PowerCut Killed R - is my code retrievable?

On 20/08/2009, at 9:57 AM, Polwart Calum (County Durham and

I've been tweaking code for several days on and off in R, cut and  
pasting in from a text editor (I just leave them open all the  
time).  I think I got something that was usable but then a  
powersurge tripped the fuses and unfortunately the machine I was  
working on doesn't have a UPS.

Does R hold the command data in cache some place?  I've  
purposefully not opened R since the crash so that if it did I don't  
over write it?

I guess what I'm wanting is the equivalent of the linux up arrow  
which repeats the last line.  i know that exists in R but from what  
I recall it didn't work when you close the R session.  Is that  
stored in a hidden file someplace that I could copy?

Its not a huge piece of code or anything - but it was code I  
tweaked over several stages as I'm new to R and so it was part of  
my learning process.

Also - is there a better way for the future?  I know some people  
use IDE's but is that for serious programming or for building a  
small function and tweaking it?

If you've been cut-and-pasting from a text editor, then your commands
*might* be in the file .Rhistory.  Unfortunately this history gets saved
only when you exit R (and by default only when you also say ``yes'' to
saving the workspace) or if you explicitly savehistory().

After a powersurge, the R workspace and history almost surely will  
not be
saved, so it is highly probable that you are SOL.  Unless you closed
the R session (and save the workspace) before the power cut.  Bummer.

Good luck.

	cheers,

		Rolf Turner

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On Wed, Aug 19, 2009 at 10:57 PM, Polwart Calum (County Durham and

I've been tweaking code for several days on and off in R, cut and pasting in from a text editor (I just leave them open all the time). ?I think I got something that was usable but then a powersurge tripped the fuses and unfortunately the machine I was working on doesn't have a UPS.

So you were just using the text editor as a scratch pad, and not
saving it? A half-decent text editor should be saving things to disk
as you go. For example, in emacs, if your emacs dies while editing a
file then when you restart it, it will notice and offer to restore it
from its "restore" file. If you were using emacs you might have files
like #foo.R# which are emacs' auto-restore files. Other editors might
do other things - possibly leaving files in /tmp on a Linux system
(but they might get zapped by a reboot).

Also - is there a better way for the future? ?I know some people use IDE's but is that for serious programming or for building a small function and tweaking it?

Tip #1 is save your text file scratchpads!
 Tip #2 is save your R session regularly (just do 'save.image()' and
it will save your current R session objects in a .RData file)
 Tip #3 is you could use emacs + ESS as an IDE - you run R within
emacs, giving you cut n paste of code, syntax highlighting, session
transcripts, and emacs' protection from data loss on a crash!

Barry

On Wed, Aug 19, 2009 at 10:57 PM, Polwart Calum (County Durham and
Darlington NHS Foundation Trust)<calum.polwart at nhs.net> wrote:

I've been tweaking code for several days on and off in R, cut and
pasting in from a text editor (I just leave them open all the time).
_I think I got something that was usable but then a powersurge tripped
the fuses and unfortunately the machine I was working on doesn't have

a UPS.

 So you were just using the text editor as a scratch pad, and not
saving it? A half-decent text editor should be saving things to disk
as you go. For example, in emacs, if your emacs dies while editing a
file then when you restart it, it will notice and offer to restore it
from its "restore" file. If you were using emacs you might have files
like #foo.R# which are emacs' auto-restore files. Other editors might
do other things - possibly leaving files in /tmp on a Linux system
(but they might get zapped by a reboot).

To follow up on what Barry wrote above: Don't be put off by the
recommendation to use EMACS (which is not to everyone's taste).
I use vim, which does much the same sort of thing: there is a hidden
".whatever.swp" file which contains a back-trackable history of
the editing changes that have been made to the file. So, if you get
a crash, on re-opening the file in vim you are asked if you want to
"recover". The ".swp" file is *not* zapped by a reboot!

But, in any case, it is very wise to frequently and deliberately
save the current state of your file. In vim's command mode, all you
need to do is to type ":w" and it is saved. And to get into command
mode (or make sure that you are in it), just press "<ESC>".
So "<ESC>:w" does it. Takes 0.5 seconds.

Again, what I routinely do (in Linux) when developing R code is to
have two terminal windows open. In one I am running R. In the other,
beside it, I am editing a file of R code. To run code in R that has
been entered in the "code" window, I just highlight it with the
mouse in the "code" window, and then paste it into the "R" window.

This method also has the advantage that it is easy to scroll back
to code entered earlier, and either paste it into the R window,
or copy it down in the "code" window if you want to modify it.
(The "code" window does not have to be a ".R" file to be sourced
by R -- though it may later become one. Its function is to preserve
a trace of what you have done, and make it easy to modify things
until you get what you want).

Ted.

Also - is there a better way for the future? _I know some people use
IDE's but is that for serious programming or for building a small
function and tweaking it?

 Tip #1 is save your text file scratchpads!
 Tip #2 is save your R session regularly (just do 'save.image()' and
it will save your current R session objects in a .RData file)
 Tip #3 is you could use emacs + ESS as an IDE - you run R within
emacs, giving you cut n paste of code, syntax highlighting, session
transcripts, and emacs' protection from data loss on a crash!

Barry

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E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
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Date: 20-Aug-09                                       Time: 00:21:42
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[....]

|> Again, what I routinely do (in Linux) when developing R code is to
|> have two terminal windows open. In one I am running R. In the
|> other, beside it, I am editing a file of R code. To run code in R
|> that has been entered in the "code" window, I just highlight it
|> with the mouse in the "code" window, and then paste it into the "R"
|> window.

