Re: [Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

Thanks Herve! I can confirm that after updating to IRanges 2.13.24, GenomicRanges 1.31.18 and Biostrings 2.47.9 all works again. thanks, jo > On 9 Feb 2018, at 10:31, Hervé Pagès wrote: > > Hi Johannes, > > This should be fixed by now. > > I also committed a small

Re: [Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

Hi Johannes, This should be fixed by now. I also committed a small change to ensembldb (commit e4b9ffc54a35d8f4d8c398b94a53e0b65b48cbab) to fix a problem introduced by some recent changes to GenomicRanges so ensembldb should turn green again on Saturday's build report. Let me know if you still

Re: [Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

OK, seems we're getting closer - just updated all packages. Now the error is: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'windows' for signature '"DNAString"' my sessionInfo: > sessionInfo() R Under development (unstable) (2018-01-08

[Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

Dear all, one of the unit tests in ensembldb is failing because of a problem in GenomicFeatures::extractTranscriptSeqs (I guess): library(BSgenome.Hsapiens.NCBI.GRCh38) bsg <- BSgenome.Hsapiens.NCBI.GRCh38 library(EnsDb.Hsapiens.v86) all <- extractTranscriptSeqs(bsg, EnsDb.Hsapiens.v86) Error