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Kasper Daniel Hansen | 7 Aug 19:33

the R help system

I have two things which are either enhancement requests or just me not  
doing the right thing. Both are related to the R help system. My  
examples below are for a S4 class from package Biobase, but it should  
be generally applicable.

1) S4 classes. If I do C-c C-v and try to find the help page on the  
class ExpressionSet, I can get the help page if I type "ExpressionSet- 
class", but not via TAB completion. If I (from the R command prompt)  
type ?"ExpressionSet-class" I get a normal help page buffer, but if I  
do class?ExpressionSet, the help is printed in the R buffer instead of  
its own window.

2) conflicting help pages. If I have two packages, both with a help  
page linking to the same term (an excellent example right now is the  
Bioconductor package "affy" and the help page for image), I used to  
get an annoying tcltk window popping up. It was annoying and slow, but  
worked. Recently I put the following in my Rprofile
   options(menu.graphics = FALSE)
If I now do ?image from an R session, the little selection menu is not  
displayed at the R prompt, but rather in a separate read-only help  
buffer. If I try to do C-c C-v image, the same happens.

Kasper

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xiaopeng hu | 7 Aug 04:25

I can not use install.packages

I use ess and emacs under windows xp.
I use M-x R to start R in ESS.
when I input install.packages("MASS"),
only display
--- Please select a CRAN mirror for use in this session ---,
then nothing happens.

Why? Have you ever happened to this questions?
Thanks

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Patrick Drechsler | 7 Aug 02:42
Face

bug: exclude version control stuff for stable versions

Hi,

trying to update to ess version 5.3.8 and including it in "mysitelisp"
worked fine.  Until I updated my version control repository..

REQUEST: PLEASE refrain from including .svn directories (or other VC
stuff such as .git, .hg, etc) in official RELEASES. The VC stuff is fine
in development.

Cheers,

Patrick

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Kevin Wright | 5 Aug 19:50

Language setting for ESS help buffer

My setup: GNU Emacs 22.2.1 (i386-mingw-nt5.1.2600), ESS 5.3.8, Windows XP

Sometimes in my ESS help buffer I see:

\221Character indices\222

instead of 'Character indices'.

Is this normal? Is there a setting that controls this? I experimented
with MULE settings, but that did not seem to have any effect.

Thanks for any tips,

Kevin

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enno_sandkasten | 31 Jul 11:16

German umlaute in ESS, Emacs & R

Hi list,

I use GNU Emacs 22.2.1 (i386-mingw-nt5.1.2600) of 2008-03-26 on Windows XP and ESS Version 5.3.7, both
downloaded from http://vgoulet.act.ulaval.ca/en/ressources/emacs/, and R version 2.7.1 for Windows.

My problem is that Emacs cannot handle german umlaute as R variable names:

> รค <- 3
Error: unexpected input in "\201"

This does not occur in RGui.exe. I think this is more an emacs than ess problem, but maybe there are any suggestions.

Thanks, Sven

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Rodney Sparapani | 30 Jul 22:25

Re: SAS + SUDAAN + ESS

Ken wrote:
> Hi Rodney,
>
> ESS 5.3.0
>
> I want to run it for the Interactive SAS session.  Could you please tell me how to set it up for the interactive SAS?
>
> Thanks,
> Ken
>   
Hi Ken:

That's a really old version of ESS, but this might work. You don't
mention which
version of SAS that you are using. But, I think the easiest way to fix
this is to
add a -path ... entry to the system sasv9_local.cfg or to your personal
sasv9.cfg
(assuming SAS v. 9). Or you can add that to the ESS variables
inferior-SAS-args.
But, it seems to me that this should be done at the system level. The user
should not have to deal with this complexity.

