Question

I am sifting through a package and scripts that utilize the package, and would like to identify external dependencies. The goal is to modify scripts to specify library(pkgName) and to modify functions in the package to use require(pkgName), so that these dependencies will be more obvious later.

I am revising the code to account for each externally dependent package. As an example, though it is by no means definitive, I am now finding it difficult to identify code that depends on data.table. I could replace data.table with Matrix, ggplot2, bigmemory, plyr, or many other packages, so feel free to answer with examples based on other packages.

This search isn’t particularly easy. The approaches I have tried so far include:

• Search the code for library and require statements
• Search for mentions of data.table (e.g. library(data.table))
• Try running codetools::checkUsage to determine where there may be some issues. For the scripts, my program inserts the script into a local function and applies checkUsage to that function. Otherwise, I use checkUsagePackage for the package.
• Look for statements that are somewhat unique to data.table, such as :=.
• Look for where objects’ classes may be identified via Hungarian notation, such as DT

The essence of my searching is to find:

• loading of data.table,
• objects with names that indicate they are data.table objects,
• methods that appear to be data.table-specific

The only easy part of this seems to be finding where the package is loaded. Unfortunately, not all functions may explicitly load or require the external package – these may assume it has already been loaded. This is a bad practice, and I am trying to fix it. However, searching for objects and methods seems to be challenging.

This (data.table) is just one package, and one with what seems to be limited and somewhat unique usage. Suppose I wanted to look for uses of ggplot functions, where the options are more extensive, and the text of the syntax is not as idiosyncratic (i.e. frequent usage of + is not idiosyncratic, while := seems to be).

I don’t think that static analysis will give a perfect answer, e.g. one could pass an argument to a function, which specifies a package to be loaded. Nonetheless: are there any core tools or packages that can improve on this brute force approach, either via static or dynamic analysis?

For what it’s worth, tools::pkgDepends only addresses dependencies at the package level, not the function or script level, which is the level I’m working at.

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Update 1: An example of a dynamic analysis tool that should work is one that reports which packages are loaded during code execution. I don’t know if such a capability exists in R, though – it would be like Rprof reporting the output of search() instead of the code stack.

Answer 1

First, thanks to @mathematical.coffee to putting me on the path of using Mark Bravington’s mvbutils package. The foodweb function is more than satisfactory.

To recap, I wanted to know about about checking one package, say myPackage versus another, say externalPackage, and about checking scripts against the externalPackage. I’ll demonstrate how to do each. In this case, the external package is data.table.

1: For myPackage versus data.table, the following commands suffice:

library(mvbutils)
library(myPackage)
library(data.table)
ixWhere <- match(c("myPackage","data.table"), search())
foodweb(where = ixWhere, prune = ls("package:data.table"), descendents = FALSE)

This produces an excellent graph showing which functions depend on functions in data.table. Although the graph includes dependencies within data.table, it’s not overly burdensome: I can easily see which of my functions depend on data.table, and which functions they use, such as as.data.table, data.table, :=, key, and so on. At this point, one could say the package dependency problem is solved, but foodweb offers so much more, so let’s look at that. The cool part is the dependency matrix.

depMat  <- foodweb(where = ixWhere, prune = ls("package:data.table"), descendents = FALSE, plotting = FALSE)
ix_sel  <- grep("^myPackage.",rownames(depMat))
depMat  <- depMat[ix_sel,]
depMat  <- depMat[,-ix_sel]
ix_drop <- which(colSums(depMat) == 0)
depMat  <- depMat[,-ix_drop]
ix_drop <- which(rowSums(depMat) == 0)
depMat  <- depMat[-ix_drop,]

This is cool: it now shows dependencies of functions in my package, where I’m using verbose names, e.g. myPackage.cleanData, on functions not
in my package, namely functions in data.table, and it eliminates rows and columns where there are no dependencies. This is concise, lets me survey dependencies quickly, and I can find the complementary set for my functions quite easily, too, by processing rownames(depMat).

NB: plotting = FALSE doesn’t seem to prevent a plotting device from being created, at least the first time that foodweb is called in a sequence of calls. That is annoying, but not terrible. Maybe I’m doing something wrong.

2: For scripts versus data.table, this gets a little more interesting. For each script, I need to create a temporary function, and then check for dependencies. I have a little function below that does precisely that.

listFiles <- dir(pattern = "myScript*.r")
checkScriptDependencies <- function(fname){
    require(mvbutils)
    rawCode  <- readLines(fname)
    toParse  <- paste("localFunc <- function(){", paste(rawCode, sep = "\n", collapse = "\n"), "}", sep = "\n", collapse = "")
    newFunc  <- eval(parse(text = toParse))
    ix       <- match("data.table",search())
    vecPrune <- c("localFunc", ls("package:data.table"))
    tmpRes   <- foodweb(where = c(environment(),ix), prune = vecPrune, plotting = FALSE)
    tmpMat   <- tmpRes$funmat
    tmpVec   <- tmpMat["localFunc",]
    return(tmpVec)
}

listDeps <- list()
for(selFile in listFiles){
    listDeps[[selFile]] <- checkScriptDependencies(selFile)
}

Now, I just need to look at listDeps, and I have the same kind of wonderful little insights that I have from the depMat above. I modified checkScriptDependencies from other code that I wrote that sends scripts to be analyzed by codetools::checkUsage; it’s good to have a little function like this around for analyzing standalone code. Kudos to @Spacedman and @Tommy for insights that improved the call to foodweb, using environment().

(True hungaRians will notice that I was inconsistent with the order of name and type – tooBad. 🙂 There’s a longer reason for this, but this isn’t precisely the code I’m using, anyway.)

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Although I’ve not posted pictures of the graphs produced by foodweb for my code, you can see some nice examples at http://web.archive.org/web/20120413190726/http://www.sigmafield.org/2010/09/21/r-function-of-the-day-foodweb. In my case, its output definitely captures data.table’s usage of := and J, along with the standard named functions, like key and as.data.table. It seems to obviate my text searches and is an improvement in several ways (e.g. finding functions that I’d overlooked).

All in all, foodweb is an excellent tool, and I encourage others to explore the mvbutils package and some of Mark Bravington’s other nice packages, such as debug. If you do install mvbutils, just check out ?changed.funs if you think that only you struggle with managing evolving R code. 🙂