[R] Error in installing packages

Thu Jun 7 00:09:51 CEST 2012

On 06/06/2012 01:41 PM, Andreia Leite wrote:
> Yes it's windows (vista). It's not a specific package. I've tried more than
> a CRAN mirror and the message it's always date (the list with the packages
> simply doesn't appear).
> What proxy settings should I verify specifically (sorry I don't know a lot
> on informatics)? I've installed a few packages before this and I never had
> such a message.

With a brand-new 2.9.2 I did this

 > utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Error in read.dcf(file = tmpf) :
   Line starting '<!DOCTYPE html PUBLI ...' is malformed!
 > traceback()
4: read.dcf(file = tmpf)
3: available.packages(contriburl = contriburl, method = method)
2: install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type)
1: utils:::menuInstallPkgs()
 >
 > trace(available.packages, tracer=quote(print(contriburl)))
Tracing function "available.packages" in package "utils"
[1] "available.packages"
 > utils:::menuInstallPkgs()
Tracing available.packages(contriburl = contriburl, method = method) on 
entry
[1] "http://cran.cs.wwu.edu/bin/windows/contrib/2.9"
[2] "http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.9"
Error in read.dcf(file = tmpf) :
   Line starting '<!DOCTYPE html PUBLI ...' is malformed!

and that second url is no longer valid (redirected to the institution 
home page). Perhaps

 > getOption("repos")
                       CRAN                            CRANextra
   "http://cran.cs.wwu.edu" "http://www.stats.ox.ac.uk/pub/RWin"
 > options(repos=getOption("repos")["CRAN"])
 > utils:::menuInstallPkgs()

A similar problem came up on the Bioconductor mailing list, where our 
installer was pointing Mac users to the non-existent

   http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15

Martin

>
> Thanks
>
> On Wed, Jun 6, 2012 at 6:11 PM, Uwe Ligges
> <ligges at statistik.tu-dortmund.de>wrote:
>
>>
>>
>> On 06.06.2012 17:14, Andreia Leite wrote:
>>
>>> Dear list,
>>>
>>> I'm trying to install a package but every time I select the option form
>>> the
>>> menu this error message appears:
>>>
>>>   utils:::menuInstallPkgs()
>>>>
>>> Error in read.dcf(file = tmpf) :
>>>    Line starting '<!DOCTYPE html PUBLI ...' is malformed!
>>>
>>> Do you have any clue of the reason why is it happening? I'm using a older
>>> version (2.9.2) but it always worked perfectly!
>>>
>>
>> Have you checked proxy settings?
>> Is this Windows?
>> Have you checked if the (also unstated) CRAN mirror you are using  works
>> correctly and delivers that part of the repository?
>>
>> Uwe ligges
>>
>>
>>
>>
>>
>>
>>
>>
>>> Best regards,
>>> Andreia LEite
>>>
>>> --
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>>>
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>>
>
>

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