Hi Valerie & Hervé, Thanks a lot, I will try adding the new alias!
I am still baffled by the other half of the mystery, i.e. that the build check warning appeared to the reports about a week ago and I still cannot see it on my own R-3.1.0 alpha build.
Any ideas why this would work differently on the build daemon machines compared to http://cran.r-project.org/src/base-prerelease/R-alpha_2014-03-16_r65200.tar.gz?
Antti On 2014-03-17 20:38 , Hervé Pagès wrote:
Hi Antti, Yes it's a little bit surprising (and questionable) that 'R CMD check' requires you to define an alias that is inconsistent with: - Your setMethod statement: setMethod("[", signature(x="scoreList"), ... - The output of showMethods: showMethods("[") Function: [ (package base) x="AffyBatch" [...] x="scoreList" [...] - The behavior of dispatch and selectMethod(): selectMethod("[", "scoreList") # works as expected But, as Val pointed out, 'R CMD check' is the boss, and the only way to make the warning go away is by adding the alias that 'R CMD check' wants to see. Note that this alias suggests that the [ generic has only 2 arguments in its signature so is not even consistent with the signature of the generic (the [,scoreList,ANY,ANY,ANY-method alias would be). Note that the primary purpose of an alias is to make your man page accessible by the user, not to please 'R CMD check'. So since the user looking for documentation about the "[" method for scoreList objects is more likely to access your man page thru your original [,scoreList-method alias, I would recommend you keep it. Just add the [,scoreList,ANY-method alias to please 'R CMD check'. Cheers, H. On 03/17/2014 10:49 AM, Valerie Obenchain wrote:Hi Antti, It's looking for \alias{[,scoreList,ANY-method} The generic '[' can dispatch on arguments 'x', 'i' and 'j'.getGeneric("[")standardGeneric for "[" defined from package "base" function (x, i, j, ..., drop = TRUE) standardGeneric("[", .Primitive("[")) <bytecode: 0x237af30> <environment: 0x21d9f18> Methods may be defined for arguments: x, i, j, drop Use showMethods("[") for currently available ones.The method you wrote for scoreList dispataches on 'x' as a scoreList object but doesn't specify 'i' or 'j'. One of these indices must be present in order for subsetting to happen. In this case (I believe) the default is assuming 'i' as ANY and 'j' as missing. For example, with the VCF class I've specified the method for ANY, ANY: setMethod("[", c("VCF", "ANY", "ANY"), function(x, i, j, ..., drop=TRUE) { ... To see more examples, showMethods('[') Valerie On 03/17/2014 08:13 AM, Antti Honkela wrote:Hi all, The latest build check report shows one warning for 'tigre': --------------------------------------- * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'scoreList,ANY' --------------------------------------- As far as I can tell the method in question should be documented, as one of the .Rd files contains an alias: \alias{[,scoreList-method} Furthermore I cannot reproduce it on my own using the latest R-alpha (or R-devel from last week): R CMD check on the source tar-ball downloaded directly from Bioconductor runs cleanly. Can someone please help in figuring out what is going on? Antti
-- Antti Honkela antti.honk...@hiit.fi - http://www.hiit.fi/u/ahonkela/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
