[R] saveRDS() and readRDS() Why?

Discussion:

Patrick Connolly

2018-11-07 07:56:21 UTC

Permalink

From a Windows R session, I do

object.size(rawData)

31736 bytes # from scraping a non-reproducible web address.

saveRDS(rawData, file = "rawData.rds")

Then copy to a Linux session

rawData <- readRDS(file = "rawData.rds")
rawData

[1] "rawData"

object.size(rawData)

112 bytes

rawData

[1] "rawData" # only the name and something to make up 112 bytes
Have I misunderstood the syntax?

It's an old version on Windows. I haven't used Windows R since then.

major 3
minor 2.4
year 2016
month 03
day 16

I've tried R-3.5.0 and R-3.5.1 Linux versions.

In case it's material ...

I couldn't get the scraping to work on either of the R installations
but Windows users told me it worked for them. So I thought I'd get
the R object and use it. I could understand accessing the web address
could have different permissions for different OSes, but should that
affect the R objects?

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

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

______________________________________________
R-***@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.

Eric Berger

2018-11-07 08:13:40 UTC

Permalink

What do you see at the OS level?
i.e. on windows
DIR rawData.rds
on linux
ls -l rawData.rds
compare the file sizes on both.

Post by Patrick Connolly
From a Windows R session, I do

object.size(rawData)

31736 bytes # from scraping a non-reproducible web address.

saveRDS(rawData, file = "rawData.rds")

Then copy to a Linux session

rawData <- readRDS(file = "rawData.rds")
rawData

[1] "rawData"

object.size(rawData)

112 bytes

rawData

[1] "rawData" # only the name and something to make up 112 bytes
Have I misunderstood the syntax?
It's an old version on Windows. I haven't used Windows R since then.
major 3
minor 2.4
year 2016
month 03
day 16
I've tried R-3.5.0 and R-3.5.1 Linux versions.
In case it's material ...
I couldn't get the scraping to work on either of the R installations
but Windows users told me it worked for them. So I thought I'd get
the R object and use it. I could understand accessing the web address
could have different permissions for different OSes, but should that
affect the R objects?
TIA
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
______________________________________________
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.

[[alternative HTML version deleted]]

______________________________________________
R-***@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

2018-11-07 08:28:13 UTC

Permalink

They're both about 3kb.

Post by Eric Berger
What do you see at the OS level?
i.e. on windows
DIR rawData.rds
on linux
ls -l rawData.rds
compare the file sizes on both.
On Wed, Nov 7, 2018 at 9:56 AM Patrick Connolly
From a Windows R session, I do

object.size(rawData)

31736 bytes # from scraping a non-reproducible web address.

saveRDS(rawData, file = "rawData.rds")

Then copy to a Linux session

rawData <- readRDS(file = "rawData.rds")
rawData

[1] "rawData"

object.size(rawData)

112 bytes

rawData

[1] "rawData" # only the name and something to make up 112 bytes
Have I misunderstood the syntax?
It's an old version on Windows. I haven't used Windows R since then.
major 3
minor 2.4
year 2016
month 03
day 16
I've tried R-3.5.0 and R-3.5.1 Linux versions.
In case it's material ...
I couldn't get the scraping to work on either of the R installations
but Windows users told me it worked for them. So I thought I'd get
the R object and use it. I could understand accessing the web address
could have different permissions for different OSes, but should that
affect the R objects?
TIA
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
______________________________________________
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

2018-11-07 08:45:30 UTC

Permalink

On Wed, 07-Nov-2018 at 08:27AM +0000, Robert David Burbidge wrote:

|> Hi Patrick,
|>
|> From the help: "save writes a single line header (typically
|> "RDXs\n") before the serialization of a single object".
|>
|> If the file sizes are the same (see Eric's message), then the
|> problem may be due to different line terminators. Try serialize and
|> unserialize for low-level control of saving/reading objects.

I'll have to find out what 'serialize' means.

On Windows, it's a huge table, looks like it's all hexadecimal.

On Linux, it's just the text string 'rawData' -- a lot more than line
terminators.

Have I misunderstood what the idea is? I thought I'd get an identical
object, irrespective of how different the OS stores and zips it.

