similar to: codetools

Dear list members, I frequently program small scripts and wrap them into functions to be able to check them with checkUsage. In case these functions (loaded via source or copy pasted to the R console) use functions from other packages, I get this error: no visible global function definition for ?xxxxxxx? For example: test = function() { require(plotrix) color.legend() }

Dear R Users, Using codetools I obtained the text representation of the parse tree for this snippet z=quote({x[1]<-2}) showTree(z) > ("{" (<- ([ x 1) 2)) (A) If I understand correctly, x[1]<-2 ought to be "[<-"(x,1,2), so shouldn't i see ("{" ( [<- x 1 2 ) ) If indeed the parse tree in (A) is correct, the operation ([ x 1) returns the

Hello, Is this a bug in codetools: > codetools::showTree( body( glm) ) ("{" (<- call (match.call)) (if (is.character family) (<- family (get family "function" (parent.frame)))) (if (is.function family) (<- family(family))) (if (is.null ($ family family)) ("{" (print family) (stop "'family' not recognized"))) (if (missing data)

I put the idea below into a function that gives nicer looking results. Here's the new code: dupnames <- function(path = ".") { Rfiles <- pkgload:::find_code(path) allnames <- data.frame(names=character(), filename=character(), line = numeric()) result <- NULL for (f in Rfiles) { exprs <- parse(f, keep.source = TRUE) locs <-

Sorry for reposting, i keep forgetting this should be plain text. Will not make this mistake again Hello, The following code moo <- function(a=1){ x=1; x=x+y} funs <- new.env() enter <- function(type, v, e, w){ assign(v, TRUE, funs) } library(codetools) collectUsage(moo, enterGlobal = enter) adds + to the environment funs i.e. funs: "=" "{" "+"

Hi the list, Considere the following: f <- function(x){apply(x,2,mean)} findGlobals(f) findGlobals consideres mean as a global variable, which it is not. Is there a way to tell to findGlobals that mean is a function ? Thanks Christophe

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in

After upgrading to R 2.5.1 on Debian, R CMD check gives * checking Rd cross-references ... WARNING Error in .find.package(package, lib.loc) : there is no package called 'codetools' Execution halted * checking for missing documentation entries ... WARNING etc The NEWS file says (for 2.5.0; I was on 2.4 before the recent upgrade) o New recommended package 'codetools' by Luke

Both codetools and compiler get by without this. codetools uses source refs to generate messages; I don't recall if compiler does but it could easily do so. I would be wary about committing to this sort of implementation specific stuff -- we might want to go to completely different parser technology at tome point, which would be harder if we committed to these sort of details. Best, luke On

UseMethod has since the beginning had the 'feature' that local variables in the generic are added to the environment in which the method body is evaluated. This is documented in ?UseMethod and R-lang.texi, but use of this 'feature' has been explicitly discouraged in R-lang.texi for many years. This is an unfortunate design decision for a number of reasons (see below), so the plan

Hi the list Is there any tutorial to learn codetools ? It seems to be a very interesting pacakge, but the help gives not that much detail, and there is not that much examples provided... Christophe

In a package, I define a method for not-yet-generic function 'qr.X' like so: > setOldClass("qr") > setMethod("qr.X", signature(qr = "qr"), function(qr, complete, ncol) NULL) The formals of the newly generic 'qr.X' are inherited from the non-generic function in the base namespace. Notably, the inherited default value of formal

Hello the list, I am trying to write a "cleanProgramming" function to test the procedure I use. For example, I want to be sure that I am not using globals variables. The function "findGlobals" detect that. To list the globals used in function "fun", the syntax is : "findGlobals(fun,FALSE)$variable" My problem is that I want to use it in a function,

>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com> >>>>> on Tue, 13 Mar 2018 10:12:55 -0700 writes: > FYI, in R devel (to become 3.5.0), there's isFALSE() which will cut > some corners compared to identical(): > > microbenchmark::microbenchmark(identical(FALSE, FALSE), isFALSE(FALSE)) > Unit: nanoseconds > expr

Hi all Is there any compiler for R ? By compiler, I mean something that check the cleanliness of the code : if we declare all the variables we use, if we don't use external variable from a function and so on... For exemple, something that will ring a bell on the following code (saying "line 4 : 'pp' undefine in function 'power' ") 1. pp <- 3 2. power <-

Here's a dummy example that I think illustrates the problem: toto <- function() { if (runif(1) < 0.5) function(a) a else function(a,b) a+b } > fcn <- toto() > fcn(1,2) [1] 3 > fcn <- toto() > fcn(1,2) [1] 3 > fcn <- toto() > fcn(1,2) Error in fcn(1, 2) : unused argument (2) How can you use the returned function, if you get different arguments?

This is just a note/wishlist/for the record: With foo1 <- function() { res; } foo2 <- function() { for (i in c()) res <- 1; res; } foo3 <- function() { while (FALSE) res <- 1; res; } foo4 <- function() { if (FALSE) res <- 1; res; } we get: > foo1() Error in foo1() : object 'res' not found > foo2() Error in foo2() : object 'res' not

I've recently hunted down a troublesome bug in my own code, and am looking for an easy mechanism to detect this kind of error in other R code. The problem was an undefined variable inside of a function. Unfortunately, R looked for that variable in the global environment and found it since there was variable with that name in my testing scripts (note to self: do not name things "x").

Hi, I was wondering if I could get R to warn me, or give me a rude awakening somehow, if I'm accessing a variable that is out of my function's scope. For example, often times I'm creating a function as I'm testing it in the REPL, copying and pasting between both. As a simple example, I might end up with a function like: f <- function(a, b) { a + b.test } Where

You can file it as a wishlist item in the bug trackign system. Without a compelling case or a complete and well tested patch or both I doubt it will rise to the top of anyone's priority list. Best, luke On Sun, 15 Sep 2019, Jan Gorecki wrote: > Thank you Luke for prompt reply. > Is it possible then to request a new function to R C API "message" > that would equivalent to