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Make timeout configurable in downloadFile() #139

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Merged
merged 1 commit into from
Jul 4, 2023
Merged

Make timeout configurable in downloadFile() #139

merged 1 commit into from
Jul 4, 2023
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yihui
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@yihui yihui commented Dec 14, 2022

The default 120 seconds may not be enough, e.g., #138 and https://d.cosx.org/d/423763

Timeout was reached: [] Operation timed out after 120000 milliseconds with 47824896 out of 156738322 bytes received...

After this PR, they can increase the value by, e.g., options(timeout = 600) (10 mins).

options('timeout') defaults to 60 in base R, so this PR won't change your default (max(60, 120) == 120).

@yihui
Make timeout configurable in downloadFile()

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Users can increase `options(timeout)` if the default is not enough, e.g., #138 and https://d.cosx.org/d/423763
@khughitt
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Nice and simple fix 👍

It's probably also worth modifying the similar call in getGEOSuppFiles.R.

@khughitt
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One more place that needs to be modified is parseGEO.R:getAndParseGSEMatrices:

Error in open.connection(x, "rb") :
  Timeout was reached: [ftp.ncbi.nlm.nih.gov] Resolving timed out after 10000 milliseconds
Calls: download_geo ... getAndParseGSEMatrices -> getDirListing -> <Anonymous> -> read_html.default
Execution halted

@yihui
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yihui commented Mar 19, 2023

I can definitely do that, but first we need to get @seandavi's attention.

@seandavi seandavi merged commit 58225fa into seandavi:devel Jul 4, 2023
@yihui yihui deleted the patch-1 branch July 5, 2023 02:13
@jacorvar
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Hi,

in spite of increasing timeout with options(timeout=3000), downloadFile keeps using 120 seconds. Am I doing something wrong?

I've installed the latest version using install_github('seandavi/GEOquery') and R version 4.3.1 (2023-06-16).

@seandavi seandavi mentioned this pull request Oct 30, 2023
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@yihui
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yihui commented Oct 30, 2023

Make sure to restart R after (re)installing a package.

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@yihui @khughitt @jacorvar @seandavi