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

Francois Pepin fpepin at cs.mcgill.ca
Fri Oct 27 23:50:29 CEST 2006

Hi Daniel,

Bioconductor 2.0 is the development version. Bioconductor 1.9 is quite
recent (Oct 9th to be precise), so I wouldn't expect any new
capabilities for it.

If you give us a bit more information as to why your data is not
accepted (error message, sessionInfo() output, example code) then I
think the people on the list might be able to help.

I have moved this discussion to the main bioconductor mailing list. It
has a wider readership of people who can help you and the bioc-devel
list is mostly used for discussing bioconductor development.

You might want to take a look at the bioconductor posting guide as well
(http://www.bioconductor.org/docs/postingGuide.html). Following it makes
our life a lot easier and means that you're much more likely to get an
useful answer.

hope this helps,


On Fri, 2006-10-27 at 19:44 -0200, Daniel Macedo Lorenzini wrote:
> Dear Developing Team,
> First I would like to thank you for your effort to develop such a nice
> code as Bioconductor.
> Unfortunately I have found many difficulties during the installation of
> Bioconductor. I have started on Bioconductor to analyse a Nimblegen chip
> dataset at probe level. Initially I worked on a Debian etch system, with
> R 2.4 installed. In the current stable Bioconductor distro the Nimblegen
> data is not accepted. So I tried to install the Bioconductor 2.0, which
> needs R 2.5 (I don t understand why). There is no debian package for R
> 2.5, so I got the R source code. R source doesn t compile because it doesn
> t like my xorg installation (I do have the x11-dev package installed). So
> I gave up my linux installation (shame on me) and went into the Window$ R
> 2.5. I got it correctly installed, all the affy and oligo packages I
> needed were download and I prepared my Nimblegen chip design library with
> commands such as the following:
> > library(makePlatformDesign)
> > makePDpackage("2004-11-09_Human_60mer_TEST.ndf", "ngsExpression1.xys", manufacturer="nimblegen")
> for my surprise I could not install such package with the R CMD INSTALL.
> Searching some more I found that Perl and MinGW would be useful. Still
> didn t make it. I find nothing else to change.
> I wonder why the Bioconductor developing team cannot work on a widely
> distributed R version. After one week of work I found out that it will be
> easier to come back home (linux), prepare a Perl script to fake Nimblegen
> data as Affymatrix data and then work on the stable bioconductor version.
> Regards,
> Daniel Lorenzini
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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