[Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

[Rainer Johannes]

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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