R 2.14 - detect packages without namespace

Tag: r , cran Author: zhangbin8860 Date: 2011-10-18

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?

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.
Great question. thanks for asking.

Best Answer

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 

comments:

I made a correction to the original code. It should be i in seq_along(.libPaths())
fantastic! thanks, Andrie.
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.

Other Answer1

Just run :

update.packages(checkBuilt=TRUE)

comments:

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.
@Andrie Good point. No harm to refresh everything to be on safe side, though (R2.14 is quite a bit different).
I agree with you. It's just that the OP said he can't do that on his installation.
Ah. Ok I see OP's comment now.

Other Answer2

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]))