[R] [Rd] R CMD build wiped my computer

Wed Jul 28 22:18:43 CEST 2010

Ubuntu also uses ~ as a backup file syntax, but Ubuntu has a trash can
where deleted files are located, so it would be easy to restore them.  I
would be surprised if Fedora didn't also have a trash can. 

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Duncan Murdoch
Sent: Wednesday, July 28, 2010 11:12 AM
To: Jarrod Hadfield
Cc: r-help at r-project.org; Marc Schwartz
Subject: Re: [R] [Rd] R CMD build wiped my computer

On 28/07/2010 10:01 AM, Jarrod Hadfield wrote:
> Hi Marc,
>
> Thanks for the info on recovery - most of it can pieced together from 
> backups but a quick, cheap and easy method of recovery would have been

> nicer.
>
> My main concern is that this could happen again and that the "bug" is 
> not limited to R 2.9. I would think that an accidental carriage return

> at the end of a file name (even a temporary one) would be a reasonably

> common phenomenon (I'm surprised I hadn't done it before).
>   

If you can put together a recipe to reproduce the problem (or a less
extreme version of R deleting files it shouldn't), we'll certainly fix
it.  But so far all we've got are guesses about what might have gone
wrong, and I don't think anyone has been able to reproduce the problem
on current R.

Duncan Murdoch
> Cheers,
>
> Jarrod
>
>
>
> On 28 Jul 2010, at 14:04, Marc Schwartz wrote:
>
> > Jarrod,
> >
> > Noting your exchange with Martin, Martin brings up a point that 
> > certainly I missed, which is that somehow the tilde ('~') character 
> > got into the chain of events. As Martin noted, on Linuxen/Unixen 
> > (including OSX), the tilde, when used in the context of file name 
> > globbing, refers to your home directory. Thus, a command such as:
> >
> >  ls ~
> >
> > will list the files in your home directory. Similarly:
> >
> >  rm ~
> >
> > will remove the files there as well. If the -rf argument is added, 
> > then the deletion becomes recursive through that directory tree, 
> > which appears to be the case here.
> >
> > I am unclear, as Martin appears to be, as to the steps that caused 
> > this to happen. That may yet be related in some fashion to Duncan's 
> > hypothesis.
> >
> > That being said, the use of the tilde character as a suffix to 
> > denote that a file is a backup version, is not limited to Fedora or 
> > Linux, for that matter. It is quite common for many text editors 
> > (eg. Emacs) to use this. As a result, it is also common for many 
> > applications to ignore files that have a tilde suffix.
> >
> > Based upon your follow up posts to the original thread, it would 
> > seem that you do not have any backups. The default ext3 file system 
> > that is used on modern Linuxen, by design, makes it a bit more 
> > difficult to recover deleted files. This is due to the unlinking of 
> > file metadata at the file system data structure level, as opposed to

> > simply marking the file as deleted in the directory structures, as 
> > happens on Windows.
> >
> > There is a utility called ext3undel 
> > (http://projects.izzysoft.de/trac/ext3undel
> > ), which is a wrapper of sorts to other undelete utilities such as 
> > PhotoRec and foremost. I have not used it/them, so cannot speak from

> > personal experience. Thus it would be a good idea to engage in some 
> > reviews of the documentation and perhaps other online resources 
> > before proceeding. The other consideration is the Catch-22 of not 
> > copying anything new to your existing HD, for fear of overwriting 
> > the lost files with new data. So you would need to consider an 
> > approach of downloading these utilities via another computer and 
> > then running them on the computer in question from other media, such

> > as a CD/DVD or USB HD.
> >
> > A more expensive option would be to use a professional data recovery

> > service, where you would have to consider the cost of recovery 
> > versus your lost time. One option would be Kroll OnTrack UK 
> > (http://www.ontrackdatarecovery.co.uk/
> > ). I happen to live about a quarter mile from their world HQ here in

> > a suburb of Minneapolis. I have not used them myself, but others 
> > that I know have, with good success. Again, this comes at a 
> > potentially substantial monetary cost.
> >
> > The key is that if you have any hope to recover the deleted files, 
> > you not copy anything new onto the hard drive in the mean time.
> > Doing so will decrease the possibility of file recovery to near 0.
> >
> > As Duncan noted, there is great empathy with your situation. We have

> > all gone through this at one time or another. In my case, it was 
> > perhaps 20+ years ago, but as a result, I am quite anal retentive 
> > about having backups, which I have done for some time on my systems,

> > hourly.
> >
> > HTH,
> >
> > Marc Schwartz
> >
> >
> > On Jul 28, 2010, at 5:55 AM, Jarrod Hadfield wrote:
> >
> >> Hi Martin,
> >>
> >> I think this is the most likely reason given that the name in the 
> >> DESCRIPTION file does NOT have a version number. Even so, it is 
> >> very easy to misname a file and then delete it/change its name (as 
> >> I've done here) and I hope current versions of R would not cause 
> >> this problem. Perhaps Fedora should not use ~ as its back up file 
> >> suffixes?
> >>
> >> Cheers,
> >>
> >> Jarrod
> >>
> >>
> >> On 28 Jul 2010, at 11:41, Martin Maechler wrote:
> >>
> >>>>>>>> Jarrod Hadfield <j.hadfield at ed.ac.uk>  on Tue, 27 Jul 2010 
> >>>>>>>> 21:37:09 +0100 writes:
> >>>
> >>>> Hi, I ran R (version 2.9.0) CMD build under root in Fedora (9). 
> >>>> When it tried to remove "junk files" it removed EVERYTHING in my 
> >>>> local account! (See below).
> >>>
> >>>> Can anyone tell me what happened,
> >>>
> >>> the culprit may lay here:
> >>>>> * removing junk files
> >>>>> unlink MCMCglmm_2.05/R/   residuals.MCMCglmm.R
> >>>>> ~
> >>>
> >>> where it seems that someone (you?) have added a newline in the 
> >>> filname, so instead of 'residuals.MCMCglmm.R~'
> >>> you got
> >>>
> >>> 'residuals.MCMCglmm.R
> >>> ~'
> >>>
> >>> and the unlink / rm  command interpreted '~' as your home 
> >>> directory.
> >>>
> >>> But I can hardly believe it.
> >>> This seems explanation seems a bit doubtful to me.. ...
> >>>
> >>>> and even more importantly if I can I restore what was lost.
> >>>
> >>> well, you just get it from the backup. You do daily backups, do 
> >>> you?
> >>>
> >>> Regards,
> >>> Martin Maechler, ETH Zurich
> >>>
> >
> >
>
>
>

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
***************************************************************

This message is for the named person's use only. It may\...{{dropped:20}}