R devel - Nov 2006 - CRAN task views work only once per session (PR#9330)

Cran task views seems to be a "once-per-session" process -- the first
attempt to access views in a (RGui for Windows) session works, but
subsequent attempts fail. There is a noticeably long pause before
the failing call returns.

Example session with two calls to "available.views" follows, but
similar
effects have been observed with two calls to "install.views" and even
a call to "available.views" followed by a call to
"install.views".


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.
> 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"     
> available.views(repos="http://cran.uk.r-project.org")
Error: could not find function
"available.views"
> library(ctv)
> available.views(repos="http://cran.uk.r-project.org")
CRAN Task Views
---------------
Name: Bayesian
Topic: Bayesian Inference
Maintainer: Jong Hee Park
Repository: http://cran.uk.r-project.org
---------------
Name: Cluster
Topic: Cluster Analysis & Finite Mixture Models
Maintainer: Friedrich Leisch and Bettina Gruen
Repository: http://cran.uk.r-project.org
---------------
Name: Econometrics
Topic: Computational Econometrics
Maintainer: Achim Zeileis
Repository: http://cran.uk.r-project.org
---------------
Name: Environmetrics
Topic: Analysis of ecological and environmental data
Maintainer: Gavin Simpson
Repository: http://cran.uk.r-project.org
---------------
Name: Finance
Topic: Empirical Finance
Maintainer: Dirk Eddelbuettel
Repository: http://cran.uk.r-project.org
---------------
Name: Genetics
Topic: Statistical Genetics
Maintainer: Giovanni Montana
Repository: http://cran.uk.r-project.org
---------------
Name: Graphics
Topic: Graphic Displays & Dynamic Graphics & Graphic Devices &  
   Visualization
Maintainer: Nicholas Lewin-Koh
Repository: http://cran.uk.r-project.org
---------------
Name: MachineLearning
Topic: Machine Learning & Statistical Learning
Maintainer: Torsten Hothorn
Repository: http://cran.uk.r-project.org
---------------
Name: Multivariate
Topic: Multivariate Statistics
Maintainer: Paul Hewson
Repository: http://cran.uk.r-project.org
---------------
Name: SocialSciences
Topic: Statistics for the Social Sciences
Maintainer: John Fox
Repository: http://cran.uk.r-project.org
---------------
Name: Spatial
Topic: Analysis of Spatial Data
Maintainer: Roger Bivand
Repository: http://cran.uk.r-project.org
---------------
Name: gR
Topic: gRaphical models in R
Maintainer: Claus Dethlefsen
Repository: http://cran.uk.r-project.org
> available.views(repos="http://cran.uk.r-project.org")
CRAN Task Views
no views found
> 
--please do not edit the information below--

Version:
 platform = i386-pc-mingw32
 arch = i386
 os = mingw32
 system = i386, mingw32
 status = 
 major = 2
 minor = 4.0
 year = 2006
 month = 10
 day = 03
 svn rev = 39566
 language = R
 version.string = R version 2.4.0 (2006-10-03)

Windows XP Professional (build 2600) Service Pack 2.0

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

Search Path:
 .GlobalEnv, package:ctv, package:methods, package:stats,
package:graphics, package:grDevices, package:utils, package:datasets,
Autoloads, package:base

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One comment - taken from the FAQ - in advance:
  Bug reports on contributed packages should be sent first to the package
  maintainer, and only submitted to the R-bugs repository by package
  maintainers, mentioning the package in the subject line.

In this case, posting to R-devel (but not R-bugs) and Cc to me (as the
maintainer of ctv) would also have been ok.

As for your problem: On my Linux machine, the code

  library("ctv")
  x <- available.views(repos = "http://CRAN.uk.R-project.org")
  y <- available.views(repos = "http://CRAN.uk.R-project.org")

runs without any problem, x and y are also identical afterwards. As I
haven't got a Windows XP machine, could someone on the list please run the
code above and confirm (or disconfirm) that the second call takes longer
and finally finds no views.

thx in advance,
Z

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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> -----Original Message-----
> From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
> Sent: 06 November 2006 11:42
> To: Keith Ponting
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] CRAN task views work only once per session (PR#9330)
> 
> 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.
R-patched runs the offending code repeatedly without complaint (and my
original problem with ctv available.views is also solved) so I will look
forward to the next release.

Thankyou for your time (and to you and all responsible for R itself!).

Keith Ponting 


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