[R] Corrupting files while copying (was Re: saveRDS() and readRDS() Why? [solved, pretty much anyway])

Patrick Connolly p_connolly @ending from @ling@hot@co@nz
Sat Dec 1 07:38:18 CET 2018


I'd be interested to know if anyone can replicate what I experienced.

VBox version: 5.1.22 r115126 (Qt5.6.2) Versions of R and OSes below:


On Sun, 18-Nov-2018 at 09:44PM +1300, Patrick Connolly wrote:

|> Sequence of steps:
|> 
|> Using R-3.5.1 and Windows 7 with the latest Rstudio, shared directory
|> as working directory on Virtual Box host machine:
|> 
|> > x <- airquality
|> > saveRDS(x, file = "x.rds")
|> > saveRDS(x, file = "y.rds")
|> 
|> On guest machine Mint Linux 17.3, KDE desktop, copy x.rds & y.rds to
|> working directory PWD using file manager Dolphin.
|> 
|> (Don't have the precise version of VirtualBox right now.)

Update:
VBox version: 5.1.22 r115126 (Qt5.6.2)

|> 
|> > x <- readRDS(file =  "x.rds")
|> Error in readRDS(file = "x.rds") : error reading from connection
|> > x <- readRDS(file =  "y.rds")
|> 
|> >   tools::md5sum(c("x.rds", "y.rds"))
|>                              x.rds                              y.rds
|> "5fef054848f39b4be02b7c54f1c71a20" "978a64d1dd342d16a381c9ca728d3665"
|> 
|> Yet, if instead of using Dolphin, use bash commands from the shared
|> directory 
|> 
|> $ cp *.rds ~/PWD/
|> 
|> no error reading from the connection or other differences between
|> x.rds and y.rds.
|> 
|> head(x)
|> 
|> > head(datasets::airquality)
|>   Ozone Solar.R Wind Temp Month Day
|> 1    41     190  7.4   67     5   1
|> 2    36     118  8.0   72     5   2
|> 3    12     149 12.6   74     5   3
|> 4    18     313 11.5   62     5   4
|> 5    NA      NA 14.3   56     5   5
|> 6    28      NA 14.9   66     5   6
|> > 
|> 
|> On Thu, 15-Nov-2018 at 09:53AM -0500, Ista Zahn wrote:
|> 
|> |> Hi Patrick,
|> |> 
|> |> I think it would help to start from the beginning and give complete
|> |> (but concise!) replication instructions, including telling us what
|> |> host and gest operating systems you are using (including the
|> |> versions), the version
|> |>  of virtualbox you used, and exactly what steps are needed to
|> |> reproduce the surprising behavior.
|> |> 
|> |> Best,
|> |> Ista
|> |> On Wed, Nov 14, 2018 at 2:36 AM Patrick Connolly
|> |> <p_connolly using slingshot.co.nz> wrote:
|> |> >
|> |> > Thanks William,
|> |> >
|> |> > I've used Dolphin for years and never encountered that phenomenon.
|> |> > Even so, that description doesn't fit what's going on here.  1.7
|> |> > kilobytes is hardly a 'large directory'.
|> |> >
|> |> > The problem seems to be with the way VirtualBox mounts directories
|> |> > which isn't an R issue, nor is the fact that copying from Linux to
|> |> > Windows isn't affected.  But the fact that it happens only with rds
|> |> > files that use the name of the R object as part of their own names
|> |> > must be an R issue (that surfaces only when other conditions are
|> |> > present).
|> |> >
|> |> > Theories short of divine intervention appreciated.
|> |> >
|> |> >
|> |> >
|> |> > On Tue, 13-Nov-2018 at 02:22PM -0800, William Dunlap wrote:
|> |> >
|> |> > |> Perhaps you got bitten by Dolphin's non-modal dialogs, as described in
|> |> > |> https://userbase.kde.org/Dolphin/File_Management:
|> |> > |>
|> |> > |> Non Modal Dialogs
|> |> > |>
|> |> > |> When Moving, Copying or Deleting files/directories the dialog disappears
|> |> > |> even when the operation has not yet completed. A progress bar then appears
|> |> > |> in the bottom right of the screen, this then disappears also, if you want
|> |> > |> see the progress you need to click a small (i) information icon in the
|> |> > |> system tray.
|> |> > |>
|> |> > |>
|> |> > |> Warning
|> |> > |> New users who are not used to this way of working (and even experienced
|> |> > |> users) can get caught out by this, if you are Moving, Copying or Deleting
|> |> > |> large directories then you need to use the icon to monitor the progress of
|> |> > |> your operation. If you don't then any subsequent actions you do, may well
|> |> > |> use an incomplete file structure resulting in corrupted files. You have
|> |> > |> been warned!
|> |> > |>
|> |> > |> Bill Dunlap
|> |> > |> TIBCO Software
|> |> > |> wdunlap tibco.com
|> |> > |>
|> |> > |> On Tue, Nov 13, 2018 at 2:10 PM, p_connolly <p_connolly using slingshot.co.nz>
|> |> > |> wrote:
|> |> > |>
|> |> > |> > This is getting more strange.
|> |> > |> >
|> |> > |> > I normally copy from the shared folder to the appropriate directory using
|> |> > |> > Dolphin, the KDE file manager.  If instead I use the standard bash cp
|> |> > |> > command, no corruption happens -- at least with the limited testing I have
|> |> > |> > done.  There also seems to be no problem copying from Linux to Windows.  I
|> |> > |> > installed R-3.5.1 for Windows just to eliminate that possible issue.
|> |> > |> >
|> |> > |> > However, R has *something* to do with it because it was used to make the
|> |> > |> > .rds file.  Just how the relationship between the name of the R object and
|> |> > |> > the name of the .rds file comes into it, I can't imagine.
|> |> > |> >
|> |> > |> > Thanks for the suggestion William.
|> |> > |> >
|> |> > |> >
|> |> > |> > On 2018-11-14 06:26, William Dunlap wrote:
|> |> > |> >
|> |> > |> >> It seems like copying the files corrupted them. How did you copy them
|> |> > |> >> (with R
|> |> > |> >> or cp or copy or ftp, etc.)?  I don't see how this has anything to do
|> |> > |> >> with R.
|> |> > |> >>
|> |> > |> >> Bill Dunlap
|> |> > |> >> TIBCO Software
|> |> > |> >> wdunlap tibco.com [1]
|> |> > |> >> On Mon, Nov 12, 2018 at 7:10 PM, p_connolly
|> |> > |> >> <p_connolly using slingshot.co.nz> wrote:
|> |> > |> >>
|> |> > |> > [...]
|> |> > |> >
|> |> > |> >
|> |> >
|> |> > --
|> |> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> |> >    ___    Patrick Connolly
|> |> >  {~._.~}                   Great minds discuss ideas
|> |> >  _( Y )_                 Average minds discuss events
|> |> > (:_~*~_:)                  Small minds discuss people
|> |> >  (_)-(_)                              ..... Eleanor Roosevelt
|> |> >
|> |> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> |> >
|> |> > ______________________________________________
|> |> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
|> |> > 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.
|> 
|> -- 
|> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
|>    ___    Patrick Connolly   
|>  {~._.~}                   Great minds discuss ideas    
|>  _( Y )_  	         Average minds discuss events 
|> (:_~*~_:)                  Small minds discuss people  
|>  (_)-(_)  	                      ..... Eleanor Roosevelt
|> 	  
|> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> 
|> ______________________________________________
|> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
|> 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.

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.



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