R help - Aug 2016 - package.skeleton, environment argument causes error

Hello, I have been using package.skeleton from within an lapply statement
successfully (assuming good source code) with the following setup in the
past:

x=try(package.skeleton(package_name,path=pathi,code_files=file_i))


but now fails with error:

Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?

I am working in RStudio Version 0.99.896, with 64 bit R version 3.3.1
(2016-06-21)




I have been probing the code for package.skeleton a bit and noticed that
the default arguments for 'list' and 'environment' are supplied
in the
function definition, thus making it impossible to achieve the conditions

envIsMissing=TRUE
missing(list) = TRUE


as a result of the fact that missing(list) cannot be true, the classesList
argument is empty and the call

classes0 <- .fixPackageFileNames(classesList)


then fails with the error

Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?


If I remove the default arguments I get further, but get the same error  I
had before (Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?) after executing the following code:

methods0 <- .fixPackageFileNames(methodsList)


and the contents of methodsList look like

An object of class "ObjectsWithPackage":

Object:
Package:


the function .fixPackageFileNames fails when it reaches

list <- as.character(list)


where in this case the contents of 'list' look like

str(list)
Formal class 'ObjectsWithPackage' [package "methods"] with 2
slots
  ..@ .Data  : chr(0)
  ..@ package: chr(0)


I am not sure if the problem arose from changes to package.skeleton
or methods::getClasses and methods::getGenerics or if there is something
peculiar about my environment.

my current ugly fix is to define the function .fixPackageFileNames in the
global environment and add a try statement and exit when it results in an
object of class "try-error":

.fixPackageFileNamesfunction (list)
{
    list <- *try(*as.character(list)*)*
    *if(class(list)=="try-error")return(list)*
    if (length(list) == 0L)
        return(list)
    list0 <- gsub("[[:cntrl:]\"*/:<>?\\|]",
"_", list)
    wrong <-
grep("^(con|prn|aux|clock\\$|nul|lpt[1-3]|com[1-4])(\\..*|)$",
        list0)
    if (length(wrong))
        list0[wrong] <- paste0("zz", list0[wrong])
    ok <- grepl("^[[:alnum:]]", list0)
    if (any(!ok))
        list0[!ok] <- paste0("z", list0[!ok])
    list1 <- tolower(list0)
    list2 <- make.unique(list1, sep = "_")
    changed <- (list2 != list1)
    list0[changed] <- list2[changed]
    list0
}


Any assistance with this error would be greatly appreciated!

Thank you,

-- 
Jacob Strunk
strunky at gmail.com

	[[alternative HTML version deleted]]

It would be helpful for us if you provide a reproducible examples when 
the current package.skeleton fails.

Best,
Uwe Ligges



On 19.08.2016 00:12, Jacob Strunk wrote:
> Hello, I have been using package.skeleton from within an lapply statement
> successfully (assuming good source code) with the following setup in the
> past:
>
> x=try(package.skeleton(package_name,path=pathi,code_files=file_i))
>
>
> but now fails with error:
>
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> I am working in RStudio Version 0.99.896, with 64 bit R version 3.3.1
> (2016-06-21)
>
>
>
>
> I have been probing the code for package.skeleton a bit and noticed that
> the default arguments for 'list' and 'environment' are
supplied in the
> function definition, thus making it impossible to achieve the conditions
>
> envIsMissing=TRUE
> missing(list) = TRUE
>
>
> as a result of the fact that missing(list) cannot be true, the classesList
> argument is empty and the call
>
> classes0 <- .fixPackageFileNames(classesList)
>
>
> then fails with the error
>
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
>
> If I remove the default arguments I get further, but get the same error  I
> had before (Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?) after executing the following code:
>
> methods0 <- .fixPackageFileNames(methodsList)
>
>
> and the contents of methodsList look like
>
> An object of class "ObjectsWithPackage":
>
> Object:
> Package:
>
>
> the function .fixPackageFileNames fails when it reaches
>
> list <- as.character(list)
>
>
> where in this case the contents of 'list' look like
>
> str(list)
> Formal class 'ObjectsWithPackage' [package "methods"]
with 2 slots
>   ..@ .Data  : chr(0)
>   ..@ package: chr(0)
>
>
> I am not sure if the problem arose from changes to package.skeleton
> or methods::getClasses and methods::getGenerics or if there is something
> peculiar about my environment.
>
> my current ugly fix is to define the function .fixPackageFileNames in the
> global environment and add a try statement and exit when it results in an
> object of class "try-error":
>
> .fixPackageFileNames> function (list)
> {
>     list <- *try(*as.character(list)*)*
>     *if(class(list)=="try-error")return(list)*
>     if (length(list) == 0L)
>         return(list)
>     list0 <- gsub("[[:cntrl:]\"*/:<>?\\|]",
"_", list)
>     wrong <-
grep("^(con|prn|aux|clock\\$|nul|lpt[1-3]|com[1-4])(\\..*|)$",
>         list0)
>     if (length(wrong))
>         list0[wrong] <- paste0("zz", list0[wrong])
>     ok <- grepl("^[[:alnum:]]", list0)
>     if (any(!ok))
>         list0[!ok] <- paste0("z", list0[!ok])
>     list1 <- tolower(list0)
>     list2 <- make.unique(list1, sep = "_")
>     changed <- (list2 != list1)
>     list0[changed] <- list2[changed]
>     list0
> }
>
>
> Any assistance with this error would be greatly appreciated!
>
> Thank you,
>