Re: [Bioc-devel] Fwd: proteomics/MS generic

2015-01-14 Thread Laurent Gatto
Dear Bioconductor team, Following up from an email from last November, here is a list of generics that could be added to BiocGenerics to avoid conflict and unnecessary dependencies among proteomics packages: ## currently in mzR setGeneric(psms, function(object, ...) standardGeneric(psms))

[Bioc-devel] IRanges findOverlaps Result Different for Recent Update

2015-01-14 Thread Dario Strbenac
Hello, For an identical query, the matrix results are in a different order. Consider the subject hits of the last two rows : mapping# R Under development (unstable) (2015-01-13 r67453) and IRanges 2.1.35 queryHits subjectHits [1,] 1 1 [2,] 1 4

Re: [Bioc-devel] IRanges findOverlaps Result Different for Recent Update

2015-01-14 Thread Michael Lawrence
I bet there is a lot of code that depends on having the hits (conveniently) ordered by query,subject index, so we should try to restore the previous behavior. On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac dstr7...@uni.sydney.edu.au wrote: Hello, For an identical query, the matrix results

Re: [Bioc-devel] [Rd] Is the tcltk failure in affylmGUI related to R bug 15957

2015-01-14 Thread Dan Tenenbaum
[moving this to bioc-devel] - Original Message - From: Keith Satterley ke...@wehi.edu.au To: r-de...@r-project.org Sent: Tuesday, January 13, 2015 9:50:40 PM Subject: [Rd] Is the tcltk failure in affylmGUI related to R bug 15957 I maintain the package affylmGUI. It works when