Re: [Rd] parse_Rd and/or lazyload problem

From: <luke_at_stat.uiowa.edu>
Date: Wed, 04 Nov 2009 15:23:30 -0600 (CST)

Here is a more stripped down variant generates and error on OS X for me:

     mkEg <- function(tm) list(scrunge = as.POSIXct(tm))

     extract <- function(db) {
 	e<- new.env()
 	lazyLoad(db, e)
 	as.list( e)
     }

     eg <- mkEg("2009-11-04 12:49:53")
     eg1 <- mkEg("2009-11-04 12:49:28")

     tools:::makeLazyLoadDB( eg, '/tmp/ll')
     extract('/tmp/ll') # force; OK

     tools:::makeLazyLoadDB( eg1, '/tmp/ll')
     extract('/tmp/ll')

Changing the second set of /tmp/ll makes the symptom go away.

I believe this comes down to unintended use of the lazyload mechanism -- in particular it is not intended that a database be rewritten after it has been loaded. There is a chaching mechanism for improved performance on slow file systems, and I believe what is happening is that the new indices are being used to look in the old chached data. There might be some merit in having lazyLoad call R_lazyLoadDBflush.

luke

On Tue, 3 Nov 2009, Seth Falcon wrote:

> Hi,
>
> On 11/3/09 6:51 PM, Mark.Bravington_at_csiro.au wrote:
>>
>> file.copy( 'd:/temp/Rdiff.Rd', 'd:/temp/scrunge.Rd') # Rdiff.Rd from
>> 'tools' package source
>>
>> eglist<- list( scrunge=parse_Rd( 'd:/temp/scrunge.Rd'))
>> tools:::makeLazyLoadDB( eglist, 'd:/temp/ll')
>> e<- new.env()
>> lazyLoad( 'd:/temp/ll', e)
>> as.list( e) # force; OK
>>
>> eglist1<- list( scrunge=parse_Rd( 'd:/temp/Rdiff.Rd'))
>> tools:::makeLazyLoadDB( eglist1, 'd:/temp/ll')
>> e<- new.env()
>> lazyLoad( 'd:/temp/ll', e)
>> as.list( e) # Splat
>>
>> It doesn't make any difference which file I process first; the error comes
>> the second time round.
>
> If I adjust this example in terms of paths and run on OS X, I get the
> following error on the second run:
>
>> as.list(e) # Splat
> Error in as.list.environment(e) : internal error -3 in R_decompress1
>
> I haven't looked further yet.
>
> + seth
>
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>

-- 
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:      luke_at_stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

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Received on Wed 04 Nov 2009 - 21:27:51 GMT

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