[BioC] Wow, what have I done

[Loren Engrav]

Thank you
I tried and failed, you are right, I am confused
Am using R64 2.3.1 and the monster pack since it is available and I have not
installed Leopard as yet
But R64 2.3.1 monster does not include affyQCReport and I have failed at
loading it into R64 2.3.1 inspite of your trying to help

By the way, if I get Leopard up this weekend, where is an R64 for Leopard
with affyQCReport and affy?

Thank you

-- 
Loren Engrav
Univ Washington
Seattle

> From: Kasper Daniel Hansen <khansen at stat.Berkeley.EDU>
> Date: Tue, 11 Dec 2007 12:19:35 -0800
> To: Herve Pages <hpages at fhcrc.org>
> Cc: Loren Engrav <engrav at u.washington.edu>, "bioconductor at stat.math.ethz.ch"
> <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Wow, what have I done
> 
> On Dec 11, 2007, at 11:40 AM, Herve Pages wrote:
> 
>> Hi Loren,
>> 
>> Loren Engrav wrote:
>> [...]
>>> 1) does the biocLite method of packages work with R64bit
>> 
>> Like for the CRAN packages, Bioconductor universal binary packages
>> work for
>> the i386 and ppc archs only. So if you start R in 64-bit mode (with
>> --arch=x86_64
>> or --arch=ppc64), you will be able to install the universal binary
>> with biocLite()
>> but you won't be able to load it:
> 
> So this might be a bit confusing to Loren: when you install a a
> package on a mac there are two options:
> 1) Install a binary package. This is nice and quick. All that happens
> is that a zip file gets downloaded and unpackaged and mostly
> everything just works. This is probably how most people install
> packages for the mac.
> 2) install a source package. Here you just download the source code
> and then it needs to be compiled (this happens automatically). The
> drawback to this method is a) It takes longer to compiler than to
> unzip - this is not a bit issue on a fast machine and b) that you
> need a set of tools installed.
> 
>>> library(Biostrings)
>>   Error: package 'Biostrings' is not installed for 'arch=x86_64'
>> 
>> So what you need to do is install from source. Either with:
>> 
>>   options(pkgType="source")
>> 
>> or with
>> 
>>   biocLite("Biostrings", type="source")
> 
> This is how you change your option. If you type
>    getOption("pkgType")
> you see what your default option is - you probably have "mac.binary"
> 
> Kasper
> 
> 
>> Cheers,
>> H.
>> 
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