Ubuntu also uses ~ as a backup file syntax, but Ubuntu has a trash can where deleted files are located, so it would be easy to restore them. I would be surprised if Fedora didn't also have a trash can.
-----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch Sent: Wednesday, July 28, 2010 11:12 AM To: Jarrod Hadfield Cc: r-help@r-project.org; Marc Schwartz Subject: Re: [R] [Rd] R CMD build wiped my computer 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 > >>> > > > > > > > ______________________________________________ R-help@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. *************************************************************** This message is for the named person's use only. It may\...{{dropped:20}} ______________________________________________ R-help@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.
