Sorry now posting to the list

On Tue, Jan 18, 2011 at 10:01 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

>
>
> On Mon, Jan 17, 2011 at 6:45 AM, Pedro Gomez-Fabre <pedro.fabre@gmail.com>wrote:
>
>> Hi guys,
>>
>>
>>
>> I am trying to update bioconductor for an old release 2.10.1
>>
>>
>>
>> I have tried
>>
>>
>>
>> --------------------------
>>
>> BIO_R_Library <- .Library
>> BIO_R_Downloads_Allowed <- TRUE
>> source("http://bioconductor.org/biocLite.R")
>> update.packages(repos=biocinstallRepos(), ask=FALSE)
>>
>> --------------------------
>>
>>
>>
>> The error I am getting is
>>
>> ========
>>
>> Warning: unable to access index for repository
>> http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
>>
>> ========
>>
>>
>>
>> Looking at the url I could see the location is not available any longer.
>>
>>
>>
>> If I do a fresh installation of R and issue the same commands somehow it
>> passed the missing repository and looks for the information at fhcrc.org.
>>
>>
>>
>> --------------------------
>>
>> Warning: unable to access index for repository
>> http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
>>
>> also installing the dependencies 'multcomp', 'abind', 'miscTools', 'coin',
>> 'zoo', 'strucchange', 'gam', 'lmtest', 'colorspace', 'robustbase'
>>
>>
>>
>> trying URL '
>> http://cran.fhcrc.org/bin/windows/contrib/2.10/multcomp_1.2-3.zip'
>>
>> Content type 'application/zip' length 976410 bytes (953 Kb)
>>
>> opened URL
>>
>> ...
>>
>> --------------------------
>>
>>
>>
>> Issuing the same command again produce the error seen first.
>>
>>
>>
>> Do you know how I can select a valid location? Is there any way I can
>> decide
>> what server I have to be looking at? Alternatives?
>>
>>
>>
>>
> Hi Pedro,
>
> This is just a warning and can be safely ignored. Your packages should have
> updated correctly. Email the list if that is not the case, and include the
> output of sessionInfo().
>
> Thanks,
> Dan
>
>
> Hi Dan,

Thanks for responding.

Please find the information you requested.

> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
> BIO_R_Library <- .Library
> BIO_R_Downloads_Allowed <- TRUE
> source("http://bioconductor.org/biocLite.R")
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
> update.packages(repos=biocinstallRepos(), ask=FALSE)
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.10.1
>

How can I bypass the error?


>
>
>> Thanks in advance for your help.
>>
>> Pedro
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
>

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