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I need to run several scripts via the bash shell using Rscript and some functions I use require the function isGeneric. However, in this case the process end like that (for example):

Error in .getLogLik() : could not 
find function "isGeneric"
Calls: main -> dredge -> .getLik -> .getLogLik
Execution halted

This can be reproduced as follows

# in the bash shell
echo "isGeneric('apply')" > /tmp/test.R
Rscript /tmp/test.R

Result: 

Error: could not find function "isGeneric"
Execution halted

However, if we open a R session and type the following, it works:

# in the R shell
isGeneric('apply')
[1] FALSE

Would you know where the problem comes from and how to fix it?

Joshua Ulrich
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Ludovic Duvaux
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1 Answers1

24

According to help(Rscript), Rscript doesn't load the methods package by default, because it's time-consuming. So you either need to specify it on the command line:

Rscript --default-packages=methods file.R

Or library(methods) at the top of the file you're calling.

Joshua Ulrich
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  • Thanks Joshua it works just fine now. And sorry I didn't see the link between `isGeneric` and the `methods` package. – Ludovic Duvaux Oct 19 '13 at 17:03
  • @LudoDuvaux: no worries. It's not an obvious link unless you've encountered this issue before. – Joshua Ulrich Oct 19 '13 at 17:09
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    I just ran into this with `Error: could not find function "is"`. The connection there is even less obvious! – DavidC May 08 '15 at 18:20
  • the command (according to help(Rscript)) should really be: `Rscript --default-packages=methods,datasets,utils,grDevices,graphics,stats` in order to have the same default packages as R -- if you just include methods, a bunch of other stuff is then missing – Kem Mason Jan 23 '19 at 20:24