WTChimeraData() Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [experimenthub.bioconductor.org] Connection time-out
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haidan • 0
@2568c383
Last seen 4 months ago
United States

I am a newer to use Bioconductor; I have met the following question when I load data by WTChimeraData() function This is my codes:

library(MouseGastrulationData)
sce.chimera <- WTChimeraData(samples=5:10)

sometimes, returned this

sce.chimera <- WTChimeraData(samples=5:10) |======================================================================| 100%

Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [experimenthub.bioconductor.org] Connection time-out

and sometimes, returned this

Error in value[3L] : failed to connect reason: Timeout was reached: [bioconductor.org] Connection time-out Consider rerunning with 'localHub=TRUE' In addition: Warning message: Could not check database for updates. Database source currently unreachable. This should only be a temporary interruption. Using previously cached version.

I don't know why, who can help me? and thank you !

WTChimeraData MouseGastrulationData WT • 735 views
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@jonathan-griffiths-20559
Last seen 4 months ago
Cambridge UK

Looks to me like you're struggling to connect to the Bioconductor servers that hold the data.

If you have downloaded the data before, it looks like you can use the argument localHub=TRUE to avoid connecting to the servers.

If you haven't, then you could try running the code again now, after a little time has passed since the first attempt. Hopefully the servers just had some temporary downtime. If that doesn't work, then it seems like you have something set up on your network that is blocking that connection.

Jonny

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I tried to connect the Bioconductor servers for several times, and failed. So I decided to use the argument >localHub=True. I wonder to know how to download the data by myself.

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The processed data _might_ be on ArrayExpress, I can't remember.

I would strongly recommend you download the data from a network that isn't blocking access. I was able to download these data at the weekend when I tried. You could then save the data as an rds file and transfer it onto the machine that you are struggling with.

Unfortunately I'm not going to be able to help further on this as the underlying issue is with the network connection you have.

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Thank you very much for your advice. But, I install Biocondutor in Windows, network is fine, still cann't download data.

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