[R-SIG-Mac] Error with update.packages()
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Sep 4 21:41:06 CEST 2008
On Thu, 4 Sep 2008, Brant Inman wrote:
> 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:
You need to do this from the account you used to install the package in
the first place. It's a permissions issue.
>
> ----------
>
> ...<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
>
--
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
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