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ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
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treehouse update fails #26

Closed markgene closed 4 years ago

markgene commented 4 years ago

Hi Shixiang,

Thank you for developing the package! It is very easy to use. However, I failed to update the dataset of treehouse. See below. Thanks!

> packageVersion("UCSCXenaTools")
[1] ‘1.3.1’
> XenaDataUpdate()
=> Obtaining info from UCSC Xena hubs...
==> Searching cohorts for host https://ucscpublic.xenahubs.net...
==> Trying #1
===> #37 cohorts found.
===> Querying datasets info...
===> #114 datasets found.
...
==> Searching cohorts for host https://xena.treehouse.gi.ucsc.edu...
==> Trying #1
==> Trying #2
==> Trying #3
Error in value[[3L]](cond) : 
  Tried 3 times but failed, please check URL or your internet connection!
github-actions[bot] commented 4 years ago

Thanks for reporting, Shixiang will reply as soon as possible:)

ShixiangWang commented 4 years ago

@markgene Thanks for reporting, this isssue is typically calused by your unstable internet connection. I will try to update the datasets and push a new version.

ShixiangWang commented 4 years ago

@markgene Based on https://xenabrowser.net/hub/, the problem is that the hub is down, so we cannot connect it from R

image

ShixiangWang commented 4 years ago

You can send an email to Xena team to check the server problem, I cannot help you out from this. I am closing this issue now, feel free to reopen it.