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

Thu Jul 29 00:20:47 CEST 2010

On Thu, 29 Jul 2010, Duncan Murdoch wrote:
> 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:

It looks to me like it has already been fixed, if indeed that was the problem.  In 
R-2.10.1, I tried to reproduce the problem (using RColorBrewer, since that was the 
smallest package I have a local copy of), and the build produced this:
:
* removing junk files
* excluding invalid files from 'RColorBrewer'
Subdirectory 'R' contains invalid file names:
  residuals.MCMCglmm.R xyz
:
where the space shown between the "R" and the "xyz" was a newline character. [I didn't 
dare try using a "~" :-)]

Ray Brownrigg

> 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
>
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