|>
|> Rgds,
|>
|> Robert
|>
|>
|> On 07/11/18 08:13, Eric Berger wrote:
|> >What do you see at the OS level?
|> >i.e. on windows
|> >DIR rawData.rds
|> >on linux
|> >ls -l rawData.rds
|> >compare the file sizes on both.
|> >
|> >
|> >On Wed, Nov 7, 2018 at 9:56 AM Patrick Connolly <***@slingshot.co.nz>
|> >wrote:
|> >
|> >> From a Windows R session, I do
|> >>
|> >>>object.size(rawData)
|> >>31736 bytes # from scraping a non-reproducible web address.
|> >>>saveRDS(rawData, file = "rawData.rds")
|> >>Then copy to a Linux session
|> >>
|> >>>rawData <- readRDS(file = "rawData.rds")
|> >>>rawData
|> >>[1] "rawData"
|> >>>object.size(rawData)
|> >>112 bytes
|> >>>rawData
|> >>[1] "rawData" # only the name and something to make up 112 bytes
|> >>Have I misunderstood the syntax?
|> >>
|> >>It's an old version on Windows. I haven't used Windows R since then.
|> >>
|> >>major 3
|> >>minor 2.4
|> >>year 2016
|> >>month 03
|> >>day 16
|> >>
|> >>
|> >>I've tried R-3.5.0 and R-3.5.1 Linux versions.
|> >>
|> >>In case it's material ...
|> >>
|> >>I couldn't get the scraping to work on either of the R installations
|> >>but Windows users told me it worked for them. So I thought I'd get
|> >>the R object and use it. I could understand accessing the web address
|> >>could have different permissions for different OSes, but should that
|> >>affect the R objects?
|> >>
|> >>TIA
|> >>
|> >>--
|> >>~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >> ___ Patrick Connolly
|> >> {~._.~} Great minds discuss ideas
|> >> _( Y )_ Average minds discuss events
|> >>(:_~*~_:) Small minds discuss people
|> >> (_)-(_) ..... Eleanor Roosevelt
|> >>
|> >>~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >>
|> >>______________________________________________
|> >>R-***@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.
|> >>
|> > [[alternative HTML version deleted]]
|> >
|> >______________________________________________
|> >R-***@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-***@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.

Eric Berger

2018-11-07 09:01:16 UTC

Permalink

Your understanding is correct. It works fine for me.

Post by Patrick Connolly
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

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

Post by Patrick Connolly
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

|> >>
|> >>______________________________________________
|> >>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.
|> >>
|> > [[alternative HTML version deleted]]
|> >
|> >______________________________________________
|> >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
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
______________________________________________
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.

Jan van der Laan

2018-11-07 09:15:33 UTC

Permalink

Are you sure you didn't do saveRDS("rawData", file = "rawData.rds")
instead of saveRDS(rawData, file = "rawData.rds") ? This would explain
the result you have under linux.

In principle saveRDS and readRDS can be used to copy objects between
R-sessions without loosing information.

What does readRDS return on windows with the same file?

What type of object is rawData? Do str(rawData). Some objects created by
packages cannot be serialized, e.g. objects that point to memory
allocated by a package. The pointer is then serialized not the memory
pointed to.

Also, if the object is generated by a package, you might need to load
the package to get the printing etc. of the object right.

HTH,

Jan

Post by Patrick Connolly
|> Hi Patrick,
|>
|> From the help: "save writes a single line header (typically
|> "RDXs\n") before the serialization of a single object".
|>
|> If the file sizes are the same (see Eric's message), then the
|> problem may be due to different line terminators. Try serialize and
|> unserialize for low-level control of saving/reading objects.
I'll have to find out what 'serialize' means.
On Windows, it's a huge table, looks like it's all hexadecimal.
On Linux, it's just the text string 'rawData' -- a lot more than line
terminators.
Have I misunderstood what the idea is? I thought I'd get an identical
object, irrespective of how different the OS stores and zips it.
|>
|> Rgds,
|>
|> Robert
|>
|>
|> >What do you see at the OS level?
|> >i.e. on windows
|> >DIR rawData.rds
|> >on linux
|> >ls -l rawData.rds
|> >compare the file sizes on both.
|> >
|> >
|> >
|> >> From a Windows R session, I do
|> >>
|> >>>object.size(rawData)
|> >>31736 bytes # from scraping a non-reproducible web address.
|> >>>saveRDS(rawData, file = "rawData.rds")
|> >>Then copy to a Linux session
|> >>
|> >>>rawData <- readRDS(file = "rawData.rds")
|> >>>rawData
|> >>[1] "rawData"
|> >>>object.size(rawData)
|> >>112 bytes
|> >>>rawData
|> >>[1] "rawData" # only the name and something to make up 112 bytes
|> >>Have I misunderstood the syntax?
|> >>
|> >>It's an old version on Windows. I haven't used Windows R since then.
|> >>
|> >>major 3
|> >>minor 2.4
|> >>year 2016
|> >>month 03
|> >>day 16
|> >>
|> >>
|> >>I've tried R-3.5.0 and R-3.5.1 Linux versions.
|> >>
|> >>In case it's material ...
|> >>
|> >>I couldn't get the scraping to work on either of the R installations
|> >>but Windows users told me it worked for them. So I thought I'd get
|> >>the R object and use it. I could understand accessing the web address
|> >>could have different permissions for different OSes, but should that
|> >>affect the R objects?
|> >>
|> >>TIA
|> >>
|> >>--
|> >>~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >> ___ Patrick Connolly
|> >> {~._.~} Great minds discuss ideas
|> >> _( Y )_ Average minds discuss events
|> >>(:_~*~_:) Small minds discuss people
|> >> (_)-(_) ..... Eleanor Roosevelt
|> >>
|> >>~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >>
|> >>______________________________________________
|> >>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.
|> >>
|> > [[alternative HTML version deleted]]
|> >
|> >______________________________________________
|> >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.

