Error in download.file while installing rhdf5lib
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charlotte ▴ 10
@bbcc9ab6
Last seen 6 weeks ago
Hong Kong

Hi I am installing rhdf5lib on R 4.1.0 on ubuntu and I met some installation problems.

BiocManager::install("Rhdf5lib",force=TRUE)

Here is the error and warning messages.

Error in download.file(url, destfile, method, mode = "wb", ...) :
  download from 'https://bioconductor.org/packages/3.13/bioc/src/contrib/Rhdf5lib_1.14.2.tar.gz' failed
In addition: Warning messages:
1: In .inet_warning(msg) :
  downloaded length 1146192 != reported length 9991926
2: In .inet_warning(msg) :
  URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/Rhdf5lib_1.14.2.tar.gz': Timeout of 300 seconds was reached
Warning message:
In .inet_warning(msg) : download of package ‘Rhdf5lib’ failed

I think maybe it is the problem of slow internet, but I don't know how to fix it.

rhdf5 rhdf5filters Rhdf5lib • 129 views
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Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

This definitely looks like a problem with slow internet rather than anything else. You can increase the length of the timeout by running options(timeout = X) where X is the time in seconds. The default is 300 seconds as you can see in your error message. Setting options(timeout = 600) would increase it to 600 seconds.

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