saveRDS() and readRDS() Why? [solved, pretty much anyway)

On 2018-11-13 12:55, William Dunlap wrote:

You wrote:
  ## 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 to
the Linux guest, I  get this:


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"

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

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

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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.

Bill Dunlap
TIBCO Software
wdunlap tibco.com [1]

On Mon, Nov 12, 2018 at 12:42 PM, p_connolly
<p_connolly at slingshot.co.nz> wrote:

On 2018-11-12 22:49, peter dalgaard wrote:

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

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

<p_connolly at slingshot.co.nz> wrote:

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.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com