[BioC] Wow, what have I done

[Kasper Daniel Hansen]

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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