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_conno...@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_conno...@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_conno...@slingshot.co.nz> wrote:
|> |> > |> >>
|> |> > |> > [...]
|> |> > |> >
|> |> > |> >
|> |> >
|> |> > --
|> |> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> |> > ___ Patrick Connolly
|> |> > {~._.~} Great minds discuss ideas
|> |> > _( Y )_ Average minds discuss events
|> |> > (:_~*~_:) Small minds discuss people
|> |> > (_)-(_) ..... Eleanor Roosevelt
|> |> >
|> |> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> |> >
|> |> > ______________________________________________
|> |> > R-help@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@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@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.
