From berwin at maths.uwa.edu.au  Mon Aug 29 12:55:04 2005
From: berwin at maths.uwa.edu.au (Berwin A Turlach)
Date: Mon, 29 Aug 2005 18:55:04 +0800
Subject: [Rd] robustness of install.packages/update.packages (was Re:
 bug in L-BFGS-B? (PR#8099))
In-Reply-To: <Pine.LNX.4.61.0508291027350.30101@gannet.stats>
References: <20050827141028.DCE0218B9F@slim.kubism.ku.dk>
	<Pine.LNX.4.61.0508271525290.4656@gannet.stats>
	<17169.40182.935036.246380@bossiaea.maths.uwa.edu.au>
	<Pine.LNX.4.61.0508281813240.15601@gannet.stats>
	<Pine.LNX.4.61.0508291027350.30101@gannet.stats>
Message-ID: <17170.59784.707764.393102@bossiaea.maths.uwa.edu.au>

G'day Brian,

>>>>> "BDR" == Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:

    >>> However, update.packages() wanted to update quite a few
    >>> packages besides MASS (the other packages in the VR bundle,
    >>> nlme, lattice &c).  Once it failed on MASS, it terminated with
    >>> an error and did not update any of the other packages.  Would
    >>> it be possible to robustify update.packages behaviour such
    >>> that it would continue in such situations with updating the
    >>> remaining packages?
    >>  Not a good idea. Better to follow the FAQ.  At that point the
    >> dependencies have been worked out and will not be re-computed
    >> if a package installation fails.

    BDR> I checked, and I am unable to reproduce this.  I get
O.k., I tried to reproduce the behaviour.  So I installed the binary
distribution of R 2.1.1 in another directory on my laptop once more
(and then deleted the copy that I actually wanted to keep; shouldn't
do such things at this time of the day).

So below I attach what is, I believe a faithful reproduction of what I
tried to do yesterday.  Except that I did not run the file that
installs all the contributed packages that I like to have installed.

But it seems that now VR_7.2-17.zip has vanished from
mirror.aarnet.edu.au and you can see how on the first occassion the
download stops with an error.  I believe that in this case it could
have continued to download the other files.

Once I changed the mirror, the other behaviour that I mentioned
becomes apparent.  But I take your point that because of package
dependencies it might actually be not wise to continue with updating
further packages once the update of a package has failed.  But then,
shouldn't in that case (by the same argument) all the updates that
have been done already be undone again?

Cheers,

        Berwin

++++++++++++++++++ Transcript of R session ++++++++++++++++++++++++++++

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> library(MASS)
> update.packages()
boot :
 Version 1.2-22 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.2-23 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
VR :
 Version 7.2-16 installed in C:/PROGRA~1/R/rw2011/library 
 Version 7.2-17 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
cluster :
 Version 1.10.0 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.10.1 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
foreign :
 Version 0.8-8 installed in C:/PROGRA~1/R/rw2011/library 
 Version 0.8-9 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
lattice :
 Version 0.11-8 installed in C:/PROGRA~1/R/rw2011/library 
 Version 0.12-3 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
mgcv :
 Version 1.3-1 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.3-4 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
nlme :
 Version 3.1-60 installed in C:/PROGRA~1/R/rw2011/library 
 Version 3.1-62 available at http://mirror.aarnet.edu.au/pub/CRAN
Update (y/N/c)?  y
trying URL 'http://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/2.1/boot_1.2-23.zip'
Content type 'application/zip' length 767814 bytes
opened URL
downloaded 749Kb

