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lgatto / ProteomicsAnnotationHubData

Annotation hub data for proteomics data
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ProteomicsAnnotationHubData: curl timeout #14

Closed lgatto closed 8 years ago

lgatto commented 8 years ago

Issue reported by Van and Dan:

Subject: ProteomicsAnnotationHubData: curl timeout

As you know, it's broken on all platforms in release and on mac in devel, the common error is a curl timeout:

  • installing source package ‘ProteomicsAnnotationHubData’ ... * R * inst \ preparing package for lazy loading Error in curl::curl(ul, "r") : Timeout was reached Error : unable to load R code in package ‘ProteomicsAnnotationHubData’ ERROR: lazy loading failed for package ‘ProteomicsAnnotationHubData’
  • removing ‘/home/vobencha/sandbox/ProteomicsAnnotationHubData.Rcheck/ProteomicsAnnotationHubData’

The problem is this url:

ul = "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/" con <- curl::curl(ul, "r") Error in curl::curl(ul, "r") : Timeout was reached

When looking for a way to relax the timeout I found this thread and see you've gone down this path before:

https://support.bioconductor.org/p/76485/

Was the solution to set a proxy? The code in question is in

ProteomicsAnnotationHubData:::.ftpFileInfo2

I was able to very intermittently reproduce the timeout. I couldn't find any way to list files in a directory using httr, as was suggested by Dan, but I found RCurl:getURL, which I used to reimplement .ftpFileInfo2.

lgatto commented 8 years ago

Done in a11dc78f21cfd716e9ebcc0acd8fc5e0fd010518.