Command-Tab to switch back to "X11" you get whichever X11
window is active, namely the second one. Then use Command-` to get to the
original graphics window.

That's what I think is probably going on.