Boylan, Ross | 23 Jul 07:09 2016
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cannot add bindings to a locked environment

The reason I was trying to set the environment was to get around the following problem.  I was going to  post
this to the R list, but after debugging it I suspect it may be ess-related, and so I'm posting it here.

Sequence
1. start R 3.1 via ESS 16.04 in Emacs 24.4
2.in R, do library(LazarSim)
3. Attempt C-c C-t C-s to set environment, but fail with the previously reported type error.
3. Visit a file and read it in to R via C-c C-l.  The file is in the LazarSim source directory, which is below
the working directory for R.  The file contains code and classes that are not in the installed library loaded
in step 1.
4. Attempt to use those classes:
> sb <- StandBonf(alpha=.1)
 > shortName(sb)
 Error in assign(".SigLength", nsig, envir = env) (from Test.R#13)   
  cannot add bindings to a locked environment

Debugging that error showed the env in the error message was <environment: namespace:LazarSim>

I expected that the file contents of step 3 would end up in the global namespace, and suspect that ESS must
have fiddled things so that's not the case.  Of course, ideally I would like to insert them into the package
namespace, and I thought that was what ESS's developer model was supposed to do.

Here's the file for step 3, minus comments
setClass("AbstractTest", representation=representation(alpha="numeric"))

setGeneric("test", function(self, r, ...) standardGeneric("test"))

setGeneric("shortName", function(self) standardGeneric("shortName"))
setMethod("shortName", c("AbstractTest"),
          function(self) c(class(self)))
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Boylan, Ross | 23 Jul 04:20 2016
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ess-r-set-evaluation-env problems

Using ESS 16.04 from git and emacs 24.4.1 in a text only environment, when I do C-c-C-t C-s or the equivalent
command (see subject) the echo area shows "wrong type argument: stringp, nil".

After toggling on the emacs debugger:
Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  directory-file-name(nil)
  ess-r-package--find-package-path()
  ess-r-package--local-package-info()
  ess-r-package-get-info()
  ess-r--select-package-name()
  ess-r-set-evaluation-env(nil)
  call-interactively(ess-r-set-evaluation-env record nil)
  command-execute(ess-r-set-evaluation-env record)
  execute-extended-command(nil "ess-r-set-evaluation-env")
  call-interactively(execute-extended-command nil nil)
  command-execute(execute-extended-command)

Also, the info documentation seems internally inconsistent; the news indicates using the command above
is the way to go, but (ess)Top > Developing with ESS > ESS developer, section 10.3, seems to have the old
commands, which do not work--or at least C-c C-t C-a gets me the same error.

Ross Boylan
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Stephen Eglen | 17 Jul 16:52 2016
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Off-topic: In praise of github

Hi ESS team,
this is off-topic for ess-help, but I hope still of relevance to the
community:

Ten Simple Rules for Taking Advantage of Git and GitHub

http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004947

The keen reader will see a link to ess-help however (hint "commit early,
commit often").

Stephen

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Ramon Diaz-Uriarte | 9 Jul 02:21 2016
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no syntax highlighting/colors for text between quotes in iESS


Dear All,

Since my last update of ESS (ess-version: 16.04 [elpa: 20160703.731] but
also ESS from git from a few minutes ago: ess-version: 16.04 [git:
eae9e8fc9d8aa02c5831eb357969e66caa8c1e39]) in the iESS buffer text between
quotes is no longer colored. It is in the ESS buffer, though.

If instead of using the above version I use the 16.04 from the tar.gz from
http://ess.r-project.org/index.php?Section=download (ess-version: 16.04
[Released git: cccb9481389b]) I get back the usual (for me) behavior of
having text within quotes with distinct syntax coloring in both the iESS
and ESS buffers.

I can reproduce the above by using ess-site from either one or another
version.

Is this intended? Is there any way to bring back the old behavior?

Best,

R.

--

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
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olpantani | 1 Jul 18:27 2016
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R: Re: M-n s is undefined


I'm also interested in this. I also can send some money or something you're interested in, such as books on
amazon or things like that.

Dironi + tastierina = erroti ortografici

-------- Messaggio originale --------
Da: Paul Johnson <pauljohn32 <at> gmail.com> 
Data:01/07/2016  17:12  (GMT+01:00) 
A: Vitalie Spinu <spinuvit <at> gmail.com> 
Cc: ess-help <at> stat.math.ethz.ch 
Oggetto: Re: [ESS] M-n s is undefined 

Vitalie

I still think you should make some screen casts to show us how this
works for you.  I can't tell in this thread if people are not liking
polymode or they simply don't understand what is necessary to use it.
Others in the list may be like me, long time Emacs users who don't
have time to study up on new features we don't understand.

I'm willing to try anything, if you can help me understand why you do
it that way and how it works for you.