______________________________________________
R-***@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

2018-11-08 07:27:24 UTC

Permalink

Many thanks to Berwin, Eric, Robert, and Jan for their input.

I had hoped it was as simple as because I typed

saveRDS("rawData", file = "rawData.rds") on the Windows side.
but that wasn't the case.

Robert Burbridge suggested:

windows (not run)
f <- file("rawData.rds", open="w")
serialize(rawData, f, xdr = FALSE)
close(f)

# linux
rawData <- unserialize(file = "rawData.rds")

That didn't work:
Error in unserialize(file = "rawData.rds") :
unused argument (file = "rawData.rds")
(the argument isn't 'file')

Nor did

rawData <- unserialize("rawData.rds")

Error in unserialize("rawData.rds") :
character vectors are no longer accepted by unserialize()

However

readRDS(file = "rawData.rds") did!

So what I needed was serialize but not unserialize.

I still don't know Why, but I know How.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

______________________________________________
R-***@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.

Martin Maechler

2018-11-08 10:06:28 UTC

Permalink

Post by Patrick Connolly

Post by Patrick Connolly
Patrick Connolly

Many thanks to Berwin, Eric, Robert, and Jan for their input.
I had hoped it was as simple as because I typed
saveRDS("rawData", file = "rawData.rds") on the Windows side.
but that wasn't the case.
windows (not run)
f <- file("rawData.rds", open="w")
serialize(rawData, f, xdr = FALSE)
close(f)
# linux
rawData <- unserialize(file = "rawData.rds")
unused argument (file = "rawData.rds")
(the argument isn't 'file')
Nor did

rawData <- unserialize("rawData.rds")

character vectors are no longer accepted by unserialize()
However
readRDS(file = "rawData.rds") did!
So what I needed was serialize but not unserialize.
I still don't know Why, but I know How.

Hmm.. and nobody has been able to reproduce your problem, right?

IIUC, currently you are suggesting that [on Windows], if you do

saveRDS(rawdata, file="rawdata.rds")

the resulting file is does not work with readRDS() on Linux.
What again are your R versions on the two platforms?

Could you dput() -- provide a (short if possible) version of rawdata where
that problem occurs ?

Best,
Martin

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

2018-11-10 07:48:34 UTC

Permalink

On Thu, 08-Nov-2018 at 11:06AM +0100, Martin Maechler wrote:

|> >>>>> Patrick Connolly
|> >>>>> on Thu, 8 Nov 2018 20:27:24 +1300 writes:

[...]

|> >
|> > I still don't know Why, but I know How.
|>
|> Hmm.. and nobody has been able to reproduce your problem, right?
|>
|> IIUC, currently you are suggesting that [on Windows], if you do
|>
|> saveRDS(rawdata, file="rawdata.rds")
|>
|> the resulting file is does not work with readRDS() on Linux.
|> What again are your R versions on the two platforms?

It's an old version on Windows. I haven't used Windows R since then.

major 3
minor 2.4
year 2016
month 03
day 16

I've tried R-3.5.0 and R-3.5.1 Linux versions. The problem might be
entirely because of the ancient Windows version.

|>
|> Could you dput() -- provide a (short if possible) version of rawdata where
|> that problem occurs ?

I can't make a smaller version of rawdata which comes from scraping a
non-public web address, but next week when I'm back where those
machines are, I'll try it with a small data frame which is
reproducible.

|>
|> Best,
|> Martin
|>
|>
|> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> > ___ Patrick Connolly
|> > {~._.~} Great minds discuss ideas
|> > _( Y )_ Average minds discuss events
|> > (:_~*~_:) Small minds discuss people
|> > (_)-(_) ..... Eleanor Roosevelt
|> >
|> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >
|> > ______________________________________________
|> > R-***@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-***@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

2018-11-12 07:28:06 UTC

Permalink

The solution was very simple. Don't use the same name for the rds
file as used for the R object, viz a vie:

saveRDS(x, file = "x.rds")
and
x <- readRDS(file = "x.rds")

will not work; however

saveRDS(x, file = "y.rds")
and
x <- readRDS(file = "y.rds")
will work.

An undocumented feature?

Thanks to all who contributed.

