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 <hpa...@fredhutch.org> wrote: > > 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 get problems. > > Cheers, > H. > > On 02/08/2018 10:48 PM, Rainer Johannes wrote: >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o7lfXI-PMLO8dTAq5vdX3BUFPg8086_2i85m5t64YZE&s=r2MLmLPT1wOQoHhG6p9WZY_AJLlpIWGOI8ijFXTxM0s&e= >>> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=o7lfXI-PMLO8dTAq5vdX3BUFPg8086_2i85m5t64YZE&s=r2MLmLPT1wOQoHhG6p9WZY_AJLlpIWGOI8ijFXTxM0s&e= > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel