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

[Duncan Murdoch]

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
> >>>
> >
> >
>
>
>