On Sat, 10-Nov-2018 at 08:48PM +1300, Patrick Connolly wrote:

|> On Thu, 08-Nov-2018 at 11:06AM +0100, Martin Maechler wrote:
|>
|> |> >>>>> Patrick Connolly
|> |> >>>>> on Thu, 8 Nov 2018 20:27:24 +1300 writes:
|>
|> [...]
|>
|> |> >
|> |> > I still don't know Why, but I know How.
|> |>
|> |> Hmm.. and nobody has been able to reproduce your problem, right?
|> |>
|> |> IIUC, currently you are suggesting that [on Windows], if you do
|> |>
|> |> saveRDS(rawdata, file="rawdata.rds")
|> |>
|> |> the resulting file is does not work with readRDS() on Linux.
|> |> What again are your R versions on the two platforms?
|>
|>
|> It's an old version on Windows. I haven't used Windows R since then.
|>
|> major 3
|> minor 2.4
|> year 2016
|> month 03
|> day 16
|>
|>
|> I've tried R-3.5.0 and R-3.5.1 Linux versions. The problem might be
|> entirely because of the ancient Windows version.
|>
|>
|> |>
|> |> Could you dput() -- provide a (short if possible) version of rawdata where
|> |> that problem occurs ?
|>
|> I can't make a smaller version of rawdata which comes from scraping a
|> non-public web address, but next week when I'm back where those
|> machines are, I'll try it with a small data frame which is
|> reproducible.
|>
|>
|>
|> |>
|> |> Best,
|> |> Martin
|> |>
|> |>
|> |> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> |> > ___ Patrick Connolly
|> |> > {~._.~} Great minds discuss ideas
|> |> > _( Y )_ Average minds discuss events
|> |> > (:_~*~_:) Small minds discuss people
|> |> > (_)-(_) ..... Eleanor Roosevelt
|> |> >
|> |> > ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> |> >
|> |> > ______________________________________________
|> |> > R-***@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-***@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-***@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

p_connolly

2018-11-12 20:42:19 UTC

Permalink

Er, where, what, how? I can't reproduce that, at least not on 3.5.1 on

x <- airquality
saveRDS(x, file = "x.rds")
x <- NULL
x <- readRDS(file = "x.rds")
x

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
...
Looks fine to me.

It seems to work fine using the same installation to read as used for
the save.
But it's a different story if the save was done on a Windows
installation and read on a Linux installation.

## On Windows 3.4.2

x <- airquality
saveRDS(x, file = "x.rds")
saveRDS(x, file = "y.rds")

Files x.rds and y.rds are identical in size but utterly different in
content.

## On Linux 3.5.1

x <- readRDS(file = "x.rds")

Error in readRDS(file = "x.rds") : error reading from connection

x <- readRDS(file = "y.rds")
head(x)

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

It might just be the age of the Windows installation. I don't have much
use for Windows, so I haven't had much inclination to install a newer
version.

YMMV

?
-pd

On 12 Nov 2018, at 08:28 , Patrick Connolly
The solution was very simple. Don't use the same name for the rds
saveRDS(x, file = "x.rds")
and
x <- readRDS(file = "x.rds")
will not work; however
saveRDS(x, file = "y.rds")
and
x <- readRDS(file = "y.rds")
will work.
An undocumented feature?
Thanks to all who contributed.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23

p_connolly

2018-11-13 03:10:20 UTC

Permalink

Post by p_connolly
## On Windows 3.4.2

x <- airquality
saveRDS(x, file = "x.rds")
saveRDS(x, file = "y.rds")

Files x.rds and y.rds are identical in size but utterly different in
content.
Wow! Can you show us the results of
x <- datasets::airquality
saveRDS(x, file="x.rds")
saveRDS(x, file="y.rds")
tools::md5sum(c("x.rds", "y.rds"))
dput(readBin("x.rds", what="raw", n=file.size("x.rds")))
dput(readBin("y.rds", what="raw", n=file.size("y.rds")))
(Copy and paste, as text, from the R session, so we can see the input
and the output in context.

If I do that on Linux or Windows, I get identical files.

If I copy x.rds and y.rds from Windows to Linux (which is what I wish to
be able to do) using a shared folder between the Windows VirtualBox host

Post by p_connolly
x <- readRDS(file = "x.rds")

Error in readRDS(file = "x.rds") : error reading from connection

Post by p_connolly
x <- readRDS(file = "y.rds")
tools::md5sum(c("x.rds", "y.rds"))

x.rds y.rds
"5fef054848f39b4be02b7c54f1c71a20" "978a64d1dd342d16a381c9ca728d3665"

Post by p_connolly
dput(readBin("x.rds", what="raw", n=file.size("x.rds")))

as.raw(c(0x1f, 0x8b, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x06, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
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0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
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0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
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0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
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0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00))

