Re: [Bioc-devel] vectorize default dist2 function in genefilter

2013-03-12 Thread Wolfgang Huber
Dear James Thank you. What would the saved time be (e.g. compared to the overall runtime of arrayQualityMetrics)? I would be surprised if the saving was worth the added complexity, but am always happy to be surprised. A patch of the .R and .Rd file would be most welcome and expedite the change

[Bioc-devel] vectorize default dist2 function in genefilter

2013-03-12 Thread James F. Reid
Dear bioc-devel, the dist2 function in genefilter defined as: dist2 <- function (x, fun = function(a, b) mean(abs(a - b), na.rm = TRUE), diagonal = 0) { if (!(is.numeric(diagonal) && (length(diagonal) == 1L))) stop("'diagonal' must be a numeric scalar.") res = matrix(diagonal,

Re: [Bioc-devel] contradictions in the return value of predictCoding() from VariantAnnotation

2013-03-12 Thread Michael Stadler
Hi Valerie, Thank you for the quick fix - it works like a charm! Michael On 03/10/2013 02:45 AM, Valerie Obenchain wrote: > Hi Michael, > > Thanks for reporting the bug and sending a reproducible example. Sorry > it took a few days to get to this. > > A fix has been checked into versions 1.4.1