[Roxygen-devel] [roxygen2] error sourcing the R files (probably environment issue)

[Renaud Gaujoux]

Hi,

in one of the R files I have something like this, that defines a
temporary function in order to define a static variable:

f <- function(){
.a <- 0
function(x=1){
.a <<- .a + x
.a
}
}
f2 <- f()
rm(f)

When running roxygenise on this I get the error:
Error in eval(expr, envir, enclos) : object 'f' not found

No error with R CMD check.
If I use the -- very nice -- function devtools::load_all, it works
perfectly fine as well.

In this simple case I know I could do f <- f() instead and remove the
problematic call to rm (and it works fine).
But my actual use case is to define a S4 method like this:

setMethod('A', 'ANY', f())
rm(f)

Here I really need to remove not to have it remaining in my namespace.

Does roxygen2 source the R files differently?
Maybe there is an alternative way to define static variables for my use
case, that would not break roxygenise?

Thank you

Renaud



###

UNIVERSITY OF CAPE TOWN

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[Hadley Wickham]

in one of the R files I have something like this, that defines a temporary
f <- function(){
? ?.a <- 0
? ?function(x=1){
? ? ? ?.a <<- .a + x
? ? ? ?.a
? ?}
}
f2 <- f()
rm(f)
Error in eval(expr, envir, enclos) : object 'f' not found

What does traceback give you? Could you provide a small reproducible example?

Hadley

[Renaud Gaujoux]

The sample code in my post should be enough to reproduce the issue.
I have wrapped it into a package (attached to this post).

Renaud

Post by Hadley Wickham

in one of the R files I have something like this, that defines a temporary
f<- function(){
.a<- 0
function(x=1){
.a<<- .a + x
.a
}
}
f2<- f()
rm(f)
Error in eval(expr, envir, enclos) : object 'f' not found

What does traceback give you? Could you provide a small reproducible example?
Hadley

###

UNIVERSITY OF CAPE TOWN

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[Hadley Wickham]

Could you please file an issue at https://github.com/klutometis/roxygen/issues?
Thanks!
Hadley

Post by Renaud Gaujoux
The sample code in my post should be enough to reproduce the issue.
I have wrapped it into a package (attached to this post).
Renaud

in one of the R files I have something like this, that defines a temporary
f<- function(){
? ?.a<- 0
? ?function(x=1){
? ? ? ?.a<<- .a + x
? ? ? ?.a
? ?}
}
f2<- f()
rm(f)
Error in eval(expr, envir, enclos) : object 'f' not found

What does traceback give you? ?Could you provide a small reproducible
example?
Hadley

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[Renaud Gaujoux]

Done:
https://github.com/klutometis/roxygen/issues/42

Thank you

Post by Hadley Wickham
Could you please file an issue at https://github.com/klutometis/roxygen/issues?
Thanks!
Hadley

Post by Renaud Gaujoux
The sample code in my post should be enough to reproduce the issue.
I have wrapped it into a package (attached to this post).
Renaud

Post by Hadley Wickham

in one of the R files I have something like this, that defines a temporary
f<- function(){
.a<- 0
function(x=1){
.a<<- .a + x
.a
}
}
f2<- f()
rm(f)
Error in eval(expr, envir, enclos) : object 'f' not found

What does traceback give you? Could you provide a small reproducible example?
Hadley

###
UNIVERSITY OF CAPE TOWN
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[Renaud Gaujoux]

traceback()

12: eval(expr, envir, enclos)
11: eval(assignee, env)
10: parser(call, env)
9: FUN(X[[1L]], ...)
8: lapply(src_refs, parse.srcref, env = env)
7: force(code)
6: parse_cache$compute(c(env_hash, readLines(file, warn = FALSE)),
{
src_refs <- attributes(parse(srcfile$filename, srcfile =
srcfile))$srcref
pre_refs <- prerefs(srcfile, src_refs)
if (length(src_refs) == 0)
return(list())
src_parsed <- lapply(src_refs, parse.srcref, env = env)
pre_parsed <- lapply(pre_refs, parse.preref)
stopifnot(length(src_parsed) == length(pre_parsed))
mapply(c, src_parsed, pre_parsed, SIMPLIFY = FALSE)
})
5: FUN("/home/renaud/Documents/tmp/test/R/fun.R"[[1L]],
...)
4: lapply(paths, parse.file, env = env, env_hash = env_hash)
3: unlist(lapply(paths, parse.file, env = env, env_hash = env_hash),
recursive = FALSE)
2: parse.files(r_files)
1: roxygenise(".")
--
Renaud Gaujoux
Computational Biology - University of Cape Town
South Africa

in one of the R files I have something like this, that defines a temporary
f<- function(){
.a<- 0
function(x=1){
.a<<- .a + x
.a
}
}
f2<- f()
rm(f)
Error in eval(expr, envir, enclos) : object 'f' not found

What does traceback give you? Could you provide a small reproducible example?
Hadley

###

UNIVERSITY OF CAPE TOWN

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