Post by p_connolly
dput(readBin("y.rds", what="raw", n=file.size("y.rds")))

as.raw(c(0x1f, 0x8b, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x06, 0xe5, 0x97, 0x4b, 0x6c, 0x54, 0x55, 0x18, 0xc7, 0xcf, 0x9d,
0x0e, 0x7d, 0x41, 0x71, 0x2c, 0x15, 0xac, 0x65, 0xa0, 0x94, 0xa9,
0x80, 0x94, 0x52, 0xa1, 0x0b, 0xa9, 0x01, 0xa6, 0x58, 0xc4, 0xda,
0x76, 0x68, 0x99, 0x42, 0x0b, 0x2d, 0xe8, 0x08, 0x45, 0x4d, 0xca,
0x94, 0xb4, 0xc4, 0x07, 0x1b, 0x49, 0x5c, 0x10, 0x75, 0x65, 0xa2,
0x26, 0x35, 0x71, 0xad, 0x3b, 0x16, 0x2e, 0x4c, 0x7c, 0x6b, 0xc2,
0x82, 0xa8, 0x71, 0xa3, 0x71, 0x63, 0x7c, 0x2c, 0x74, 0x85, 0x2c,
0x8c, 0x0b, 0xa3, 0x40, 0xfd, 0x7f, 0xf7, 0xfc, 0xff, 0xed, 0xcd,
0x49, 0x59, 0xcf, 0xc2, 0x9b, 0xfc, 0xe6, 0xbb, 0xe7, 0x3b, 0xe7,
0x7c, 0xaf, 0x73, 0xee, 0xdc, 0x73, 0xc7, 0xeb, 0x9d, 0x73, 0x29,
0x57, 0x95, 0x4a, 0xbb, 0x54, 0x15, 0x6e, 0xab, 0xd6, 0xe0, 0xa7,
0x1a, 0x34, 0x80, 0x79, 0xb0, 0x0d, 0xe4, 0xc0, 0x2a, 0xd0, 0x78,
0xc9, 0xc5, 0xd7, 0x7a, 0xb0, 0x0e, 0xd8, 0xd8, 0x5a, 0xea, 0x6a,
0x40, 0x06, 0xac, 0x04, 0xab, 0x6d, 0x2c, 0x65, 0x1b, 0xed, 0x6d,
0x60, 0x5f, 0x44, 0x99, 0x06, 0xad, 0x36, 0x57, 0xd0, 0xe6, 0x0e,
0x30, 0x07, 0xda, 0x93, 0x7d, 0xc1, 0xb8, 0x2c, 0xe5, 0x21, 0xb0,
0x25, 0x39, 0x3f, 0x71, 0x7f, 0x8f, 0xd9, 0x00, 0x4d, 0x8c, 0xbd,
0xe1, 0x4e, 0xf6, 0x96, 0xb1, 0x7f, 0x19, 0x3c, 0xa8, 0xf8, 0x70,
0xe5, 0xc1, 0x56, 0x30, 0x04, 0x4a, 0xe4, 0x28, 0xfb, 0xac, 0x7e,
0x2d, 0x89, 0x1a, 0x74, 0x81, 0xcd, 0x60, 0x2f, 0x38, 0x0c, 0xf6,
0x5b, 0x5d, 0x12, 0xb6, 0x87, 0xc1, 0x34, 0xe3, 0xea, 0x06, 0x47,
0xc0, 0x2e, 0xfa, 0x78, 0xd8, 0xf2, 0x01, 0x75, 0xce, 0xd7, 0xb2,
0x40, 0x5b, 0x07, 0xc0, 0x45, 0x70, 0x1c, 0x94, 0x13, 0xb6, 0x3a,
0x9c, 0x5f, 0x8b, 0x5e, 0xb6, 0xd7, 0xd2, 0x86, 0xd5, 0x71, 0x23,
0xfb, 0xad, 0x0e, 0x75, 0xec, 0xb7, 0xda, 0xbe, 0x07, 0xfa, 0xd9,
0x1e, 0x04, 0xcf, 0x81, 0x51, 0xcb, 0x07, 0x3c, 0x49, 0x9f, 0xfd,
0x60, 0x02, 0xec, 0xb4, 0x1a, 0x30, 0xd6, 0x75, 0xb4, 0x75, 0x6f,
0xc2, 0xee, 0x7a, 0xc6, 0x6a, 0x7b, 0xa5, 0xd3, 0xf9, 0x35, 0x6f,
0xe0, 0x98, 0x0c, 0xef, 0x6d, 0x5e, 0x8e, 0xb5, 0xb1, 0xfd, 0xb0,
0x81, 0xbe, 0xb5, 0x47, 0x9a, 0xdc, 0xd2, 0x5e, 0xfb, 0x94, 0xf1,
0xbc, 0x89, 0x6d, 0xb2, 0x67, 0x29, 0xcf, 0x68, 0x3b, 0x7e, 0x4e,
0x3b, 0xbf, 0xdf, 0xbe, 0xa4, 0xce, 0xc0, 0xde, 0x8a, 0xcc, 0x46,
0x2f, 0x24, 0xe2, 0x8e, 0x76, 0xfb, 0xf8, 0xa3, 0x03, 0x8c, 0xb1,
0x16, 0xf7, 0x56, 0xd7, 0x66, 0x30, 0xe9, 0xeb, 0x18, 0xd5, 0xd3,
0xbf, 0xf9, 0xbc, 0x09, 0x7e, 0x86, 0x0e, 0x31, 0x46, 0xd8, 0x9f,
0x91, 0xd5, 0xec, 0x4f, 0xf0, 0x21, 0xf8, 0x11, 0x6d, 0xcc, 0x77,
0x2f, 0x41, 0xde, 0x0d, 0xb0, 0x0e, 0xd1, 0x23, 0xc0, 0x1e, 0x92,
