gmane.emacs.ess.general

Re: 2 things I wish ESS would do

Vitalie Spinu — 2008-10-06T08:50:35

Dear ESS Gurus, Sorry for renewing an old thread but the posted question is related to mine: Paul Johnson wrote: A couple of work arounds have been proposed for the above request, mainly creating a temporary transcript buffer foo.Rt, coping the region and applying ess-transcript-clean-region. Wouldn't it be easier if such a buffer exists from the very beginning of the session (say *history*) and all the input commands already cleaned of This "running history" is extremely handy as implemented in Matlab - at any time one can switch there and run/copy any range of lines. For CLI in Linux the solution was proposed here http://wiki.r-project.org/rwiki/doku.php?id=tips:using-cli:history-window To my understanding iESS command history is somewhere in the emacs memory. Is it possible somehow to flush it to an .R buffer and continuously update it? Many thanks, Vitalie. On Wed, 30 Apr 2008 17:56:34 +0200, Paul Johnson gmail.com> wrote: ____________________________________

Re: Process R hangup

karl FORNER — 2008-10-03T14:05:02

Hi I have the last sumo tarball from the xemacs mirror, but it happened with an older version too. The affyPLM is a bioconductor package, you install it with the source("http://bioconductor.org/biocLite.R"), biocListe() way Unfortunately the data file is huge, and I'm not myself a R user, so I could not narrow it to something easily reproducible for outsiders. I'll try to post something testable soon. Thanks for your time Karl ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Re: Process R hangup

Rodney Sparapani — 2008-10-03T13:34:13

Hi Karl: It's a bug, but where is it? Do you have the latest version of the SUMO packages installed? I don't recognize this particular problem, but I have seen other weirdness that can be resolved by updating those. And I don't get one other thing. I installed all R packages, but affyPLM is not here. Is there some non-obvious dependency for this package? Without it, I can't try your example. Rodney ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Process R hangup

karl FORNER — 2008-10-03T12:53:51

Hello, We're experiencing a strange problem here using xemacs + ESS on an Altix with itaniums. When we run via ESS (eval line or eval region) a R command that is not instaneous (say >= 30 seconds), the iESS window freezes with the following error message : "Process R hangup at Fri Oct 3 14:12:19 2008" I have no idea from where it comes "I tried so grep for the word "hangup"in the whole src tree of xemacs, R and ESS without any success. The problem is reproducible with the following commands : library(affyPLM); load("data.affyBatch.rda") data.affyBatch.plm <- fitPLM(data.affyBatch, model=PM~-1+probes+samples); it's the last command the produces the error after a few tens of seconds. The very same commands on another linux box run just fine. Here're the details of the computer : Altix with 1.6 Ghz Itanium 2 cpus, running SUSE LINUX Enterprise Server 9 (ia64) I tried various xemacs 21.4.x versions, including the last one. And two versions of ESS. Someone has any clue of what could cause this problem,

Re: Resume R process after Emacs/ESS crash

William Knebel — 2008-10-02T19:00:31

I am probably missing the point here but we typically use screen on the unix server then start emacs+ESS. This allows you to reconnect to the running emacs+ESS process if the X-window client crashes. However, if the emacs+ESS process itself crashes, I am not sure if there is a way to get the R process "back" in emacs+ESS. Bill On Thu, Oct 02, 2008 at 10:58:43AM -0700, Thomas Lumley wrote: ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Re: Resume R process after Emacs/ESS crash

Thomas Lumley — 2008-10-02T17:58:43

I don't know how you can get it back to iESS. You can send it SIGUSR1 to quit and save its workspace, as long as it is listening to interrupts. -thomas ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Re: Resume R process after Emacs/ESS crash

Rodney Sparapani — 2008-10-01T16:48:15

I've experimented with this. Just make up a dummy job that takes a long time. Then send it various signals to see what happens. I think the two that you are interested in are STOP and CONT, but YMMV. Most likely this would be in a terminal though. Not sure how you could get it back to iESS. ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Resume R process after Emacs/ESS crash

2008-10-01T15:19:38

Hallo, out there! I am running GNU Emacs/ESS on a remote Unix Server using an X Window client on my local Mac OS X system. After the X-Window containing Emacs crashed there's still a R process running doing some heavy computing. How can I resume this R process and catch the results? Can I start Emacs/ESS again and reconnect to this R process? Thanks in advance, Will ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Re: trace(zapsmall, edit=TRUE) problem under ESS?

