Re: [Bioc-devel] WARNING regarding imporing SummarizedExperiment

Hi guys, I have identified the problem. It's the packages I imported have same function name, so the previous functions get overwritten. Thanks Ruqian On Sun, Apr 15, 2018 at 10:18 AM, Ruqian Lyu wrote: > Hi guys, > > I'm wondering if any of you have met

[Bioc-devel] WARNING regarding imporing SummarizedExperiment

Hi guys, I'm wondering if any of you have met this warning message : Warning: replacing previous import 'SummarizedExperiment::start' by 'stats::start' when loading 'singscore' Warning: replacing previous import 'SummarizedExperiment::end' by 'stats::end' when loading 'singscore' I have import

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

On 04/14/2018 07:21 AM, Vincent Carey wrote: But Annotated is defined in S4Vectors and RNeXML; the latter is not a Bioconductor package. The likelihood of collisions among class names defined in different packages seems pretty high as S4 adoption grows. So requiring a systematic approach to

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

But Annotated is defined in S4Vectors and RNeXML; the latter is not a Bioconductor package. The likelihood of collisions among class names defined in different packages seems pretty high as S4 adoption grows. So requiring a systematic approach to disambiguating class references seems inevitable.

Re: [Bioc-devel] Error: node stack overflow

Hi Zheng, I can totally reproduce this on my Ubuntu laptop: library(rJava) library(IRanges) unique(IRanges()) # Error in validObject(.Object) : # invalid class “MethodWithNext” object: Error : C stack usage 7969396 is too close to the limit See my seesionInfo() at the end of this

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

How about renaming Annotated? Isn't having 2 classes around with the same name fundamentally a bad situation? No amount of workarounds will change that. H. On 04/12/2018 04:06 PM, Michael Lawrence wrote: Yea, good idea, I was thinking of supporting :: in class names and parsing them out. In

Re: [Bioc-devel] AAString - Amino acid code enforced?

Hi Felix, Please see my answer in the issue you opened on GitHub: https://github.com/Bioconductor/Biostrings/issues/10 Cheers, H. On 04/02/2018 06:07 AM, Felix Ernst wrote: Dear all, probably this is for Hervé Pagès: I tried the following code, which should according to ?AAString not