R 2.14 - detect packages without namespace

Question

According to the R News for v2.14:

All packages must have a namespace, and one is created on installation if not supplied in the sources. This means that any package without a namespace must be re-installed under this version of R (but data-only packages without R code can still be used).

How do I programatically detect which packages installed under 2.13.x don't have a namespace so I know what needs to be updated?

Morbilli

By the way, I can't simply call the update package function in my environment because my xcopy-deployable version of R is checked-into my source server and I use currently use SVN which makes it impossible to use the R update functions. So yes, I'm really looking for a way to detect packages without namespaces. – Morbilli

Answer 1

The function packageHasNamespace holds the key. Use it together with installed.packages:

The following code loops through all of the library locations in .libPaths:

pkgNS <- NULL
for(i in seq_along(.libPaths())){
  libLoc <- .libPaths()[i]
  pkgs <- installed.packages(lib.loc=libLoc)[, 1]
  pkgNS <- c(pkgNS, 
      sapply(unname(pkgs), packageHasNamespace, package.lib=libLoc)
  )
}

The result of this code is a named logical vector pkgNS that is TRUE if the package has a namespace, FALSE if it doesn't.

To get only those packages that don't have a namespace, create a subset of pkgNS where pkgNS is FALSE:

pkgNS[!pkgNS]

      abind      bitops   CircStats    combinat     corpcor      deldir 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
     Design         evd   financial         fpc      getopt      gsubfn 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 
       ineq       magic     mlbench    optparse     plotrix       ppcor 
      FALSE       FALSE       FALSE       FALSE       FALSE       FALSE 

Shira

I made a correction to the original code. It should be i in seq_along(.libPaths()) – Shira

NP. Let me know if it doesn't work. Each time I run this function it seems something else stops working. In my latest incarnation I need to unlist the result of sapply. Good luck. – Shira

Answer 2

Just run :

update.packages(checkBuilt=TRUE)

Forewoman

Very nice answer, but this will give a list of all packages that haven't been build in R2.14 - not just those that don't have a namespace. Most of the packages I use daily have had namespaces for quite some time. – Shira

@Shira Good point. No harm to refresh everything to be on safe side, though (R2.14 is quite a bit different). – Forewoman

I agree with you. It's just that the OP said he can't do that on his installation. – Shira

Ah. Ok I see OP's comment now. – Forewoman

Answer 3

Great thread. I was stuck on the same problem. To finish all that needs to be done you can:

remove.packages(names(pkgNS[!pkgNS]))
install.packages(names(pkgNS[!pkgNS]))

Cropland