It's even easier using ESS -- highlight in your "code" buffer, press
your designated function key and the code will be run in the *R*
buffer -- or you can use another function key to run code line by
line, or, etc. etc.  

I must admit I didn't like Emacs for the first week or so but when I
saw how easy it was to manage code, I decided it was worth the effort
to get used to the strange old paradigm which had been developed
before the invention of the mouse.

I'd also admit that I've seen people do things amazingly quickly using
vi -- despite its strange jumping from command mode to insert mode.

As others have indicated, whatever you use, it makes good sense to
keep a file of the code that you use.  Rerunning is something I do as
a rule, not an exception.  It's particularly useful when follow up
work arrives which can reuse the same code or a slightly modified
version of it.


[...]

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   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
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Also - is there a better way for the future? ?I know some people use IDE's
but is that for serious programming or for building a small function and
tweaking it?

What about a version control system to (locally) save the different
stages of your script files?
(I use git but Subversion (SVN) may be easier and do the job).

Cheers,
Hans-Peter

Rolf Write:

If you've been cut-and-pasting from a text editor, then your commands
*might* be in the file .Rhistory.  Unfortunately this history gets saved
only when you exit R (and by default only when you also say ``yes'' to
saving the workspace) or if you explicitly savehistory().

Was hoping there was some thing like that... but like you say it wasn't a planned exit so its not there

--

So you were just using the text editor as a scratch pad, and not
saving it?

Exactly

A half-decent text editor should be saving things to disk
as you go. For example, in emacs, if your emacs dies while editing a
file then when you restart it, it will notice and offer to restore it
from its "restore" file.

Yeh thats what I was expecting to happen.  I can't actually remember but I think it was gedit that I had open although sometimes I use kate.  Neither have autorecoverry as I now know.  Both can recover (possibly) files that had once been saved but it seems I never saved it - nit was literally just a big temporary, editable clipboard!

If you were using emacs you might have files
like #foo.R# which are emacs' auto-restore files. Other editors might
do other things - possibly leaving files in /tmp on a Linux system
(but they might get zapped by a reboot).

It seems only if you hit save once then you may get temporary copies...!

I've never liked emacs for other programming stuff - but will take another look at it.

--

To follow up on what Barry wrote above: Don't be put off by the
recommendation to use EMACS (which is not to everyone's taste).

Took the words out of my mouth

I use vim, which does much the same sort of thing: there is a hidden
".whatever.swp" file which contains a back-trackable history of
the editing changes that have been made to the file. So, if you get
a crash, on re-opening the file in vim you are asked if you want to
"recover". The ".swp" file is *not* zapped by a reboot!

Good to know.  I used to use vi quite a lot in my command line linux days.
These days it seems cumbersome on my linux PC but works fine on my server!
Must be a configuration issue...

Again, what I routinely do (in Linux) when developing R code is to
have two terminal windows open. In one I am running R. In the other,
beside it, I am editing a file of R code. To run code in R that has
been entered in the "code" window, I just highlight it with the
mouse in the "code" window, and then paste it into the "R" window.

Exactly what I was doing.  Sounds like emacs with ESS has this even
slicker - highlight and run.  I just need to save the stuff!

--

Use a text editor or something specific to R like Tinn-R and _save early
and often_.

Tinn-R is window$ only.  I've played with RKWard and found it cumbersome plus it doesn't put my commands and its commands together so you don't get a command line History.

Looking at sciViews-K just now.

I currently use Eclipse as my DIE for PHP programming so I'll look at that too.  I guess where I'm struggling is I don't really rate what I'm doing as programming becasue I'm not writing R plugins just some functions... Mind you just having some R context sensitive text / syntax highlighting may be an advantage.

--

What about a version control system to (locally) save the different
stages of your script files?
(I use git but Subversion (SVN) may be easier and do the job).

My changes were typically one line at a time - and re-run it.  I could remember what it was if it didn't do it (or use undo).  But if this gets big then SVN etc might be worth it.  I have no hands on expereince with GIT - one of my PHP projects has been discussing moveing to GIT / Bazzar for about 6 months.  I see the advantage for them as they have multiple coders - is there some advanatge i might have missed for a lone programmer (sorry going well OT).

Clearly either doesn't work if I don't save the file!

Thanks BTW for all the posts back - one of my best responded to queries!

Calum





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On Thu, 2009-08-20 at 20:46 +0100, Polwart Calum (County Durham and
<snip />

A half-decent text editor should be saving things to disk
as you go. For example, in emacs, if your emacs dies while editing a
file then when you restart it, it will notice and offer to restore it
from its "restore" file.

Yeh thats what I was expecting to happen.  I can't actually remember
but I think it was gedit that I had open although sometimes I use
kate.  Neither have autorecoverry as I now know.  Both can recover
(possibly) files that had once been saved but it seems I never saved
it - nit was literally just a big temporary, editable clipboard!

In gedit, Edit > Preferences, then select the Editor tab. Check the
Autosave files box and set a low-ish number to suit your needs.

By the looks of things, gedit will create backup files, but IIRC this
happens when you save, so the backup contains the version before your
most recent save. It doesn't maintain a recovery file like emacs. So the
autosave option is the best option to avoid large losses if you use
gedit.

HTH

G

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