[BioC] MacOS Package installation problems

Thu May 31 20:12:48 CEST 2012

Hi everyone,

Just a quick note to say that the new version of BiocInstaller is
available, so this issue (of biocLite() not working on Mac systems)
should not recur. When you use biocLite() it automatically updates you
to the latest version of BiocInstaller.

Thanks,
Dan

On Wed, May 30, 2012 at 12:39 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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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>>>>>
>>>>
>>>