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.hadfi...@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
>>>
>
>
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