On Saturday 18 August 2007 12:36:41 Soeren Sonnenburg wrote: > On Tue, 2007-08-14 at 21:26 -0500, Dirk Eddelbuettel wrote: > First of all I really like your efforts of debianizing R packages. I > think debian is currently well suited to be used in ``science'' but yes > there is a lot more one can do. I was indeed missing the nowadays quite > standard bioconductor packages when I had to do some microarray > analysis. It is what we feel. Many thanks for your positive feedback. > Regarding machine generated debian packages it is a first step and > probably the only way given this amount of R-packages. I also don't > think they could be in debian. This especially holds for the more > esoteric/brand new research/unstable R-packes. However I would want to > see the more mature bioconductor packages in debian... Again, I think we can agree on this, > Thinking about it, *I* think it would be best to proceed in a similar > way as the texlive people, i.e. have debian packages for all major > categories which include the major mature R-packages of that category > > r-bioc-base > r-bioc-microarray > r-bioc-annotation > r-bioc-statistics > r-bioc-graphs > r-bioc-technology Hm. I kind of like it, though I rather see this implemented as virtual packages that come rather naturally from the Biotags that BioConductor assigns to itself. > The remaining R-packages could be packaged as single debian-packages as > you proposed to do it and maybe even hosted a bioconductor.org? In case > a package seems more mature it can enter any of the categories and one > could add proper conflicts/replaces as an upgrade path. BTW, this also > solves the `not-up-to-date issue', as more mature packages don't require > weekly/monthly updates. Hm. I am not sure. The problem with hiding it all is that we also do not use apt-cache search to find the proper BioC packages in the first place. We hide this information away in the superpackages. It also impedes the communication of Debian users with R developers and the assignment of Bugs. Btw, wouldn't you be interested to join our effort? I'd offer sponsoring SHOGUN for Debian as a compensation :-) Many greetings from the fairly sunny Baltic Sea to my former home Berlin Steffen -- Dr. Steffen Möller University of Lübeck Institute for Neuro- and Bioinformatics Ratzeburger Allee 160 23538 Lübeck Germany T: +49 451 500 5504 F: +49 451 500 5502 moeller@inb.uni-luebeck.de
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