Re: [Rd] R CMD build wiped my computer (from R-help)

From: Ray Brownrigg <Ray.Brownrigg_at_ecs.vuw.ac.nz>
Date: Thu, 29 Jul 2010 12:10:49 +1200

NOTE: Now submitted to R-devel, as this seems more appropriate.

I may have spoken too soon about this having been fixed. (see below).

If I create another "unusual but not 'invalid'" filename in the R subdirectory, the behaviour is different from that reported below, and is similar to the original poster's output (the third "unlink" command, where "xyz" was "~"):

circa> ls -al RColorBrewer/R
total 140

-rwxr-xr-x  1 ray  ecs  43988 Apr 17  2005    ColorBrewer.R~*
-rw-r--r--  1 ray  ecs      0 Jul 29 09:57    residuals.MCMCglmm.R?xyz
drwxr-xr-x  2 ray  ecs   4096 Jul 29 12:02 ./
drwxr-xr-x  5 ray  ecs   4096 Jul 29 11:49 ../
-rwxr-xr-x  1 ray  ecs  43988 Jul 29 09:57 ColorBrewer.R*
-rwxr-xr-x  1 ray  ecs  43988 Apr 17  2005 ColorBrewer.R~*
-rw-r--r--  1 ray  ecs      0 Jul 29 09:58 residuals.MCMCglmm.R
circa>

circa>
circa> R CMD build RColorBrewer
* checking for file 'RColorBrewer/DESCRIPTION' ... OK
* preparing 'RColorBrewer':
* checking DESCRIPTION meta-information ... OK
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* removing junk files
unlink RColorBrewer/R/   ColorBrewer.R~

unlink RColorBrewer/R/ColorBrewer.R
unlink RColorBrewer/R/ residuals.MCMCglmm.R xyz
unlink RColorBrewer/R/residuals.MCMCglmm.R unlink RColorBrewer/R/ColorBrewer.R~
rmdir RColorBrewer/R
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'RColorBrewer_1.0-3.tar.gz'

circa>

Ray Brownrigg

On Thu, 29 Jul 2010, Ray Brownrigg wrote:
> 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
> >
> > ______________________________________________
> > R-help_at_r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html and provide commented,
> > minimal, self-contained, reproducible code.



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