[Orgmode] [babel] writing my .Rprofile in orgmode, issue with emacsclient

[Erik Iverson]

Hello,

In the spirit of the examples of writing your .emacs file in orgmode, I wrote my 
.Rprofile (R's startup file) in orgmode.  I do have one issue where I have no 
idea what is going wrong, and would appreciate any information!

Basic setup, GNU Emacs 23.1, latest git org-mode, running on Linux.  I start 
emacs with emacs --daemon on startup, and always just use emacsclient to do 
everything.  So for my org-mode .Rprofile,

1) I create a ~/.Rprofile.org file that uses org-mode syntax and includes all R 
code in R source blocks that will be tangled into a .Rprofile.R file.

2) In my actual .Rprofile, I have the following, which actually works.  The 
basic idea was taken from 
http://orgmode.org/worg/org-contrib/babel/reference.php#sec-6 .  I simply want 
to tangle the .Rprofile.org file from (1) above into .Rprofile.R and source it. 
I know the lisp isn't as simple as it could be, since I adapted it from the more 
complex setup referenced, but this actually works for me.

#BEGIN .Rprofile
invisible(system("emacsclient -t --eval \"(progn
(add-to-list 'load-path (expand-file-name \\\"~/lisp/org-mode/lisp/\\\"))
(add-to-list 'load-path (expand-file-name 
\\\"~/lisp/org-mode/contrib/lisp/\\\"))
(require 'org)(require 'org-exp)(require 'org-babel)
(mapc (lambda (file)
       (find-file (expand-file-name file \\\"/home/erik\\\"))
       (org-babel-tangle)) '(\\\".Rprofile.org\\\")))\"", intern = TRUE, 
ignore.stderr = TRUE))

source("~/.Rprofile.R")
#END .Rprofile

Then I do 'M-x R' in emacs, and R tangles the org-mode file, sources the result, 
and everything works.  This even works without the '-t' option given above to 
emacsclient.

The problem is when I try to C-c C-c on an R source block in an org-mode file. 
My issue is, that *without* the '-t' option to emacsclient, (-t says it "opens a 
new emacs frame on the current terminal"), org-babel-execute-src-block hangs 
when I press C-c C-c in an R code block using the above setup.  It definitely 
relates to the emacsclient call in my .Rprofile,  because I can simply comment 
that system call out of my .Rprofile and all is well.  If I use :session, 
everything is fine.

The best lead I have is that if I change org-babel-R-evaluate in the following 
way, my setup also works without the -t option:

Give the R call in the following line

(point-min) (point-max) "R --no-save" nil 'replace (current-buffer)))

the --vanilla option.  Obviously this just doesn't run my problematic .Rprofile, 
but the point is that this is the exact location in the chain of calls where 
it's getting 'stuck'.  Emacs just hangs with the 'busy' mouse cursor until I C-g.

If I watch the system process list, the R process does get started, and a new 
(2nd) instance of emacsclient is also started, but it doesn't return.

Like I said, I have 'fixed' this with -t, but I really want to know why it 
wasn't working in the first place, and if this is really a fix.  Notice how I 
have to also ignore.stderr = TRUE in my 'system' R call, because if I don't, all 
my org-babel output contains

#+results:
: emacsclient: could not get terminal name
...further output...

if my source block has :results output as opposed to :results value.

I just don't get why my setup works with M-x R but not with 
org-babel-execute-src-block, there is some interaction between those two and I 
can't see what it is.

Sorry for the long post, I hope my question makes sense!

Best Regards,
Erik Iverson