Trouble loading Roadmap data from AnnotationHub
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bletteb18 • 0
@bletteb18-14222
Last seen 4.0 years ago

I'm getting an error when trying to load data from AnnotationHub. Here's an example of my code:

 

library(AnnotationHub)
ah <- AnnotationHub()

dat <- ah[["AH29067"]]

 

This gives:

Error: failed to load resource
 name: AH29067
 title: E017-DNase.hotspot.broad.bed.gz
 reason: solving row 1: range cannot be determined from the supplied arguments (too many NAs)

 

This seems to happen for some but not all values of names in ah[["name"]]. My session info is:

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] rtracklayer_1.36.6   GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 
[4] IRanges_2.10.5       S4Vectors_0.14.7     AnnotationHub_2.8.3 
[7] BiocGenerics_0.22.1  BiocInstaller_1.26.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13                  compiler_3.4.1               
 [3] XVector_0.16.0                bitops_1.0-6                 
 [5] tools_3.4.1                   zlibbioc_1.22.0              
 [7] digest_0.6.12                 bit_1.1-12                   
 [9] BSgenome_1.44.2               lattice_0.20-35              
[11] RSQLite_2.0                   memoise_1.1.0                
[13] tibble_1.3.4                  pkgconfig_2.0.1              
[15] rlang_0.1.2                   Matrix_1.2-10                
[17] DelayedArray_0.2.7            shiny_1.0.5                  
[19] DBI_0.7                       curl_3.0                     
[21] yaml_2.1.14                   GenomeInfoDbData_0.99.0      
[23] httr_1.3.1                    knitr_1.17                   
[25] Biostrings_2.44.2             grid_3.4.1                   
[27] bit64_0.9-7                   Biobase_2.36.2               
[29] R6_2.2.2                      AnnotationDbi_1.38.2         
[31] BiocParallel_1.10.1           XML_3.98-1.9                 
[33] blob_1.1.0                    matrixStats_0.52.2           
[35] GenomicAlignments_1.12.2      Rsamtools_1.28.0             
[37] htmltools_0.3.6               SummarizedExperiment_1.6.5   
[39] mime_0.5                      interactiveDisplayBase_1.14.0
[41] xtable_1.8-2                  httpuv_1.3.5                 
[43] RCurl_1.95-4.8  

 

Does anyone know how to resolve this error? Thanks!

annotationhub • 565 views
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Entering edit mode
shepherl 2.8k
@lshep
Last seen 10 hours ago
United States

We are looking into this ERROR and may involve a fix on our side for loading a specific bed format from the source url.

A temporary work around would be something like the following:

library(AnnotationHub)
ah <- AnnotationHub()

# this will fail but download the file 
dat <- ah[["AH29067"]]


fpath = cache(ah["AH29067"])
tbl = read.delim(fpath, sep="\t", header=FALSE, 
                 col.names=c("seqnames", "start", "end", "strand", "score"))
dat = GRanges(tbl)
dat
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Entering edit mode

Great, thanks! This does work in the meantime.

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