On Saturday 18 August 2007 22:45:56 Soeren Sonnenburg wrote: > On Sat, 2007-08-18 at 14:44 +0200, Steffen Moeller wrote: > > On Saturday 18 August 2007 12:36:41 Soeren Sonnenburg wrote: [...] > Well I don't know how much should be split up. But I guess this depends > also on the number of debian ready packages we are talking about? The > next problem is I don't really know how to judge whether a package is > 'ready for debian' or not. > > One could of course start with the core/essential packages and then > slowly increase the package number. Robert Gentlemen suggested to start > with the packages in BioCLite, which is > > affy affydata affyPLM annaffy annotate Biobase Biostrings DynDoc gcrma > genefilter geneplotter hgu95av2 limma marray matchprobes multtest > reposTools ROC vsn xtable. > > What do yo think?
For the packages you listed above you do not really need our Debian gimmicks for. It is easily installed with a few commands of R. But yes, except that I would rather go for hgu133 they should all be in, ok the example data needs the hgu95. I think I am aiming at affylmGUI and RBGL and such that are standard but do not compile too easily for novices since they require to install some extra bits. This way we (I include you here :-) ) can show off with how cool Debian is a bit more. > > > 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. > > Yes you are right, that may be problematic. If we don't talk about > hundreds of packages it is probably also OK... Fine. I personally think we are at about 25 packages in BioC that I'd consider part of core use cases. We did not have discussed this yet. The packaging is automated. Some more pretty printing should probably be done before we move bits into Debian main. Technically the packages are functional. Updates are happening more frequently than you may think, actually, I would not want to do it manually. > > Btw, wouldn't you be interested to join our effort? I'd offer sponsoring > > SHOGUN for Debian as a compensation :-) > > Indeed I am interested, but I don't have any experience with debian+R > other than from packaging shogun-r. So I wonder whether for there exist > general cdbs helpers for r & bioc. Well, check out http://wiki.debian.org/AliothPkgBioc. For more detailed R-packaging related issues Dirk <[EMAIL PROTECTED]> is your man. > Regarding shogun, Torsten Werner is already sponsoring the uploads - so > don't worry :-) Nice. > > Many greetings from the fairly sunny Baltic Sea to my former home Berlin > > Actually I am planning to be at the baltic sea next weekend to take part > in the 'vilmschwimmen'! Enjoy Ruegen, then. Steffen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
