Question

recount

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nathan-temple • 0

@746d7519

Last seen 2.4 years 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 • 1.0k views

ADD COMMENT • link updated 5 weeks ago by Leonardo Collado Torres ★ 1.1k • written 2.4 years 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 2.4 years ago Henry • 0

score 0 · Answer 1 · 2024-08-23

Hmm, I missed this question from like 2 years ago. It looks like it was a network transient issue as the code you provided above does work nowdays.

Sorry for the super late response.

Leo

## Load library
suppressPackageStartupMessages(library("recount"))

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

## Download the gene-level RangedSummarizedExperiment data
download_study(project_info$project)
#> 2024-08-23 10:41:14.400833 downloading file rse_gene.Rdata to SRP009615

load("SRP009615/rse_gene.Rdata", verbose = TRUE)
#> Loading objects:
#>   rse_gene
rse_gene
#> class: RangedSummarizedExperiment 
#> dim: 58037 12 
#> metadata(0):
#> assays(1): counts
#> rownames(58037): ENSG00000000003.14 ENSG00000000005.5 ...
#>   ENSG00000283698.1 ENSG00000283699.1
#> rowData names(3): gene_id bp_length symbol
#> colnames(12): SRR387777 SRR387778 ... SRR389083 SRR389084
#> colData names(21): project sample ... title characteristics

packageVersion("recount")
#> [1] '1.31.0'

^{Created on 2024-08-23 with [reprex v2.1.1](https://reprex.tidyverse.org)}