R CMD build wiped my computer

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