[Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

[Rainer Johannes]

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 <hpages at 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.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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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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