From ripley at stats.ox.ac.uk  Mon Nov  6 12:42:26 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 6 Nov 2006 11:42:26 +0000 (GMT)
Subject: [Rd] CRAN task views work only once per session (PR#9330)
In-Reply-To: <6583C92252A35A4C97E64E50716110F8034FFB8E@mailx03.virtual-email.net>
References: <6583C92252A35A4C97E64E50716110F8034FFB8E@mailx03.virtual-email.net>
Message-ID: <Pine.LNX.4.64.0611061140410.21505@gannet.stats.ox.ac.uk>

I think the following item in NEWS for R-patched may be relevant:

     o   load()ing from a connection had a logic bug in when it closed
         the connection. (PR#9271)

so please try R-patched.


On Mon, 6 Nov 2006, Keith Ponting wrote:

> Thankyou to those who have replied to this thread.
>
> I have now reproduced similar effects in a way which does not directly
> involve CRAN task views. (I have also reproduced the original problem on
> a different machine within
> our site and using a different mirror.)
>
> The following sequence of commands works repeatedly within plain Rterm
> (actually running under XEmacs) on Windows XP:
>
> x<-url("http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds",open="rb"
> );
> showConnections()
> .readRDS(x);
> showConnections()
> close(x)
> showConnections()
>
> However under RGui on the same system, second and subsequent attempts
> time out in .readRDS (see session log below) and note that although the
> connection is shown as open immediately before the second .readRDS call,
> it is shown as closed immediately after that (failing) call.
>
> I wonder whether something in RGui is holding on to connections after
> they have been closed. Even while .readRDS is timing out in one RGui
> session, I can run that sequence of calls in plain Rterm or (once!) in
> another RGui session without problems, which I hope eliminates the
> possibility that it is our company firewall or something else on my PC
> holding on to the connection in some way.
>
> ---------- session log starts
> ------------------------------------------------
>
> R version 2.4.0 (2006-10-03)
> Copyright (C) 2006 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>>
> x<-url("http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds",open="rb"
> );
>> showConnections()
>  description                                             class mode
> text
> 3 "http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds" "url" "rb"
> "binary"
>  isopen   can read can write
> 3 "opened" "yes"    "no"
>> .readRDS(x);
>> showConnections()
>  description                                                    class
> mode
> 3 "gzcon(http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds)" "gzcon"
> "rb"
>  text     isopen   can read can write
> 3 "binary" "opened" "yes"    "no"
>> close(x)
>> showConnections()
>     description class mode text isopen can read can write
>>
> x<-url("http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds",open="rb"
> );
>> showConnections()
>  description                                             class mode
> text
> 3 "http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds" "url" "rb"
> "binary"
>  isopen   can read can write
> 3 "opened" "yes"    "no"
>> .readRDS(x);
> Error in .readRDS(x) : connection is not open
> In addition: Warning message:
> InternetOpenUrl failed: 'The operation timed out'
>> showConnections()
>     description class mode text isopen can read can write
>> close(x)
>> showConnections()
>     description class mode text isopen can read can write
>>
> x<-url("http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds",open="rb"
> );
>> showConnections()
>  description                                             class mode
> text
> 3 "http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds" "url" "rb"
> "binary"
>  isopen   can read can write
> 3 "opened" "yes"    "no"
>> .readRDS(x);
> Error in .readRDS(x) : connection is not open
> In addition: Warning message:
> InternetOpenUrl failed: 'The operation timed out'
>> showConnections()
>     description class mode text isopen can read can write
>> close(x)
>> showConnections()
>     description class mode text isopen can read can write
>>
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"
>>
>
> ---------- session log ends
> ------------------------------------------------
>
> If I remove the .readRDS(x) call, there is no problem - the following
> command sequence does work repeatedly:
> x<-url("http://www.sourcekeg.co.uk/cran/src/contrib/Views.rds",open="rb"
> );
> showConnections()
> close(x)
> showConnections()
>
> Dr. Keith Ponting
> Principal Scientist
>
> Aurix Ltd
> Malvern Hills Science Park
> Geraldine Rd  Malvern  Worcestershire  WR14 3SZ  UK
>
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-- 
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



[Rd] CRAN task views work only once per session (PR#9330)
Prof Brian Ripley