trying URL 'http://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/2.1/VR_7.2-17.zip'
Error in download.file(url, destfile, method, mode = "wb") : 
        cannot open URL 'http://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/2.1/VR_7.2-17.zip'
In addition: Warning message:
cannot open: HTTP status was '404 Not Found' 
> options(repos=c(CRAN="http://cran.au.r-project.org/"))
> options()$repos
                           CRAN 
"http://cran.au.r-project.org/" 
> update.packages()
boot :
 Version 1.2-22 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.2-23 available at http://cran.au.r-project.org
Update (y/N/c)?  y
VR :
 Version 7.2-16 installed in C:/PROGRA~1/R/rw2011/library 
 Version 7.2-19 available at http://cran.au.r-project.org
Update (y/N/c)?  y
cluster :
 Version 1.10.0 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.10.1 available at http://cran.au.r-project.org
Update (y/N/c)?  y
foreign :
 Version 0.8-8 installed in C:/PROGRA~1/R/rw2011/library 
 Version 0.8-10 available at http://cran.au.r-project.org
Update (y/N/c)?  y
lattice :
 Version 0.11-8 installed in C:/PROGRA~1/R/rw2011/library 
 Version 0.12-5 available at http://cran.au.r-project.org
Update (y/N/c)?  y
mgcv :
 Version 1.3-1 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.3-6 available at http://cran.au.r-project.org
Update (y/N/c)?  y
nlme :
 Version 3.1-60 installed in C:/PROGRA~1/R/rw2011/library 
 Version 3.1-64 available at http://cran.au.r-project.org
Update (y/N/c)?  y
trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/boot_1.2-23.zip'
Content type 'application/zip' length 767814 bytes
opened URL
downloaded 749Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/VR_7.2-19.zip'
Content type 'application/zip' length 1575000 bytes
opened URL
downloaded 1538Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/cluster_1.10.1.zip'
Content type 'application/zip' length 480389 bytes
opened URL
downloaded 469Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/foreign_0.8-10.zip'
Content type 'application/zip' length 176663 bytes
opened URL
downloaded 172Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/lattice_0.12-5.zip'
Content type 'application/zip' length 713040 bytes
opened URL
downloaded 696Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/mgcv_1.3-6.zip'
Content type 'application/zip' length 795159 bytes
opened URL
downloaded 776Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/nlme_3.1-64.zip'
Content type 'application/zip' length 2142405 bytes
opened URL
downloaded 2092Kb

package 'boot' successfully unpacked and MD5 sums checked
bundle 'VR' successfully unpacked and MD5 sums checked
Error: cannot remove prior installation of package 'MASS'
> search()
 [1] ".GlobalEnv"        "package:MASS"      "package:methods"  
 [4] "package:stats"     "package:graphics"  "package:grDevices"
 [7] "package:utils"     "package:datasets"  "Autoloads"        
[10] "package:base"     
> detach(2)
> update.packages()
VR :
 Version 7.2-16 installed in C:/PROGRA~1/R/rw2011/library 
 Version 7.2-19 available at http://cran.au.r-project.org
Update (y/N/c)?  y
cluster :
 Version 1.10.0 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.10.1 available at http://cran.au.r-project.org
Update (y/N/c)?  y
foreign :
 Version 0.8-8 installed in C:/PROGRA~1/R/rw2011/library 
 Version 0.8-10 available at http://cran.au.r-project.org
Update (y/N/c)?  y
lattice :
 Version 0.11-8 installed in C:/PROGRA~1/R/rw2011/library 
 Version 0.12-5 available at http://cran.au.r-project.org
Update (y/N/c)?  y
mgcv :
 Version 1.3-1 installed in C:/PROGRA~1/R/rw2011/library 
 Version 1.3-6 available at http://cran.au.r-project.org
Update (y/N/c)?  y
nlme :
 Version 3.1-60 installed in C:/PROGRA~1/R/rw2011/library 
 Version 3.1-64 available at http://cran.au.r-project.org
Update (y/N/c)?  y
trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/VR_7.2-19.zip'
Content type 'application/zip' length 1575000 bytes
opened URL
downloaded 1538Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/cluster_1.10.1.zip'
Content type 'application/zip' length 480389 bytes
opened URL
downloaded 469Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/foreign_0.8-10.zip'
Content type 'application/zip' length 176663 bytes
opened URL
downloaded 172Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/lattice_0.12-5.zip'
Content type 'application/zip' length 713040 bytes
opened URL
downloaded 696Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/mgcv_1.3-6.zip'
Content type 'application/zip' length 795159 bytes
opened URL
downloaded 776Kb

trying URL 'http://cran.au.r-project.org/bin/windows/contrib/2.1/nlme_3.1-64.zip'
Content type 'application/zip' length 2142405 bytes
opened URL
downloaded 2092Kb

bundle 'VR' successfully unpacked and MD5 sums checked
Error: cannot remove prior installation of package 'MASS'
> search()
[1] ".GlobalEnv"        "package:methods"   "package:stats"    
[4] "package:graphics"  "package:grDevices" "package:utils"    
[7] "package:datasets"  "Autoloads"         "package:base"     
>



[Rd] robustness of install.packages/update.packages (was Re: bug in L-BFGS-B? (PR#8099))
Berwin A Turlach