[Rd] robustness of install.packages/update.packages (was Re: bug in L-BFGS-B? (PR#8099))
Berwin A Turlach
berwin at maths.uwa.edu.au
Mon Aug 29 12:55:04 CEST 2005
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 ++++++++++++++++++++++++++++
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> 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"
>
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