[BioC] MacOS Package installation problems

Wed May 30 21:39:36 CEST 2012

On Wed, May 30, 2012 at 12:28 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Wed, May 30, 2012 at 12:02 PM, Michael Salbaum
> <Michael.Salbaum at pbrc.edu> wrote:
>> Thanks for the help, I thought it was just me...
>>
>>
>>
>> michael
>>
>>
>> -----Original Message-----
>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
>> Sent: Wed 5/30/2012 1:57 PM
>> To: Michael Salbaum
>> Cc: Sean Davis; bioconductor at r-project.org
>> Subject: Re: [BioC] MacOS Package installation problems
>>
>> Hi Michael,
>>
>>
>> On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum
>> <Michael.Salbaum at pbrc.edu> wrote:
>>> Hi Dan,
>>>
>>> I tried setting BioC as well as CRAN mirror as suggested.
>>
>>>
>>
>> It looks like there is a problem with the CRAN mirrors.
>> I tried installing DESeq on my own Mac and got the same problem as
>> you. I got it even if I tried the master mirror in Switzerland
>> (http://stat.ethz.ch/CRAN).
>>
>> I will report this to the CRAN people and let you know what I hear from
>> them.
>
> Actually, it turns out the problem was on our end. The BiocInstaller
> package should not include CRANextra in its list of repositories if
> you are not on Windows. That repository is meant for Windows only and
> going to the Mac portion of the URL will cause an error.
>
> This is fixed in BiocInstaller 1.4.5 (release) and 1.5.9 (devel). It
> will not propagate to you until late tomorow (Thursday) morning
> Seattle time, so in the meantime you could try something like this:
>
> library(BiocInstaller)
> repos <- biocinstallRepos()
> repos <- repos[!names(repos) %in% "CRANextra"]
> install.packages("DEseq", repos=repos)
>

There was a typo, that last line should be:
install.packages("DESeq", repos=repos)

Thanks,
Dan


> I apologize for the inconvenience.
>
> Dan
>
>
>>
>> In the meantime, you might try
>> biocLite("DESeq", type="source")
>> If you have the right development tools installed, that should work.
>> The "tedious" solution you came up with will also work until this is
>> resolved.
>>
>> Dan
>>
>>
>>
>>> Using
>>>
>>>
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("DESeq")
>>>
>>> still directed to the resources listed below, with access problems, and
>>> single packages listed as missing.
>>>
>>> So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming
>>> that
>>> it's close to Louisiana),
>>> and used the R package installer to fetch the 'missing' packages one by
>>> one
>>> (things like: xtable, genefilter, geneplotter and a few more).
>>>
>>> I apologize for my clumsiness in the ways of R, but I'm originally a
>>> wetbench person...
>>>
>>>
>>> Cheers, michael
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
>>> Sent: Wed 5/30/2012 1:21 PM
>>> To: Michael Salbaum
>>> Cc: Sean Davis; bioconductor at r-project.org
>>> Subject: Re: [BioC] MacOS Package installation problems
>>>
>>> Hi Michael,
>>>
>>> On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum
>>> <Michael.Salbaum at pbrc.edu> wrote:
>>>> Got it to work.
>>>> A bit tedious, loading single packages by hand, but nevertheless.
>>>
>>> What do you mean by this? You should not have to *install* single
>>> packages by hand.
>>> The following should install DESeq and all its dependencies in one
>>> step (assuming you set your CRAN mirror to a working mirror as
>>> discussed earlier):
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("DESeq")
>>>
>>> Then, to *load* DESeq, the following should load it and all its
>>> dependencies:
>>>
>>> library(DESeq)
>>>
>>> What was the tedious part?
>>> Dan
>>>
>>>
>>>
>>>> Thanks for the help,
>>>>
>>>> Cheers, michael
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
>>>> Sent: Wed 5/30/2012 11:35 AM
>>>> To: Sean Davis
>>>> Cc: Michael Salbaum; bioconductor at r-project.org
>>>> Subject: Re: [BioC] MacOS Package installation problems
>>>>
>>>> On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>>>> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>>>>> wrote:
>>>>>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum
>>>>>> <Michael.Salbaum at pbrc.edu> wrote:
>>>>>>> Hi everyone,
>>>>>>>
>>>>>>> Newbie question:
>>>>>>>
>>>>>>> I'm having trouble with package installation on a Mac (OS 10.6.8)
>>>>>>>
>>>>>>>>  source("http://bioconductor.org/biocLite.R")
>>>>>>>>     biocLite("DESeq")
>>>>>>> BioC_mirror: http://bioconductor.org
>>>>>>> Using R version 2.15, BiocInstaller version 1.4.4.
>>>>>>> Warning: unable to access index for repository
>>>>>>>
>>>>>>>
>>>>>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15
>>>>>>> Installing package(s) 'DESeq'
>>>>>>> Warning: unable to access index for repository
>>>>>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15
>>>>>>> Error: Line starting '<!DOCTYPE html PUBLI ...' is malformed!
>>>>>>>
>>>>>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux
>>>>>>> directory, but no macosx
>>>>>>>
>>>>>>> Advice  is greatly appreciated - thanks!
>>>>>>
>>>>>> I would suggest using bioconductor.org as your repository.
>>>>>> Try:
>>>>>> chooseBioCmirror()
>>>>>> And choose the "Seattle" option.
>>>>>
>>>>> Dan, did you mean CRAN mirror?
>>>>>
>>>>> chooseCRANmirror()
>>>>>
>>>>> It looks like the CRAN mirror was the issue.
>>>>
>>>> You are correct, my mistake.
>>>> Dan
>>>>
>>>>
>>>>
>>>>>
>>>>> Sean
>>>>>
>>>>>> Dan
>>>>>>
>>>>>>
>>>>>>>
>>>>>>> J. Michael Salbaum, Ph.D.
>>>>>>> Associate Professor
>>>>>>> Pennington Biomedical Research Center
>>>>>>> Louisiana State University System
>>>>>>> 6400 Perkins Road
>>>>>>> Baton Rouge, LA 70808
>>>>>>>
>>>>>>> (225) 763-2782
>>>>>>>
>>>>>>>
>>>>>>>        [[alternative HTML version deleted]]
>>>>>>>
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>>>>>>
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>>>>
>>>
>>