Re: [Rd] xtabs and NA
On 09.02.2015 16:59, Gabor Grothendieck wrote: On Mon, Feb 9, 2015 at 8:52 AM, Kirill Müller kirill.muel...@ivt.baug.ethz.ch wrote: Passing table the output of model.frame would still allow the use of a formula interface: mf - model.frame( ~ data, na.action = na.pass) do.call(table, c(mf, useNA = ifany)) abc NA 1111 Fair enough, this qualifies as a workaround, and IMO this is how xtabs should handle it internally to allow writing xtabs(~data, na.action = na.pass) -- or at least xtabs(~data, na.action = na.pass, exclude = NULL) if backward compatibility is desired. Would anyone with write access to R's SVN repo care enough about this situation to review a patch? Thanks. -Kirill __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Bioc-devel] OrganismDb and associated TxDb
Gviz has a nice way of working with TxDb instances to derive gene models. It can be cumbersome to refer to a TxDb instance, and the Homo.sapiens OrganismDb instance is very convenient to work with. I do not see any straightforward way to extract a reference to a TxDb from Homo.sapiens. I could traverse the graph slot but class?OrganismDb makes no reference to this. In summary, I think it would be good to document the OrganismDb API and to think about preferences for using OrganismDb as opposed to TxDb and OrgDb (org.Hs.eg.db) whenever possible. BTW I attempted to 'patch' Gviz by substituting OrganismDb for TxDb -- there are only two references to TxDb in Gviz ... and it would seem that the necessary operations apply to OrganismDb just as well as to TxDb. But the APIs are not in sync ... I ran into seqlevels0 ... and that is something of a mystery. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] update.packages with ask = FALSE will sometimes ask about updates
On 13 February 2015 at 10:11, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 11/02/2015 10:46, Richard Cotton wrote: The 'at a minimum' information required by the posting guide is conspicuous by its absence. At a guess, this is R-devel and Windows. What I'm running doesn't matter if I'm asking for general opinion on the best behaviour. It has to work for everyone. He missed the documented options (and the NEWS items, the posting guide ...). All this is irrelevant. Whatever my OS, and whatever the documented options are, if I explicitly say I don't want interactive behaviour by specifying ask = FALSE, then R stopping to ask me things feels like incorrect behaviour. Since there seems to be resistance to making any changes to the behaviour, for future readers, the solution that has been suggested to me to ensure that you don't get asked any questions is: Make sure you can compile packages (on Windows this involves installing Rtools). Then explicitly set type = source when you use ask = FALSE. update.packages(ask = FALSE, type = source) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Bioc-devel] OrganismDb and associated TxDb
Hi Vince, First of all thank you for using OrganismDb objects. You raise some interesting points though about keeping these APIs better synchronized that I feel point to some deficiencies in the current design. I spoke with Herve about this and we are puzzling over possibly using inheritance to make this a bit easier for maintenance. Marc On 02/13/2015 10:01 AM, Vincent Carey wrote: Gviz has a nice way of working with TxDb instances to derive gene models. It can be cumbersome to refer to a TxDb instance, and the Homo.sapiens OrganismDb instance is very convenient to work with. I do not see any straightforward way to extract a reference to a TxDb from Homo.sapiens. I could traverse the graph slot but class?OrganismDb makes no reference to this. In summary, I think it would be good to document the OrganismDb API and to think about preferences for using OrganismDb as opposed to TxDb and OrgDb (org.Hs.eg.db) whenever possible. BTW I attempted to 'patch' Gviz by substituting OrganismDb for TxDb -- there are only two references to TxDb in Gviz ... and it would seem that the necessary operations apply to OrganismDb just as well as to TxDb. But the APIs are not in sync ... I ran into seqlevels0 ... and that is something of a mystery. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
