[BioC] MacOS Package installation problems

Fri Jun 1 17:39:53 CEST 2012

On Fri, Jun 1, 2012 at 8:35 AM, Chinedu Orekie <Chinedu at tntcmedia.us> wrote:
> Working from the drop down menu, I pointed to the CRAN mirror and on selecting "Install Packages" I get the error "Error in read.dcf(file = tmpf):  Line starting '<DOCTYPE html PUBLI...' is malformed".
>
> I see the same error when I select "Update Packages" as well.
>
> This is bug is certainly not package specific since i never get to where I can request one.
>

I am not sure if this is a Bioconductor issue, but what happens if you
try biocLite() as suggested earlier?
Dan

> Chinedu
> "TNTC: The need to connect" | P: (908) 514-TNTC
>
> On May 31, 2012, at 10:00 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>> 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
>>>>
>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>