Question

recount

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nathan-temple • 0

@746d7519

Last seen 23 months ago

United States

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When I try to execute the code in the 'recount quick start guide' (https://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#1_Basics):


## Load library
library("recount")

## Find a project of interest
project_info <- abstract_search("GSE32465")

## Download the gene-level RangedSummarizedExperiment data
download_study(project_info$project)

It seems to find the 'project_info' correctly, but the cannot find the url:

library(recount) project_info <- abstract_search('GSE32465') download_study(project_info$project) 2022-05-08 21:05:43 downloading file rse_gene.Rdata to SRP009615 trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata' trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata' trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata' Error in download_retry(url = url, destfile = file.path(outdir, filename), : 'download_retry()' failed: URL: http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata error: cannot open URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'

recount • 722 views

ADD COMMENT • link updated 24 months ago by Henry • 0 • written 24 months ago by nathan-temple • 0

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Entering edit mode

Same. I tried this:

## Install recount from Bioconductor
install.packages("BiocManager")
BiocManager::install('recount')

## Browse the vignetets for a quick description of how to use the package
library('recount')
browseVignettes('recount')

## Download the RangedSummarizedExperiment object at the gene level for 
## study SRP009615
url <- download_study('SRP009615')

The result:

2022-05-09 06:15:52 downloading file rse_gene.Rdata to SRP009615
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Error in download_retry(url = url, destfile = file.path(outdir, filename),  : 
  'download_retry()' failed:
  URL: http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata
  error: cannot open URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
In addition: Warning messages:
1: In download.file(url, method = method, ...) :
  URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata': status was 'Couldn't resolve host name'
2: In download.file(url, method = method, ...) :
  URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata': status was 'Couldn't resolve host name'
3: In download.file(url, method = method, ...) :
  URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata': status was 'Couldn't resolve host name'

ADD REPLY • link 24 months ago Henry • 0