Sebastian P. Luque — 2008-10-01T03:46:20

Hi Spencer, On Fri, 26 Sep 2008 03:40:50 -0700, Spencer Graves pdf.com> wrote: I don't use XEmacs, but I'll take a stab at it since no XEmacs users have followed up. Are you sure gnuclient was started in your XEmacs session? Looks like your 'editor' option is set to use that. I think a (gnuserv-start) needs to be called in ~/.emacs or whatever XEmacs uses at start-up. gnuclient might need other things to be set up, so check its docs. With the native Emacs server, I have: (server-start) and then in ~/.bashrc: export EDITOR="emacsclient --alternate-editor emacs +%d %s" This is surely different with XEmacs and its gnuclient, and under MS Windows, but hope it provides some hints.

Re: trace(zapsmall, edit=TRUE) problem under ESS?

John Chambers — 2008-09-26T12:06:22

It would help to quote my comment fully enough to make sense: ------------------ Spencer Graves wrote: .... Your example "trace(zapsmall, edit=TRUE)" (p. 70) seems to malfunction under ESS (XEmacs 21.4.20 with ESS 5.3.6, if I understand correctly how to get this information) running Rterm 2.7.2. This has nothing to do with the example or, really, with trace. As ?trace mentions under the "edit" argument, it calls the function edit(), which in turn uses options("editor") to choose an editor. One needs to set the editor to something that works with the GUI you're using (many GUI's do this themselves). I don't use ESS to run examples, but I recollect this question was discussed on the ESS mailing list. ------------------------ John Spencer Graves wrote: ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

trace(zapsmall, edit=TRUE) problem under ESS?

Spencer Graves — 2008-09-26T10:40:50

Hello: I have an ESS problem with an example in Chambers (2008) Software for Data Analysis (Springer, p. 70): He describes using "trace(zapsmall, edit=TRUE)", which gives me the following: > trace(zapsmall, edit=TRUE) Error in edit(name, file, title, editor) : unable to run editor 'gnuclient.exe' I asked John about this. He replied, "I don't use ESS to run examples, but I recollect this question was discussed on the ESS mailing list." If someone can help me with this, it will likely help more than just me, because it will likely go into a script file in the SoDA package, companion to Chambers (2008), following the Bates model in "system.file('scripts', package='nlme')". Thanks, Spencer SESSION INFO: Running ESS 5.3.8 with GNU Emacs 22.3.1 (i386-mingw-nt5.1.2600) of 2008-09-06 on SOFT-MJASON sessionInfo() R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1

ESS newbie - font color blues

Derek Eder — 2008-09-26T10:28:55

Hello, I am an R user migrating from Windows to Linux and have started using ESS (a matter of hours ago). My R style working style leans heavily towards from source files (in one window) and pasting code into R (GUI) for execution. TINN was a good friend in this regard and engrained a heavy reliance on mouse work in me. I.e., highlight --> right click /copy --> right click/paste or highlight --> press button to eval. Working in Xemacs/ESS (under Linux and Windows) has made me feel a little clumsy as I automatically use old habits with no results! May I shamelessly (not having digested the EMACS manual) ask a basic question? (1) ESS (or is it emacs) changes the font color of text between quotation marks to a light grey which strains my eyes enourmously! I have not been able to locate this parameter in the options. Can someone point me in the right direction? (2) C-c copies input ...but what pastes input (analagous to C-v in many applications) ? I understand

Re: the R help system

Spencer Graves — 2008-09-26T00:13:45

ESS locks up on my with "RSiteSearch" (ESS version & session info below). It releases with -g and produces the search. In Rgui, "RSiteSearch('anything')" still works as normally. Sundar Dorai-Raj and I have developed an enhancement to "RSiteSearch" for "restrict='fun'" that returns the results in a data.frame. I've found this to be a very quick way to find functions (or man pages) with certain attributes. Jonathan Baron invited us to add it as an option to RSiteSearch{utils}. However, before we send *.R and *.Rd files to him, I'd like to get it working better under ESS. Thanks, Spencer Graves ########################## For me, the response to requesting help with a conflict (described below) depends on the specific history in that session. I also have another problem with ESS that may be related: SIMPLEST ISSUE: If I try "select.list(letters[1:2])" in a new R session, it locks up. If I do [-g, -c, -c] multiple times, it eventually comes u

Re: the R help system

Spencer Graves — 2008-09-25T02:53:34

For me, the response to requesting help with a conflict (described below) depends on the specific history in that session. I also have another problem with ESS that may be related: SIMPLEST ISSUE: If I try "select.list(letters[1:2])" in a new R session, it locks up. If I do [-g, -c, -c] multiple times, it eventually comes unlocked. After that, if I repeat "select.list(letters[1:2])", it seems to work fine. HELP PROBLEM I get several different responses to a request for help for something with a conflict: Sometimes it locks up. At other times, I've gotten a separate window with a selection box, which I think I should get. More often, I get the list of options in a separate split buffer but with no ability to select which one I want. For example, the "zoo" package has a function "as.zoo.numeric" that masks the function of that name in the "base" package. If I request help('as.zoo.numeric', 'base'), that help page scrolls by in the "*R* *" buffer.