0x7f, 0xc0, 0x1b, 0xb8, 0x1f, 0xa4, 0xaf, 0xcf, 0x20, 0xad, 0x16,
0xb6, 0xdf, 0x5e, 0x00, 0xaf, 0x80, 0xb7, 0xb8, 0x16, 0x13, 0x1c,
0x7f, 0xd9, 0xdb, 0x8a, 0x6b, 0xfa, 0x14, 0xd7, 0xe7, 0x55, 0xcc,
0xb3, 0x38, 0xfe, 0x06, 0xd7, 0xc1, 0x14, 0xb8, 0x02, 0x5d, 0x0f,
0x40, 0x5d, 0x22, 0x3c, 0x27, 0x51, 0xc6, 0xeb, 0xdc, 0x6b, 0x8c,
0xe7, 0x8a, 0x8f, 0xc5, 0xf6, 0x59, 0x94, 0xf6, 0xf9, 0x47, 0x59,
0xb4, 0x3f, 0xf2, 0x31, 0x5b, 0x9d, 0xa3, 0x14, 0xc0, 0x3e, 0x8a,
0xee, 0xf7, 0xf9, 0xb9, 0x11, 0xe7, 0xf7, 0xd9, 0xf7, 0xd0, 0x59,
0x0d, 0x6f, 0x81, 0xdb, 0xa0, 0xc8, 0xb5, 0x1a, 0x52, 0xad, 0x59,
0x9b, 0x05, 0xf0, 0x1b, 0xf8, 0x16, 0xfc, 0xc4, 0x7c, 0x3e, 0xf7,
0x75, 0x70, 0xef, 0x38, 0xbf, 0x57, 0xed, 0xd9, 0xb3, 0x7a, 0xdb,
0xb3, 0xfa, 0x97, 0x5f, 0xbb, 0xb8, 0x36, 0x39, 0xce, 0xff, 0x0e,
0xdc, 0x00, 0x3f, 0x70, 0x6d, 0xbf, 0x02, 0xbf, 0x82, 0x3f, 0xc0,
0xc7, 0xe0, 0x5d, 0x70, 0x15, 0x7c, 0x00, 0x3e, 0x01, 0x4f, 0x70,
0x8d, 0x6e, 0x32, 0x8f, 0xdf, 0x69, 0xef, 0x3a, 0xe5, 0x0d, 0xc6,
0x7a, 0x9e, 0x36, 0x7e, 0x01, 0x2d, 0xd4, 0x5f, 0xa3, 0x5c, 0xed,
0xeb, 0x14, 0x3f, 0xbb, 0xb6, 0xaf, 0xbe, 0x00, 0xaf, 0xfb, 0xf5,
0x71, 0x2f, 0xb3, 0x16, 0x36, 0x66, 0x3e, 0x9f, 0x9d, 0xb7, 0xeb,
0xed, 0x7c, 0xab, 0x4f, 0x38, 0xbf, 0x6d, 0x77, 0x7c, 0xe5, 0xb7,
0xb0, 0xdd, 0xc1, 0xfe, 0x1d, 0x5f, 0xdb, 0xf5, 0x4d, 0x7e, 0x13,
0xfb, 0xb7, 0x53, 0xdf, 0xdd, 0xec, 0xa5, 0xf4, 0x2d, 0xd4, 0x6f,
0x3e, 0x1b, 0x5f, 0xf9, 0x36, 0xca, 0x76, 0xce, 0x7f, 0x80, 0x6d,
0xd9, 0xdf, 0x4a, 0xb9, 0x2b, 0xd0, 0x6b, 0xbe, 0x64, 0x57, 0x60,
0x57, 0xf3, 0xba, 0x82, 0xf8, 0x5a, 0x03, 0xbb, 0xd2, 0xaf, 0xa5,
0x54, 0xbe, 0x8a, 0x77, 0xd1, 0x3e, 0xf3, 0x50, 0xbc, 0xea, 0xef,
0x08, 0xfc, 0x2a, 0x3f, 0xe5, 0xaf, 0x78, 0x95, 0x9f, 0xe6, 0x2b,
0x8e, 0x70, 0x9c, 0xe2, 0xe9, 0x7e, 0xdf, 0xdb, 0x6f, 0x0b, 0xf2,
0xce, 0x71, 0x7c, 0xb3, 0xf7, 0xbf, 0xff, 0x5f, 0xc6, 0xd1, 0xc8,
0x71, 0xd4, 0x2f, 0xda, 0x6f, 0x0d, 0xe6, 0x85, 0x7e, 0xd4, 0x9f,
0x09, 0xd6, 0x23, 0x5c, 0x97, 0xc6, 0xa0, 0xdd, 0x14, 0xf8, 0xbb,
0x53, 0xfd, 0xc2, 0xfd, 0x21, 0x29, 0xbd, 0xea, 0x15, 0xe4, 0xb5,
0x68, 0x5f, 0xf1, 0x86, 0xfb, 0x46, 0xfa, 0x4d, 0x41, 0xbe, 0x6a,
0x6b, 0x7d, 0x15, 0x4f, 0x28, 0x95, 0x5f, 0xb8, 0x5e, 0xd9, 0x20,
0x2e, 0xb5, 0x95, 0x7f, 0x26, 0xa8, 0x67, 0xe8, 0x57, 0x71, 0x85,
0x32, 0x8c, 0x3b, 0xcc, 0x57, 0x7e, 0x54, 0x5f, 0xf5, 0xef, 0x0c,
0x9e, 0x33, 0x3d, 0x7f, 0xb2, 0xb7, 0x32, 0xc8, 0x5f, 0xeb, 0xa0,
0xfe, 0x54, 0xb0, 0x4e, 0x92, 0xca, 0x4f, 0x75, 0xae, 0xa6, 0x54,
0x9e, 0xd9, 0xc0, 0x7f, 0x18, 0x57, 0x7b, 0xe0, 0x47, 0xeb, 0xaa,
0xf1, 0xf2, 0xa3, 0x71, 0xe1, 0x3a, 0xaa, 0xde, 0xb9, 0x40, 0x2a,
