Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2016-01-19 Thread Rainer Johannes
Thanks Hervé! I’ll check it out but don’t expect any problems. cheers, jo > On 19 Jan 2016, at 22:31, Hervé Pagès wrote: > > Hi Jo, > > In GenomicFeatures 1.23.18 I've modified the default > "extractTranscriptSeqs" method so it can be called with additional > arguments when the 2nd argument i

Re: [Bioc-devel] GenomicFeatures::extractTranscriptSeqs setMethod suggestion

2016-01-19 Thread Hervé Pagès
Hi Jo, In GenomicFeatures 1.23.18 I've modified the default "extractTranscriptSeqs" method so it can be called with additional arguments when the 2nd argument in not a GRangesList object. These additional arguments then get passed to the internal call to exonsBy(). With this change, the user shou

Re: [Bioc-devel] Versioned (Biobase) "initialize" method

2016-01-19 Thread Morgan, Martin
Hi Michael -- sorry not to respond sooner. The lessons in the StackOverflow post were learned by the mistakes in Biobase; many of the classes there fail to follow its advice. Also, there are a number of packages in Bioconductor that depend on the existing Biobase formulation. Unfortunately, the

[Bioc-devel] Conference: BioC 2016: Where Software and Biology Connect, Stanford, 24-26 June

2016-01-19 Thread Morgan, Martin
Bioconductors! Please plan to attend BioC2016: Where Software and Biology Connect, June 24 (Developer Day) - 26, Stanford University, Stanford, CA. See http://bioconductor.org/help/course-materials/2016/BioC2016/ for additional information. DEVELOPERS: Please consider offering a user-orien

Re: [Bioc-devel] bplapply Processes Sometimes Stall

2016-01-19 Thread Morgan, Martin
Please ensure that your Debian system is running R-devel and using the current BiocParallel by providing the output of sessionInfo(). From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Dario Strbenac [dstr7...@uni.sydney.edu.au] Sent: Sunday,