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

Benilton Carvalho bcarvalh at jhsph.edu
Sat Oct 28 18:29:14 CEST 2006

Hi Daniel,

sorry for the late reply.

Although oligo and makePlatformDesign are available through the BioC  
2.0 devel branch, they do not require R 2.5.

Btw, these packages lack documentation. So, if you see yourself in  
trouble, don't hesitate contacting me (but don't forget to copy the  
list, so others can also share opinions).


ps: to install the packages, you can always use biocLite() setting  
the repository argument to


Begin forwarded message:

> ---------- Forwarded message ----------
> Date: Fri, 27 Oct 2006 19:44:01 -0200 (BRST)
> From: Daniel Macedo Lorenzini <dlorenzini at cbiot.ufrgs.br>
> To: bioc-devel at stat.math.ethz.ch
> Subject: [Bioc-devel] I will succeed (hopefully) the installation of
>     Bioconductor 2.0
> 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  
> 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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