0x0f, 0xe5, 0xa9, 0x75, 0x0a, 0xc7, 0xe9, 0xb9, 0x96, 0x3d, 0xfd,
0x6f, 0x74, 0x04, 0x76, 0xe8, 0xd7, 0x2d, 0xbd, 0x3b, 0xf1, 0x6e,
0x72, 0x8f, 0x81, 0xc7, 0xc1, 0x3e, 0xf0, 0x90, 0xf3, 0xe7, 0x06,
0xbc, 0x1b, 0xe3, 0xf7, 0x90, 0x9d, 0x47, 0x0e, 0xb2, 0xff, 0x20,
0xfb, 0xfa, 0x40, 0x8f, 0xf3, 0xff, 0xe7, 0xd6, 0xde, 0x43, 0xdd,
0x3e, 0xce, 0xe9, 0xe7, 0xbc, 0xbd, 0xec, 0xeb, 0xa1, 0x34, 0x5f,
0xf6, 0x4e, 0xb1, 0xf3, 0x8d, 0x9d, 0x21, 0x0a, 0xb4, 0x6b, 0x7a,
0x9d, 0x25, 0xac, 0xcf, 0xde, 0x39, 0x63, 0xe0, 0x04, 0xe5, 0x49,
0xe7, 0xff, 0xe3, 0x4d, 0x3f, 0xcc, 0x31, 0x43, 0x8c, 0xbb, 0x97,
0xfe, 0x06, 0xa9, 0x1b, 0x4c, 0x30, 0xe0, 0x96, 0xce, 0x25, 0xc3,
0xec, 0x2f, 0x26, 0x7c, 0x8d, 0xf0, 0xbe, 0x48, 0xc6, 0xe9, 0xc7,
0x38, 0x4e, 0x7f, 0xfd, 0x1c, 0x37, 0x41, 0x1b, 0x7a, 0x27, 0x8e,
0x32, 0xb6, 0xa3, 0xcc, 0x41, 0xfa, 0x63, 0xd4, 0xe9, 0x7e, 0x9c,
0xb2, 0xc8, 0x31, 0x23, 0xcb, 0x8c, 0x1d, 0xa3, 0xbf, 0x13, 0x64,
0x92, 0x7d, 0xc7, 0x96, 0xc9, 0x39, 0x59, 0xbb, 0x42, 0xa2, 0x0e,
0x03, 0xec, 0x1b, 0x49, 0xf8, 0xb5, 0xf3, 0xe6, 0x29, 0xe7, 0xcf,
0x67, 0xa7, 0x98, 0xc3, 0x24, 0xeb, 0x79, 0x92, 0x7e, 0x47, 0x69,
0xbf, 0x40, 0x1b, 0xca, 0x57, 0xf5, 0x3c, 0x44, 0x0a, 0x5c, 0x27,
0xd3, 0xf7, 0x31, 0xae, 0x3c, 0xfb, 0x6c, 0xbc, 0xed, 0x0d, 0x3b,
0xb3, 0x3e, 0xca, 0x79, 0x03, 0x89, 0xb1, 0xda, 0x6b, 0x2b, 0x2a,
0x48, 0x75, 0x85, 0xa8, 0xa9, 0x20, 0xb5, 0x15, 0xa4, 0xae, 0x42,
0x68, 0xaf, 0xd9, 0x41, 0x1f, 0xe7, 0x59, 0x67, 0x67, 0x40, 0xfb,
0x66, 0xd4, 0x1e, 0x50, 0x5d, 0x6c, 0xac, 0x7d, 0x83, 0xd9, 0x37,
0xe5, 0x2a, 0xce, 0xb3, 0x33, 0xde, 0x5d, 0xce, 0x7f, 0x83, 0xd8,
0x99, 0xd5, 0xbe, 0x11, 0xec, 0xdc, 0x6b, 0x67, 0x42, 0xfb, 0x6e,
0xb1, 0xef, 0x24, 0xfb, 0x2e, 0xb1, 0xf3, 0xa4, 0x7d, 0x1b, 0xdc,
0xe7, 0xfc, 0x59, 0xd2, 0xce, 0xf0, 0x76, 0x96, 0xb6, 0x6f, 0xd5,
0x8d, 0x15, 0xf4, 0xfd, 0x7f, 0xcc, 0xb9, 0x82, 0xbe, 0xd3, 0xa9,
0xd8, 0x77, 0x3a, 0xb6, 0xbf, 0xa2, 0x5c, 0x3a, 0x37, 0x35, 0x47,
0x83, 0xd5, 0x52, 0x1e, 0xbe, 0x38, 0x53, 0x9e, 0x62, 0xa3, 0xa6,
0x38, 0x33, 0x5d, 0x9a, 0xed, 0x3c, 0xc2, 0x66, 0x7a, 0xec, 0xd9,
0xf2, 0x19, 0xdd, 0x8f, 0x4e, 0x9d, 0x3b, 0xaf, 0x39, 0x43, 0x33,
0xe5, 0x0b, 0xcf, 0xb0, 0x51, 0xd5, 0x57, 0x7a, 0x31, 0x74, 0x74,
0x7a, 0xba, 0x34, 0x27, 0x47, 0x52, 0xd6, 0x9f, 0x29, 0x5d, 0x28,
0x75, 0x9e, 0x9d, 0x45, 0x0c, 0xc1, 0xf0, 0xba, 0xd9, 0x99, 0xe7,
0x3b, 0x15, 0x9b, 0x25, 0x9e, 0xba, 0x84, 0x9f, 0x85, 0x85, 0x85,
0xa7, 0x21, 0x6e, 0xff, 0x07, 0x03, 0xf3, 0xcf, 0x7e, 0xc7, 0x11,
0x00, 0x00))
The issue is evidently with the shared folder. I've been doing that
(sharing the folder) for years and never encountered a problem.

