Exported variable starting with a period are not loaded

[HenrikBengtsson]

Although batchExport() successfully exports variables starting with periods, they are not loaded in the job sessions. This is in turn because loadExports() does not load those variables.

Example

> library(BatchJobs)
> reg <- makeRegistry(id="test")
> objs <- list(a=1, b=2, .c=3, d=4)
> str(objs)
List of 4
 $ a : num 1
 $ b : num 2
 $ .c: num 3
 $ d : num 4
> batchExport(reg, li=objs)
> keys <- loadExports(reg)
Loading RData files: a,b,d
> keys
[1] "a" "b" "d"

Troubleshooting

All four variables are indeed exported:

> list.files(path=BatchJobs:::getExportDir(reg$file.dir), all.files=TRUE, no..=TRUE)
[1] ".c.RData" "a.RData"  "b.RData"  "d.RData"

But the ls() method for fail objects in loadExports() uses the default all.files=FALSE;

> library(fail)
> f = fail(BatchJobs:::getExportDir(reg$file.dir), extension = "RData", simplify=TRUE)
> f$ls()
[1] "a" "b" "d"
> f$ls
function (pattern = NULL)
{
    Ls(.self, pattern)
}
<bytecode: 0x000000000c108dc8>
<environment: 0x000000000c715348>
> fail:::Ls
function (.self, pattern = NULL)
{
    keys = fn2key(.self, list.files(.self$path, pattern = sprintf("\\.%s$",
        .self$extension)))
    if (!is.null(pattern))
        keys = keys[grepl(pattern, keys)]
    return(keys)
}
<bytecode: 0x000000000afff9b8>
<environment: namespace:fail>

Suggestions

• At a minimum, batchExport() should give an error, or at least a warning, if variable names starting with a period are specified, cf. Issue batchExport() and objects with non-standard names #93.
• If fixed, the list.files() call of fail:::Ls() needs all.files=TRUE in order to pick up variables starting with a period. Simple tests, indicates that this is enough, that is, with .c in keys, then f$assign(keys, envir = .GlobalEnv) does indeed load and assign .c to the global environment.

[mllg]

Should be fixed with fail v1.3 and 7ab2e11.

[HenrikBengtsson]

Thxs.