ESS - R freezes on startup error

Pedro Barros — 2008-09-23T09:49:22

Hi All, I am using R version 2.7.2, XEmacs version 21.4 and ESS version 5.3.8, but I've had this behaviour before. Upon starting XEmacs and R, I usually load several functions, using the .Rprofile startup files. Sometimes, there is an error in one of the functions being loaded at this stage (often because they were incomplete from last session), and what happens is that I get an "error Timeout waiting for prompt. Check inferior-ess-prompt or ess-loop-timeout". I started XEmacs with the --debug-init option, but the -debug-init buffer comes completely empty. My problem is that when this happens I lose the R prompt, and I cannot find out how to regain access to R. I tried the C-g suggestion (many times) but it does not work. I would really appreciate any assistance. Pedro

Re: [R] [ess] no waiting after submitting the command

tyler — 2008-09-17T18:11:52

This may be related to something I frequently run into. I'm running a lot of simulations lately, and sometimes I can run the code via ESS, and still continue editing code, reading mail etc. in other Emacs buffers. Other times, Emacs becomes completely unresponsive until the simulation completes. I haven't come up with a reproducible way to produce either behaviour consistently. In other words, I can enter the command to run the simulation directly in the inferior process buffer, or send it from a script file with C-c C-r. In both cases _sometimes_ Emacs locks, but other times it doesn't. On occasion, I'll get a few seconds at the beginning of a simulation where I can still interact with Emacs in another buffer, and then it freezes. This is a separate issue from the execution speed differences associated with C-c C-l vs C-c C-r, which are largely avoidable by using the ess-eval-visibly-p variable. I've been assuming that this problem arises from something in the way Emacs communicates with comint process

Re: [R] [ess] no waiting after submitting the command

Vincent Goulet — 2008-09-17T16:32:26

[Moved to ess-help where this belongs] Le mer. 17 sept. à 02:56, whizvast a écrit : Well, this is not a very accurate description of this issue, but: Have you tried using the Load File command (C-c C-l)? It's an interface to source(), so it does not echo code to the console. It is generally very fast. HTH Vincent ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Re: Emacs 22.3 released

Vincent Goulet — 2008-09-15T16:08:56

I have updated my Modified Emacs for Windows distribution accordingly: http://vgoulet.act.ulaval.ca/en/emacs/ The latest version is now 22.3-modified-1. --- Vincent Goulet, Associate Professor École d'actuariat Université Laval, Québec Vincent.Goulet< at >act.ulaval.ca http://vgoulet.act.ulaval.ca Le mar. 9 sept. à 13:33, Stephen Eglen a écrit : ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

How the right decoding for ess

Ralph Scherer — 2008-09-14T09:37:05

Hello, when I use emacs 22 with ess under Debian Lenny, the R Buffer is not in the right decoding form. I use the german version and the "Umlaute" are not rightly written. How can I change the decoding for that? Bests, Ralph ______________________________________________ ESS-help< at >stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/ess-help

Re: looking for input on possible ess-rdired improvement

A.J. Rossini — 2008-09-14T08:16:35

Erik - I don't know if you fed in the changes, but in general, "JUST DO IT". (applies to ideas, code, changes, etc). That is what version control is for :-). If you ask, you might have to wait until someone actually gets around to responding to the mailing list... On Thu, Jun 12, 2008 at 4:53 AM, Erik Iverson biostat.wisc.edu> wrote:

Emacs 22.3 released

Stephen Eglen — 2008-09-09T17:33:36

Emacs users can get a new release of Emacs today -- nothing major, as this is a bug fix release. (I think most attention will now turn to Emacs 23, which offers antialiased text, at last... I've routinely been using this for several months, and its stable under my usage. See emacswiki.org if you want more info about getting Emacs to use antialiased text.) Stephen ---------------------------------------------------------------------- Subject: Emacs 22.3 released Newsgroups: gnu.emacs.announce To: info-gnu-emacs< at >gnu.org Date: Sat, 06 Sep 2008 12:24:04 -0400 GNU Emacs 22.3 has been released, and is now available at ftp.gnu.org/gnu/emacs/ and the GNU FTP mirrors (see http://www.gnu.org/order/ftp.html). The MD5 check-sum for the source tarball is: aa8ba34f548cd78b35914ae5a7bb87eb emacs-22.3.tar.gz Please send any bug reports to bug-gnu-emacs< at >gnu.org. Within Emacs, you can do this using the command M-x report-emacs-bug. Emacs 22.3 is a bugfix release. ______________________________________________ E