the generic for "trimws" hides base::trimws

[sgibb]

Since MSnbase 1.19.9 the import of Spectrum.xml files in synapter isn't working anymore. That happens because MSnbase maskes base::trimws by defining a new generic.

To reproduce:

Rdevel> R.version$version.str
[1] "R Under development (unstable) (2015-11-08 r69614)"
Rdevel> trimws(" xx ")
[1] "xx"
Rdevel> library("MSnbase"); packageVersion("MSnbase")
# ...
The following object is masked from ‘package:base’:

    trimws

[1] ‘1.19.9’
Rdevel> trimws(" xx ")
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘trimws’ for signature ‘"character"’

IMHO there are two possible solutions:

• 1. Defining a generic that uses all arguments of trimws:

# AllGenerics.R
setGeneric("trimws", function(x, which = c("both", "left", "right"))standardGeneric("trimws"))
# utils.R
setMethod("trimws", c("data.frame", "character"), function(x, which) { ... })

• 2. Or creating a new trimws that in contrast to the base::trimws accepts the ... argument (as BiocGenerics does it for is.unsorted: https://github.com/Bioconductor-mirror/BiocGenerics/blob/master/R/is.unsorted.R)

[lgatto]

Thanks - fixed in 3c07de7