R help - Feb 2011 - Error of 'memory not mapped' in ff Package with VirtualBox

Dear R Helpers,

I would like to report on an error in the ff package here.
The ff package is an R package which enables us to store large data on disk
systematically and have fast access to the database.
I used the package in Linux as a guest OS of VirtualBox, and executed the
following commands.

library(ff)
x<-ff(1:5,length=5,update=TRUE,vmode="double",filename="header.ff",overwrite=TRUE)

Afterwards, I got the following error message.

*** caught segfault ***
address 0xffffffff, cause 'memory not mapped'

Traceback:
 1: .Call("get_vector", .ffmode[vmode], attr(x, "physical"),
index,
nreturn, PACKAGE = "ff")
 2: `[.ff`(ret, 1)
 3: ret[1]
 4: as.vector(ret[1])
 5: identical(as.vector(initdata[1]), as.vector(ret[1]))
 6: ff(1:5, length = 5, update = TRUE, vmode = "double", filename
"header.ff",     overwrite = TRUE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

Can anyone give an advice to solve the problem?

Best Regards,
Ryan

-----
Wonsang You
Leibniz Institute for Neurobiology
-- 
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This is clearly a problem occuring in the C code of the ff package. 
Please report to the package maintainer, Cced here (with the 'at a 
minimum' information requested in the posting guide, most importantly 
the Linux architecture and the versions involved).

FWIW it works for me on
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
...
other attached packages:
[1] ff_2.2-1  bit_1.1-6

If possible, try running this under valgrind (see 'Writing R 
Extensions') to get more info on the cause: at least run under gdb to 
get more precise info on what was not mapped.

You don't say what the host OS of VirtualBox was.  We've found I/O 
under VirtualBox with a x86_64 Linux host to be slow, but R to run 
reliably.


On Wed, 2 Feb 2011, Wonsang You wrote:
>
> Dear R Helpers,
>
> I would like to report on an error in the ff package here.
> The ff package is an R package which enables us to store large data on disk
> systematically and have fast access to the database.
> I used the package in Linux as a guest OS of VirtualBox, and executed the
> following commands.
>
> library(ff)
>
x<-ff(1:5,length=5,update=TRUE,vmode="double",filename="header.ff",
         overwrite=TRUE)
>
> Afterwards, I got the following error message.
>
> *** caught segfault ***
> address 0xffffffff, cause 'memory not mapped'
>
> Traceback:
> 1: .Call("get_vector", .ffmode[vmode], attr(x,
"physical"), index,
> nreturn, PACKAGE = "ff")
> 2: `[.ff`(ret, 1)
> 3: ret[1]
> 4: as.vector(ret[1])
> 5: identical(as.vector(initdata[1]), as.vector(ret[1]))
> 6: ff(1:5, length = 5, update = TRUE, vmode = "double", filename
> "header.ff",     overwrite = TRUE)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
> Can anyone give an advice to solve the problem?
>
> Best Regards,
> Ryan
>
> -----
> Wonsang You
> Leibniz Institute for Neurobiology
> -- 
> View this message in context:
http://r.789695.n4.nabble.com/Error-of-memory-not-mapped-in-ff-Package-with-VirtualBox-tp3253856p3253856.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595