I've quit entirely trying to use Emacs to compile Rmd documents, I
just run commands in the shell. At least I understand how that works.
I know it seems primitive, but I'm not the only one.  We had a visit
from a couple of the well known R programmers two years ago and they
told me they had the same conclusion, it generally always works to run
"R CMD Sweave document.Rnw" in a shell.
(Continue reading)

Riccardo Romoli | 30 Jun 14:51 2016
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ESS Plot from a remote machine

Hi, I get some trouble while I try to use ESS for a remote session via 
tramp. I followed the instruction in the manual section 3.3 but I get 
this error when I try to produce a plot:

========================================
 > plot(1)
Invalid MIT-MAGIC-COOKIE-1 keyError in .External2(C_X11, d$display, 
d$width, d$height, d$pointsize,  :
   unable to start device X11cairo
In addition: Warning message:
In (function (display = "", width, height, pointsize, gamma, bg,  :
   unable to open connection to X11 display ''
 >

========================================

This is my ./ssh/config file:

Host *
Compression yes
CompressionLevel 9
KeepAlive yes

Host erre
      HostName XX.XX.XX.XX
      User erre
      ForwardX11 yes

Host server
      HostName YY.YY.YY.YY
(Continue reading)

Paul Johnson | 28 Jun 20:40 2016
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help.start() locks up Emacs/ESS

I have a new install of Ubuntu 16.04 on a laptop.  I notice a new
problem. Running from ESS *R* help.start() succeeds and browser is
displayed, but after choosing a link on that page (say "Packages")
that the ESS session is essentially dead.  The *R* seems locked

The *R* session looks like this:

>
Making 'packages.html' ... done

And I cannot find a way to recover.

Do you see this as well?

Versions:

Emacs 25.4
ESS  15.09.2-3

I don't know why Ubuntu packaging is staying with last year's ESS,
that's the next problem I have to solve in their setup.  If you know,
let me know...

--

-- 
Paul E. Johnson   http://pj.freefaculty.org
Director, Center for Research Methods and Data Analysis http://crmda.ku.edu

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(Continue reading)

Christopher W. Ryan | 26 Jun 22:43 2016

M-n s is undefined

Hello. I just set up a new computer, running Windows 7 Professional 
64-bit. I installed R 3.3.1, then MikTeX 2.9, then Vince Goulet's 
version of emacs 24.5.1 with ESS. Those are all on drive C:\, a 250 Gb 
solid state drive.  My data files and documents are on drive E:\, a 
terabyte hard drive.

In emacs, when I have an .Rnw buffer open, M-n s  is met with the error 
message in the subject line.

Sweave.sty is in C:\LOCALTEXMF\Tex\latex\Sweave

which I listed as a root in MikTeX Admin.  And I refreshed the FNDB, 
both as a user and as Admin.

How can I get M-n s  (and I assume I'll have a problem with M-P as well) 
recognized as command to sweave my file?

Thanks.

--Chris

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Ramon Diaz-Uriarte | 5 Jun 15:15 2016
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company mode troubles

Dear All,

I just upgraded a bunch of emacs packages (including ESS) and now company
is not working well with R.

With the latest tar.gz (ess-version: 16.04 [Released git: cccb9481389b])
and with the latest from elpa (ess-version: 16.04 [elpa: 20160602.203])
when I start typing, say, "runi" (to get runif as possible completion)

I get the errors:

Company: An error occurred in auto-begin

Company: Back-end (company-R-args company-R-objects :sorted) error
"Symbol's function definition is void: :sorted" with args (ignore-case)

If I then try "?" at the R prompt, I get the error

Symbol's function definition is void: :sorted

If I install (from melpa-stable) v. 15.9 none of those issues arise.

I reinstalled company (even if I've had the same 0.8.12 for the last few
months), but nothing changes. Note that company seems to be working fine in
C++ and text buffers.

Best,

R.
--

-- 
(Continue reading)

Laurent Gatto | 1 Jun 10:52 2016
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fill-paragraph shoudn't break inline R code chunks


Dear all,

Has anybody a suggestion or a solution for avoiding fill-paragraph to
break inline R code chunks when editing Rmd buffers. For example, typing
M-q on this sentence in an Rmd buffer

These data are directly available from the `r Biocexptpkg("pRolocdata")`
package.

produces

These data are directly available from the `r
Biocexptpkg("pRolocdata")` package

which is then simply formatted as inline code, rather then being
executed, as illustrated in the attached screenshot.

Thank you in advance.

Best wishes,

Laurent

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(Continue reading)

Sparapani, Rodney | 24 May 17:28 2016
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Re: [ESS-bugs] \Sexpr



>Footnote: before sending this I made sure to get the latest ESS. On an Xubuntu box I tried 
>the instructions and they just didn't work.  It turns out that I had to remove 
>/usr/share/emacs23/site-lisp/savefile/*ess* before anything would take; until that point 
>it continued to load 13.09-1, the version from the Ubuntu repository.
>   make install:  puts a new one in /etc/share/emacs
>   remove /etc/share/emacs23/ess and /etc/share/emacs23/savefile/*ess*
>   add /etc/share/emacs/site-lisp to my emacs path
>Now I see the new one.
>
>
>Terry T.

Hi Terry:



Not sure about the bug itself.  But, I looked at your installation problem.
And, frankly, I can’t imagine what went wrong.  Here, I don’t have a 
savefile/*ess* nor can I see anyway that make install would create one.

Rodney
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Gmane