gmane.comp.lang.r.mac

Re: history & comments behaviour

Robert J Goedman — 2012-05-23T22:06:56

Peter,

Is it possible you have you have 'Strip comments in history entries' checked as well? 

On my system:

[1] 12

Pressed up-arrow:

[1] 12

Checked 'Strip comments in history entries' and entered:

[1] 12

Pressed up-arrow:

[1] 12

Regards,
Rob

R version 2.15.0 Patched (2012-05-21 r59376)
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     

loaded via a namespace (and not attached):
[1] Rcpp_0.9.10

On May 23, 2012, at 1:36 PM, Peter Dixon <peter.dixon< at >ualberta.ca> wrote:

  version?


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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

Re: Trouble installing rgdal --- libcurl.4.dylib

Simon Urbanek — 2012-05-18T16:57:52

On May 18, 2012, at 12:34 PM, de Larminat, Pierre wrote:


Please wait for the CRAN version, it should be up today or tomorrow. Alternatively you can upgrade you system (we will be removing Leopard support soon anyway). My understanding is that the CRANextras binaries are now cross-compiled, so they don't always work on Leopard anymore.

Cheers,
Simon

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

Re: .First for R.app called twice?

Simon Urbanek — 2012-05-17T01:22:49

On May 16, 2012, at 7:09 PM, R. Michael Weylandt wrote:


No, since the GUI is interactive -- note that the GUI doesn't do anything to the R afterwards. If we did not support changing working directories on document open we could start R without any flags. Another possible "fix" would be to run R with --no-profile and source it by hand, but I already feel bad about the somewhat strange sequence and the user typically wants to run .Rprofile from the home directory and not the dropped one.



The only reason I called it a hack is that we need to store a copy of the first .First so we can compare it after the workspace is loaded. But at least this way .First is guaranteed to run once (unless you change .First in .First() in which case it will still run twice anyway ...) - so it may not be that bad ;).

Cheers,
Simon

Re: .First for R.app called twice?

R. Michael Weylandt — 2012-05-16T23:09:30

On Wed, May 16, 2012 at 3:04 PM, Simon Urbanek
<simon.urbanek< at >r-project.org> wrote:

Thanks for your note, Simon. I think that I understand, but I'll dig
around in the source just to make sure. I'm likely revealing my
ignorance here, but is there any reason one or the other loads
couldn't run as R --vanilla or with the interactive() flag turned off?
[My actual .Rprofile has the whole thing wrapped in
if(interactive()){} to avoid trouble in R CMD .... scenarios] This
might be a nonsense suggestion though -- I don't really use R other
than starting a fresh workspace each time so I've never really thought
through how that would be managed.


Hadn't thought of this -- I'll add it to my .Rprofile


Don't uglify the code base on my account, particularly when such an
easy fix is available and I use the Terminal so much more.

Thanks again,
Michael

Re: .First for R.app called twice?

Simon Urbanek — 2012-05-16T19:04:25


It is somewhere between intention and a bug. It is caused by the necessity of the R.app GUI to deal with launches in a different working directory -- e.g. when you drag a folder on the GUI. Because the GUI has to setup R and start the event loop before it can accept open events it emulates the regular R behavior after receiving the open event by starting R with --no-restore-data first and then loading the workspace "by hand" and running .First(). This is all fine if you use your workspace to populate .First, but if you do that in .Renviron then .First gets called twice: first when R starts without a workspace and then by the GUI because it doesn't know that your .First does not come from the loaded workspace. 

Obviously, an easy work-around is to check with bindingIsLocked().

That said, I have added a very, very ugly hack to work around your case in the GUI.

Cheers,
Simon

.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

Re: FastRWeb Questions

Simon Urbanek — 2012-05-10T23:22:12

On May 10, 2012, at 7:01 PM, Carl pfisterer <carl_pfisterer< at >yahoo.com> wrote:


Even easier is
print "Location: $url\n\n";
but make sure you do NOT print Content-type before that.



Clearly, since all relative paths will be off as you are serving this from a different URL



You should use Cairo instead.

Cheers,
Simon



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Re: FastRWeb Questions

Carl pfisterer — 2012-05-10T23:01:30

I am a web development novice so there is no particular reason it has to be perl other than that is what I started with.  Seemed like an easy way to interface with MySQL and allowed me to execute R scripts as well.  I have figured out one way to execute run() from within perl but it is not elegant, it redirects to the new page entirely instead of showing the plot inline.

my $url = "http://localhost/cgi-bin/R/carls_test?Projects=$Projects&Species=$Species&Year=$Year&Normalize=$normalize&Lag=$lag";
print "<META HTTP-EQUIV=refresh CONTENT=\"0;URL=$url\">\n\n";

I also tried
my $url = "http://localhost/cgi-bin/R/carls_test?Projects=$Projects&Species=$Species&Year=$Year&Normalize=$normalize&Lag=$lag";
my $content = get $url;
die "Couldn't get $url" unless defined $content;
print $content;

This would display the data values and tables inline, but not the images(image not found box).  It seems I can't draw to a png device from within run() so my best/easiest method at the moment is redirecting to the new page.

