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

[Brant Inman]

Thank you for your suggestion.  I did as you suggested and switched  
from USA (NC) to USA (IA).

Again, the packages seemed to download OK but this time a single error  
message appeared:

----------

...<snip>...

==================================================
downloaded 168 Kb

trying URL 
'http://streaming.stat.iastate.edu/CRAN/bin/macosx/universal/contrib/2.7/zoo_1.5-4.tgz'
Content type 'application/x-gzip' length 749912 bytes (732 Kb)
opened URL
==================================================
downloaded 732 Kb

Error: cannot remove prior installation of package ‘fSeries’
>


----------

This error appears to have stopped the package updating, since when I  
type update.packages() again, the whole list of packages is generated,  
implying that they have not been updated.

Any other suggestions?  Would uninstalling R and then reinstalling it  
help?


Brant

---------


On Sep 4, 2008, at 2:59 PM, Prof Brian Ripley wrote:

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,                  [EMAIL PROTECTED]
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

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