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Based on the answer to this question: Elegant way to check for missing packages and install them?

I'm using the following code to make sure that all packages are installed when I upgrade R, or set up other users:

list.of.packages <- c("RODBC", "reshape2", "plyr")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

I've placed it in my .First function in my .Rprofile, but when I start up R it gives the following error and continues starting up:

Error in match(x, table, nomatch = 0L) : 
  could not find function "installed.packages"

If I run the code after I get a prompt it works fine. Any ideas why?

Thanks!

Community
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sinclairjesse
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1 Answers1

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It appears from reading ?Startup that:

Next, if a function .First is found on the search path, it is executed as .First(). Finally, function .First.sys() in the base package is run. This calls require to attach the default packages specified by options("defaultPackages").

Now, installed.packages is in the utils package, which is typically one of the default packages. So it's not available at the time .First is called.

Perhaps try replacing installed.packages with utils::installed.packages?

As Josh notes below my eyes skimmed over the piece that addresses this issue directly, namely:

Note that when the site and user profile files are sourced only the base package is loaded, so objects in other packages need to be referred to by e.g. utils::dump.frames or after explicitly loading the package concerned.

joran
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    Or (as described a bit earlier in `?Startup`, you can use `utils::installed.packages` or first explicitly load the package with `require(utils)`. – Josh O'Brien Jun 28 '12 at 18:23
  • Awesome. Referencing the functions as utils::installed.packages and utils::install.packages does the trick. Thanks Josh and Joran! – sinclairjesse Jun 28 '12 at 19:39