Annotatr package not loading certain features
1
@divyswar01-11905
Last seen 6.1 years ago
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
• 1.3k views
@valerie-obenchain-4275
Last seen 3.0 years ago
United States
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
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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.