--

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

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William Knebel | 29 Jul 19:48

transient mark mode

Our group uses emacs+ess to run R on a mac osx server (10.5.4). I have
an unusual issue between two ESS settings.  We standardly set

 transient-mark-mode t

When I use the above setting with

ess-eval-visibly-p nil

the text in emacs get highlighted appropriately use C-x space
and gets submitted properly using C-x c C-x r but the text in the
emacs buffer satys highlighted as though it was never submitted. Is
this an interaction between these two options.  I would to be able to
use these together. We are using R-2.7.1 and ess 5.3.7. 

Bill

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Ken | 29 Jul 20:01

SAS + SUDAAN + ESS


Dear ESS experts,

I am trying to run SUDAAN inside my SAS code.  Without using ESS, I can use the following command to run SUDAAN
correctly in the interactive SAS session:

sas -path /usr/local/SUDAAN_90x/SAS-Callable &

However, I cannot make it work in the SAS session inside XEmacs.  Here are my settings:

;; ESS for SAS
;; (setq inferior-SAS-program-name "/usr/local/bin/sas9")
;'sh default
(setq ess-sas-submit-pre-command "nohup")
;'sh default
(setq ess-sas-submit-post-command "-rsasuser -path /usr/local/SUDAAN_90x/SAS-Callable &")
;'sh example
(setq-default ess-sas-submit-command "/usr/local/bin/sas9")

The SAS works as usual, but it could not find the SUDAAN procedures.  I believe the -path options doesn't work
as I expected.  Could anyone help me with this please?  Many thanks.

Sincerely,
Ken
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David Whiting | 29 Jul 12:16

font-lock problems with sweave

Hi,

I'm getting font-lock problems with sweave documents where some R code
is causing the subsequent latex chunks to all appear in the same font
(no highlighting). It seems to be to do with the number of times the
dollar sign appears. An odd number of occurances in the R code chunk
and all subsequent latex chunks are not highlighted; an even number of
occurances and the subsequent latex chunks are fine. 

I am not sure what I might have done to cause this. Im using the
latest ESS from subversion. Emacs 21.4.1 (ubuntu dapper and ubuntu
hardy). I'm also using auctex.

I don't really understand font-locking and don't recall
mucking about with it. Any ideas how I can track this down and stamp
on it?

Thanks.

David

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Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. 
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Mark Kimpel | 28 Jul 20:42

using ess-emacs to create a script-R.workspace project

I'd like to create some sort of data-structure that contains an R workspace,
the script that generated it (not command history but a source file), and
the sessionInfo() for that session. I'd like to create this from within
ESS-emacs and then be able to load everything with one command. This would
help both with reproducibility of results and with resuming a session.

Is this possible? Wise? Another, better way?

Thanks,
Mark

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Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)

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Dan Davison | 28 Jul 17:13

submit region to R process on stdin

Dear ESS list,

I'm trying to write an elisp function which will transform the current
region into a data frame in R, and call a function with that data
frame as an argument. The motivation was that on the emacs org-mode
(highly recommended!) mailing list, there was a request to create
plots from org-mode's ASCII tables. So far I've come up with the
following, which assumes that region contains csv-format tabular data
and passes it to Rscript on stdin.

(defun r-function-on-region (&optional R-function)
"Convert region to data frame in R and apply a function to this data frame"
  (interactive)
  (unless R-function (set 'R-function "plot"))
  (shell-command-on-region
   (point-min) (point-max)
   (concat "Rscript -e 'X11() ; " R-function "(read.csv(\"stdin\")) ; system(\"sleep 60\")'")))

My first question is, should I be using ESS for this rather than
Rscript? How hard would it be to write an equivalent function, which
passes region to a running R process, which would convert it to a data
frame and pass that data frame to an arbitrary function (defaulting to
'plot'). ess-r-call-fun-with-region-as-input or something. Could
anybody give some pointers on how that would be done?

Secondly, the above defun clearly has some problems, which I'd like to
ask for help on (but I admit aren't strictly related to ESS). I've
added the 'sleep 60' command to make the plot stay around. However
that means that one has to use C-g to get control back to the emacs
process. I tried adding an & to background the shell-command, but that
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