Re: R.app ''crashing'' when trying to installbioconductor packages

Simon Urbanek — 2012-05-10T16:16:36

On May 10, 2012, at 12:05 PM, Federico Calboli wrote:


Federico,

R.app doesn't crash (you would get a crash report), it simply waits for the install to finish. There is no output and R.app cannot react until the installation has finished. BioC server can have very slow downloads so particularly for larger packages it can take a long time to install.

Cheers,
Simon

Re: R.app ''crashing'' when trying to installbioconductor packages

Federico Calboli — 2012-05-10T16:13:23

mmm, might it be that I get this warning if I istall things with biocLite

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
 
?

BW

F



On 10 May 2012, at 17:05, Federico Calboli wrote:


--
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

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

Re: More FastRWeb questions

Joe Schwab — 2012-05-09T06:34:50

Simon,

Thanks for the help. It was indeed a permissions issue. Thanks for
guiding me in the right direction. Also I will make sure to direct any
future questions to the mailing list you mentioned. Thanks!

Cheers,
Joe

On Tue, May 8, 2012 at 5:15 PM, Simon Urbanek
<simon.urbanek< at >r-project.org> wrote:

Re: More FastRWeb questions

HENRI FLECHNER — 2012-05-08T15:22:31

Hello I have tried as you.
On Mac the way to succeed might be to partition your mac on 2 systems.
The Mac os
The Ubuntu I have tried many attempts.
I decided to work to make sure I use r and r commander
Best Regards
Henri

2012/5/8 Simon Urbanek <simon.urbanek< at >r-project.org>

Re: More FastRWeb questions

Simon Urbanek — 2012-05-08T15:15:31

Joe,

On May 8, 2012, at 8:53 AM, Joe Schwab wrote:




That's entirely irrelevant since FastRWeb doesn't use TCP/IP - make sure you are running the correct Rserve settings which are *not* on port 6311. All you need to do it to use the start script.



You seem to have permission issues on the socket or the FastRWeb directory - check the permissions on
/var/FastRWeb/socket
You should make sure that _www has both read and write access. Remove it before starting if in doubt. If it's not there, make sure that the user under which you run Rserve has write permissions in /vat/FastRWeb. That applies to the other directories as well - it will need write permissions on tmp and _www must be able to read web.R and tmp.

Cheers,
Simon

PS: stats-rosuda-devel is the mailing list for Rserve/FastRWeb questions

Re: FastRWeb Questions

Simon Urbanek — 2012-05-07T23:57:55

On May 7, 2012, at 3:49 PM, Carl pfisterer wrote:


Well, you could get rid of the perl part to start with - FastRWeb automatically maps form entries into run() arguments so you should not need perl at all to process forms. If you still have some logic in perl that you don't want to push to R then your options may be thin -- you could run Rcgi from perl, use AJAX (from a page you generate with perl) or connect to Rserve directly, but I don't have an Rserve perl client, so you'd have to look elsewhere (maybe misappropriating the C++ client or something like that ... however, it should be fairly easy to write perl client for this purpose since you're only interested in strings)

Cheers,
Simon

Re: FastRWeb Questions

Carl pfisterer — 2012-05-07T19:49:55

Thanks Simon, that helps a lot.  With respect to my last question, I have a cgi script that gets user input from a form, then plots the data in R.  What I would like to do is to call run(...) from within the cgi script when the user clicks submit.  

-Carl

________________________________
 From: Simon Urbanek <simon.urbanek< at >r-project.org>

Cc: "r-sig-mac< at >r-project.org" <r-sig-mac< at >r-project.org> 
Sent: Monday, May 7, 2012 9:20 AM
Subject: Re: [R-SIG-Mac] FastRWeb Questions

Carl,

On May 7, 2012, at 1:04 PM, Carl pfisterer wrote:

Yes

typically

http://.../R?x1=1&x2=20

run <- function(x1, x2, ...) {
  x <- seq(as.integer(x1), as.integer(x2))

In theory you could use

http://.../R?x=1:20

run <- function(x, ...) {
  x <- eval(parse(text=x))

but I would not recommend that since it would allow users to inject arbitrary code which is not good for the security ...

What do you mean? R scripts are to be run from R, not perl... You could simply run the Rcgi binary, but I'm not sure where you are he

Re: FastRWeb Questions

Simon Urbanek — 2012-05-07T17:20:17

Carl,

On May 7, 2012, at 1:04 PM, Carl pfisterer wrote:


Yes



typically

http://.../R?x1=1&x2=20

run <- function(x1, x2, ...) {
  x <- seq(as.integer(x1), as.integer(x2))
  
In theory you could use

http://.../R?x=1:20

run <- function(x, ...) {
  x <- eval(parse(text=x))

but I would not recommend that since it would allow users to inject arbitrary code which is not good for the security ...



What do you mean? R scripts are to be run from R, not perl... You could simply run the Rcgi binary, but I'm not sure where you are heading with this ...



It certainly will a there is no startup delay.

Cheers,
Simon

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
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