[Bioc-devel] Updated biocLite -- please try!

[Martin Morgan]

On 06/15/2011 12:59 AM, Laurent Gatto wrote:
> Dear Martin,
>
> On 14 June 2011 23:21, Martin Morgan<mtmorgan at fhcrc.org>  wrote:
>> Hi BiocDevelopers --
>>
>> As mentioned previously, we have revised how biocLite works. Please try
>>
>>    source("http://bioconductor.org/scratch-repos/biocLite.R")
>>
>> and then installing your favorite package
>>
>>   biocLite("MyFavoritePackage")
>>
>> The 'source()' command will download, install (first time only!) and load
>> the 'BiocInstaller' package.
>>
>> biocLite does behave differently. It'll check for out-of-date packages and
>> ask, after installing MyFavoritePackage, whether you'd like to update them.
>> With no arguments, biocLite() installs just Biobase, IRanges, and
>> AnnotationDbi. biocLite(character()) will look for out-of-date packages to
>> update. And ?biocLite will provide a help page(!).
>>
>> The revised behavior should only occur in the 'devel' version of R, R-2.13
>> should behave as before.
>>
>> Any feedback most welcome.
>
> Just tested package updating with the new biocLite revision
> (sessionInfo below) and everything worked well.
>
> Could you clarify the distinction between the Bioconductor and
> BiocInstaller packages? These look very similar.

The Bioconductor package was renamed BiocInstaller, and the Bioconductor 
package is being removed.

Thanks Laurent.

Martin

>
> Best wishes,
>
> Laurent
>
>> sessionInfo()
> R version 2.14.0 Under development (unstable) (2011-06-07 r56076)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>   [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8
>   [7] LC_PAPER=C                LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.1.11
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.0
>
>> Martin
>> --
>> Computational Biology
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>>
>> Location: M1-B861
>> Telephone: 206 667-2793
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793