containsElements("H2O", "Z") returns TRUE

[sgibb]

containsElements returns TRUE (with a warning) for characters that are not valid elements:

library("MetaboCoreUtils")

containsElements("H2O", "Z")
#> Warning in (function (xx, rr) : The following names are not valid and are
#> dropped: 1
#> [1] TRUE
containsElements("H2O", "J")
#> Warning in (function (xx, rr) : The following names are not valid and are
#> dropped: 1
#> [1] TRUE
containsElements("H2O", "")
#> Warning in (function (xx, rr) : The following names are not valid and are
#> dropped: 1
#> [1] TRUE

^{Created on 2023-08-02 with reprex v2.0.2}

It should return FALSE (without a warning).

It would be possible to add something like

if (length(rr) == 1 && rr < 0)
    return(integer(0))

in the mapply of countElements

MetaboCoreUtils/R/chemFormula.R

Lines 55 to 75 in 7294eec

	mapply(function(xx, rr) {
	n <- length(rr)
	start <- attr(rr, "capture.start")
	end <- start + attr(rr, "capture.length") - 1L
	sbstr <- substring(xx, start, end)
	## set elements without a number in the formula to one
	sbstr[!nchar(sbstr)] <- 1L
	sl <- seq_len(n)
	nm <- sbstr[sl]
	r <- setNames(as.integer(sbstr[n + sl]), nm)
	valid <- .isValidElementName(nm)
	if (any(!valid)) {
	warning(
	"The following names are not valid and are dropped: ",
	paste0(names(r)[!valid], collapse = ", ")
	)
	r <- r[valid]
	}
	r
	}, xx = x, rr = rx, SIMPLIFY = FALSE, USE.NAMES = TRUE)

(after the if (is.na(xx)) statement introduced in #62 ) and test for length(x) == 0 in containsElements but that would break many unit tests in test_adducts.R (.pasteElements throws an error because of an unnamed argument instead of silently return ""; even returning a named integer(0) results in many other failures in test_adducts.R).

[sgibb]

I add (currently failing) unit tests in the issue63-containsElements-returns-TRUE-for-invalid-elements branch.
https://github.com/rformassspectrometry/MetaboCoreUtils/compare/issue63-containsElements-returns-TRUE-for-invalid-elements?expand=1

[jorainer]

Thanks for adding this issue! Can you maybe work on that?

[sgibb]

fixed by #65