William Dunlap
2018-Nov-13 22:22 UTC
[R] saveRDS() and readRDS() Why? [solved, pretty much anyway)
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 at 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 at slingshot.co.nz> wrote: >> > [...] > >[[alternative HTML version deleted]]
Patrick Connolly
2018-Nov-14 07:35 UTC
[R] Corrupting files while copying (was Re: saveRDS() and readRDS() Why? [solved, pretty much anyway])
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 at
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 at slingshot.co.nz> wrote:
|> >>
|> > [...]
|> >
|> >
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
Ista Zahn
2018-Nov-15 14:53 UTC
[R] Corrupting files while copying (was Re: saveRDS() and readRDS() Why? [solved, pretty much anyway])
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 at 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 at 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 at slingshot.co.nz> wrote: > |> >> > |> > [...] > |> > > |> > > > -- > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. > ___ Patrick Connolly > {~._.~} Great minds discuss ideas > _( Y )_ Average minds discuss events > (:_~*~_:) Small minds discuss people > (_)-(_) ..... Eleanor Roosevelt > > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. > > ______________________________________________ > R-help at 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.