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

[Jarrod Hadfield]

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).

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
>>>
>
>


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