Prevent download errors in R by increasing the timeout

If you find yourself getting a "Timeout of 60 seconds was reached" warning from download.file that's preventing you from installing a package, you can increase the timeout in R by using options().

For example, when I was trying to run the following command:

SeuratData::InstallData('ifnb')
trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz'
Content type 'application/octet-stream' length 413266233 bytes (394.1 MB)
================
downloaded 126.6 MB

Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 132779682 != reported length 413266233
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  URL 'https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz': Timeout of 60 seconds was reached
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  download from 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz' failed
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘ifnb.SeuratData’ failed
Error in loadNamespace(name) : 
  there is no package called ‘ifnb.SeuratData’

Increase the timeout by using options().

options(timeout = 1000)
SeuratData::InstallData('ifnb')
trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz'
Content type 'application/octet-stream' length 413266233 bytes (394.1 MB)
==================================================
downloaded 394.1 MB

* installing *source* package ‘ifnb.SeuratData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ifnb.SeuratData)

The downloaded source packages are in
    ‘/tmp/RtmpfhhGRo/downloaded_packages’

Some details

The options() function:

Allow the user to set and examine a variety of global options which affect the way in which R computes and displays its results.

Documentation for the timeout option:

timeout: positive integer. The timeout for some Internet operations, in seconds. Default 60 (seconds) but can be set from environment variable R_DEFAULT_INTERNET_TIMEOUT. (Invalid values of the option or the variable are silently ignored: non-integer numeric values will be truncated.) See download.file and connections.

And finally, what is an official definition of a timeout? Here's one from Wikipedia:

A specified period of time that will be allowed to elapse in a system before a specified event is to take place, unless another specified event occurs first; in either case, the period is terminated when either event takes place. Note: A timeout condition can be canceled by the receipt of an appropriate time-out cancellation signal.

For me that's a confusing statement. I would write (but am probably wrong or inaccurate):

A specified period of time a system is allowed to idle when a specified event is requested. If the allowed idle time has passed, then the specified event is terminated.

Anyway long story short, use options(timeout = 1000) if you find yourself downloading from a server that tends to stall. Or use a number you fancy, like 496 or 8128 seconds.

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