[BioC] MacOS Package installation problems

Fri Jun 1 04:00:45 CEST 2012

Hi,

On Thu, May 31, 2012 at 6:36 PM, Chinedu Orekie <Chinedu at tntcmedia.us> wrote:
> Dan:
>
> I get the same error at separate internet connections (at home and at work). Now these are locations that worked in the past. So I am doubtful that a change in net connection is explanation.
>
> The sequence to seeing that error was: utils:::menuInstallPkgs() at the console and then on selecting a mirror site.

Which mirror site did you select? Did you try to install a package?
Which one? Was there any output besides the error message you sent?

> Your thoughts.

I don't know what could cause this.
The recommended way to install Bioconductor packages, and the only
method we support and can troubleshoot, is:

source("http://bioconductor.org/biocLite.R")
biocLite("pkgName")

Also, to rule out any problems with mirrors, you should run
chooseCRANmirror()
and
chooseBioCmirror()
and choose Switzerland
and
USA (WA 1)
respectively.

Dan

>
> Chinedu
> "TNTC: The need to connect" | P: (908) 514-TNTC
>
> On May 31, 2012, at 6:57 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>> Hi Chinedu,
>>
>> On Thu, May 31, 2012 at 7:48 AM, Chinedu Orekie <Chinedu at tntcmedia.us> wrote:
>>> I am having the same problem installing packages (Line starting '<!DOCTYPE html
>>> PUBLI ...' is malformed). It has not mattered which repoistory I cite, CRAN or
>>> BioC. I first observed this yesterday, 30 Jun 2012. This all seems quite recent
>>> since I was able to access packages only two weeks ago. My computer is Windows
>>> based by the way.
>>>
>>> Could this be some generic systems error?
>>>
>>
>> This is the first I have heard of this happening on windows systems.
>> Can you send the command that caused the error, as well as the full
>> error code and the output of sessionInfo()?
>>
>> Thanks,
>> Dan
>>
>>
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>>