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
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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
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E-mail: hpa...@fredhutch.org
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