[Bioc-devel] I will succeed (hopefully) the installation of Bioconductor 2.0

[Daniel Macedo Lorenzini]

Hi Herve,

You answered exactly what I needed. For some people (including me) it is
easier to use an R 2.4 pushing the bioconductor 2.0 inside than installing
R 2.5. I think this must be presented in the 2.0 installation
instruction website, even if you cannot guarantee the funcionality. If
someone is searching a devel version (2.0), he/she already knows that
somethings may not work.

Thanks a lot,

Daniel




On Fri, 27 Oct 2006, Herve Pages wrote:

> Daniel Macedo Lorenzini wrote:
> >
> > I wonder why the Bioconductor developing team cannot work on a widely
> > distributed R version.
>
> Hi Daniel,
>
> The Bioconductor developing team is working with
> R devel for the devel version of Bioconductor (2.0,
> to be released in April 2007 just a few days after
> R 2.5.0 will be released).
> And the Bioconductor developing team has been working
> with R 2.4.0, a widely distributed R version, for the
> preparation of the current release of Bioconductor (1.9).
>
> This doesn't mean you can't use Bioconductor 2.0 packages
> with R 2.4.0, it just means that we can make no guarantee that
> they will work due to some possible incompatibilities between
> R 2.4.0 and current R devel. But nobody prevents you to try:
>   1) start R 2.4.0
>   2) source('http://bioconductor.org/biocLite.R')
>   3) biocLite('Biobase')
>   4) biocLite('affyio')
>   5) repo <- 'http://bioconductor.org/packages/2.0/bioc'
>   6) install.packages('makePlatformDesign', repo=repo, dep=TRUE)
>   7) library(makePlatformDesign)
>   8) makePDpackage("2004-11-09_Human_60mer_TEST.ndf",
> "ngsExpression1.xys", manufacturer="nimblegen")
>   9) expect some breakage since you are using a package
>      still in development and on the wrong platform (R 2.4.0
>      instead of R devel)
>  10) if something goes wrong, please help us to help
>      you by providing some usefull output
>        http://bioconductor.org/docs/postingGuide.html
>
> Thanks,
>
> H.
>
>