[Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

[Hervé Pagès]

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.triche at 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.Rainer at 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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> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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