Question: Annotatr package not loading certain features
0
gravatar for divyswar01
2.8 years ago by
divyswar010
divyswar010 wrote:

I am trying to load some features through annotatr package and I got the following error message 

'select()' returned 1:1 mapping between keys and columns
Building promoters...
snapshotDate(): 2016-11-15
Building CpG islands...
downloading from ‘https://annotationhub.bioconductor.org/fetch/5086’
retrieving 1 resource
Error: failed to load resource
  name: AH5086
  title: CpG Islands
  reason: 1 resources failed to download

 

This is the command that I used:

library(annotatr)
annots = c('hg19_genes_promoters','hg19_cpg_islands')
annots_gr = build_annotations(genome = 'hg19', annotations = annots)
annotatr • 439 views
ADD COMMENTlink modified 2.8 years ago by Valerie Obenchain6.7k • written 2.8 years ago by divyswar010
1

Hello,

Sorry for the very delayed response, despite your use of the annotatr tag, I didn't get a notification about this message. Given Valerie's response (thanks), I would guess it was a temporary blip in access to AnnotationHub. I have experienced this before, and just waited it out.

Thanks for using annotatr.

ADD REPLYlink written 2.8 years ago by rcavalca130
Answer: Annotatr package not loading certain features
3
gravatar for Valerie Obenchain
2.8 years ago by
United States
Valerie Obenchain6.7k wrote:

Hi,

Please show the output of your sessionInfo().

Behind the scenes, the function is trying to load a resource from AnnotationHub, specifically AH5086. I'm able to do this with no errors:

library(AnnotationHub)

> hub = AnnotationHub()
snapshotDate(): 2016-11-15
> hub[["AH5086"]]
require(“GenomicRanges”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/5086’
retrieving 1 resource
  |======================================================================| 100%
GRanges object with 28691 ranges and 1 metadata column:
                       seqnames           ranges strand |        name
                          <Rle>        <IRanges>  <Rle> | <character>
      [1]                  chr1 [ 28736,  29810]      * |    CpG:_116
      [2]                  chr1 [135125, 135563]      * |     CpG:_30
      [3]                  chr1 [327791, 328229]      * |     CpG:_29
      [4]                  chr1 [437152, 438164]      * |     CpG:_84
      [5]                  chr1 [449274, 450544]      * |     CpG:_99
      ...                   ...              ...    ... .         ...
  [28687]  chr9_gl000201_random [ 15651,  15909]      * |     CpG:_30
  [28688]  chr9_gl000201_random [ 26397,  26873]      * |     CpG:_43
  [28689] chr11_gl000202_random [ 16284,  16540]      * |     CpG:_23
  [28690] chr17_gl000204_random [ 54686,  57368]      * |    CpG:_228
  [28691] chr17_gl000205_random [117501, 117801]      * |     CpG:_23
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome

Here is my sessionInfo():

> sessionInfo()
R Under development (unstable) (2016-10-22 r71581)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora 24 (Workstation Edition)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] AnnotationHub_2.7.6 BiocGenerics_0.21.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                   IRanges_2.9.7                
 [3] digest_0.6.10                 mime_0.5                     
 [5] R6_2.2.0                      xtable_1.8-2                 
 [7] DBI_0.5-1                     stats4_3.4.0                 
 [9] RSQLite_1.0.0                 BiocInstaller_1.25.2         
[11] httr_1.2.1                    S4Vectors_0.13.2             
[13] Biobase_2.35.0                shiny_0.14.2                 
[15] httpuv_1.3.3                  yaml_2.1.13                  
[17] AnnotationDbi_1.37.0          htmltools_0.3.5              
[19] interactiveDisplayBase_1.13.0

 

ADD COMMENTlink written 2.8 years ago by Valerie Obenchain6.7k
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