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

Herve Pages hpages at fhcrc.org
Sat Oct 28 00:54:06 CEST 2006

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



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