Trouble loading Roadmap data from AnnotationHub
1
0
Entering edit mode
bletteb18 • 0
@bletteb18-14222
Last seen 6.4 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 • 825 views
ADD COMMENT
0
Entering edit mode
shepherl 3.8k
@lshep
Last seen 14 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
ADD COMMENT
0
Entering edit mode

Great, thanks! This does work in the meantime.

ADD REPLY

Login before adding your answer.

Traffic: 672 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6