Post by p_connolly
Bill Dunlap
TIBCO Software
wdunlap tibco.com [1]
On Mon, Nov 12, 2018 at 12:42 PM, p_connolly

Er, where, what, how? I can't reproduce that, at least not on 3.5.1
x <- airquality
saveRDS(x, file = "x.rds")
x <- NULL
x <- readRDS(file = "x.rds")
x
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
...
Looks fine to me.

x <- airquality
saveRDS(x, file = "x.rds")
saveRDS(x, file = "y.rds")

Files x.rds and y.rds are identical in size but utterly different in
content.
## On Linux 3.5.1

x <- readRDS(file = "x.rds")

Error in readRDS(file = "x.rds") : error reading from connection

x <- readRDS(file = "y.rds")
head(x)

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
It might just be the age of the Windows installation. I don't have
much use for Windows, so I haven't had much inclination to install a
newer version.
YMMV

?
-pd

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23

______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-help [2]
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html [3]
and provide commented, minimal, self-contained, reproducible code.
------
[1] http://tibco.com
[2] https://stat.ethz.ch/mailman/listinfo/r-help
[3] http://www.R-project.org/posting-guide.html

p_connolly

2018-11-13 22:10:11 UTC

Permalink

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.

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

[...]

______________________________________________
R-***@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

2018-11-14 07:35:55 UTC

Permalink

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

~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

______________________________________________
R-***@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.

Ista Zahn

2018-11-15 14:53:50 UTC

Permalink

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

Post by Patrick Connolly
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.
|> Perhaps you got bitten by Dolphin's non-modal dialogs, as described in
|>
|> 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
|>
|>
|> > 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.
|> >
|> >
|> >
|> >> 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
|> >>
|> > [...]
|> >
|> >
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___ Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) ..... Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
______________________________________________
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

2018-11-18 08:44:38 UTC

Permalink

Sequence of steps:

Using R-3.5.1 and Windows 7 with the latest Rstudio, shared directory

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.)

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

2018-12-01 06:38:18 UTC

Permalink

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