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 r74099) Platform: x86_64-apple-darwin17.4.0/x86_64 (64-bit) Running under: macOS High Sierra 10.13.4 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] EnsDb.Hsapiens.v86_2.99.0 [2] ensembldb_2.3.9 [3] AnnotationFilter_1.3.2 [4] GenomicFeatures_1.31.8 [5] AnnotationDbi_1.41.4 [6] Biobase_2.39.2 [7] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 [8] BSgenome_1.47.4 [9] rtracklayer_1.39.8 [10] Biostrings_2.47.7 [11] XVector_0.19.8 [12] GenomicRanges_1.31.16 [13] GenomeInfoDb_1.15.5 [14] IRanges_2.13.22 [15] S4Vectors_0.17.30 [16] BiocGenerics_0.25.2 [17] BiocInstaller_1.29.4 loaded via a namespace (and not attached): [1] Rcpp_0.12.15 compiler_3.5.0 [3] pillar_1.1.0 ProtGenerics_1.11.0 [5] prettyunits_1.0.2 progress_1.1.2 [7] bitops_1.0-6 tools_3.5.0 [9] zlibbioc_1.25.0 biomaRt_2.35.10 [11] digest_0.6.15 bit_1.1-12 [13] RSQLite_2.0 memoise_1.1.0 [15] tibble_1.4.2 lattice_0.20-35 [17] pkgconfig_2.0.1 rlang_0.1.6 [19] Matrix_1.2-12 DelayedArray_0.5.17 [21] DBI_0.7 curl_3.1 [23] GenomeInfoDbData_1.1.0 httr_1.3.1 [25] stringr_1.2.0 bit64_0.9-7 [27] grid_3.5.0 R6_2.2.2 [29] XML_3.98-1.9 BiocParallel_1.13.1 [31] magrittr_1.5 blob_1.1.0 [33] Rsamtools_1.31.3 matrixStats_0.53.0 [35] GenomicAlignments_1.15.10 assertthat_0.2.0 [37] SummarizedExperiment_1.9.13 stringi_1.1.6 [39] lazyeval_0.2.1 RCurl_1.95-4.10 > On 8 Feb 2018, at 21:57, Tim Triche, Jr. <tim.tri...@gmail.com> wrote: > > that is a cool feature -- I didn't even know it existed. it will be even > cooler when it resumes working ;-) > > > > --t > > On Thu, Feb 8, 2018 at 2:34 PM, Rainer Johannes <johannes.rai...@eurac.edu> > wrote: > 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 in (function (classes, fdef, mtable) : > unable to find an inherited method for function 'narrow' for signature > '"DNAStringSet"' > > Have there been any recent changes? > > thanks, jo > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
