[R] [R-SIG-Mac] Error with update.packages()

[Prof Brian Ripley]

Try another mirror: this is not the first time we've seen problems at 
www.ibiblio.org.

On Thu, 4 Sep 2008, Brant Inman wrote:

> R-helpers:
>
> I just updated from R 7.0 to R 7.2.2 today.  I am using MAC OS X
> version 10.5.4 on a Macbook to run R.
>
> ----------------------------
>
> > sessionInfo()
> R version 2.7.2 (2008-08-25)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.2
>
> ----------------------------
>
> When I tried to update my packages, I got the following messages:
>
> ----------------------------
>
> > update.packages()
> Amelia :
>  Version 1.1-30 installed in /Library/Frameworks/R.framework/
> Resources/library
>  Version 1.1-33 available at http://www.ibiblio.org/pub/languages/R/
> CRAN
> Update (y/N/c)?  y
> empiricalBayes :
>  Version 2.0 installed in /Library/Frameworks/R.framework/Resources/
> library
>  Version 2.1 available at http://www.ibiblio.org/pub/languages/R/CRAN
> Update (y/N/c)?  y
> Matrix :
>  Version 0.999375-9 installed in /Library/Frameworks/R.framework/
> Resources/library
>  Version 0.999375-11 available at http://www.ibiblio.org/pub/languages/R/CRAN
> Update (y/N/c)?  y
>
> ...<snip, all seems well>....
>
> also installing the dependencies ?sandwich?, ?strucchange?, ?vcd?,
> ?rrcov?, ?spam?
>
> trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/sandwich_2.1-0.tgz'
> Content type 'application/x-gzip' length 678518 bytes (662 Kb)
> opened URL
> ==================================================
> downloaded 662 Kb
>
> trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/strucchange_1.3-3.tgz'
> Content type 'application/x-gzip' length 777150 bytes (758 Kb)
> opened URL
> ==================================================
> downloaded 758 Kb
>
> ...<snip, the errors begin>....
>
> trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/rrcov_0.4-06.tgz'
> Content type 'application/x-gzip' length 365965 bytes (357 Kb)
> opened URL
> ==========================================
> downloaded 304 Kb
>
> trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/spam_0.15-0.tgz'
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>   cannot open URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/spam_0.15-0.tgz'
> In addition: Warning messages:
> 1: In download.file(url, destfile, method, mode = "wb", ...) :
>   downloaded length 312279 != reported length 365965
> 2: In download.file(url, destfile, method, mode = "wb", ...) :
>   unable to connect to 'mirrors.ibiblio.org' on port 80.
> Warning in download.packages(p0, destdir = tmpd, available =
> available,  :
>   download of package 'spam' failed
> trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/Amelia_1.1-33.tgz'
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>   cannot open URL 'http://www.ibiblio.org/pub/languages/R/CRAN/bin/macosx/universal/contrib/2.7/Amelia_1.1-33.tgz'
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>   unable to connect to 'mirrors.ibiblio.org' on port 80.
> Warning in download.packages(p0, destdir = tmpd, available =
> available,  :
>   download of package 'Amelia' failed
>
> ...<snip, the errors continue>....
>
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>   unable to connect to 'mirrors.ibiblio.org' on port 80.
> Warning in download.packages(p0, destdir = tmpd, available =
> available,  :
>   download of package 'zoo' failed
>
> gzip: stdin: unexpected end of file
> tar: Unexpected EOF in archive
> tar: Unexpected EOF in archive
> tar: Error is not recoverable: exiting now
> Error in sprintf(gettext(fmt, domain = domain), ...) :
>   argument is missing, with no default
>
> ----------------------------
>
> The first part of the procedure seemed to work, then came page after
> page of error messages.  Can someone tell me what is going on here and
> how I can fix the problem?  I found a similar report on R-help that
> was never resolved and also involved a MAC (http://tolstoy.newcastle.edu.au/R/e4/help/08/06/15556.html
> ).  Could this be a MAC issue?
>
> Thanks very much for your time.
>
> Brant Inman
> 	[[alternative HTML version deleted]]
>
>

-- 
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