[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,                  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