BiocGenerics breaks template filling

[mschubert]

The following call to Q no longer works when loading the BiocGenerics library:

library(BiocGenerics) # remove this line and it works
res = clustermq::Q(identity, x=1, n_jobs=1, memory=1000)
# n_jobs gets filled as "   3"

The reason for this is that in fill_template, we do the following:

clustermq/R/util.r

Lines 35 to 37 in ec01add

	is_num = sapply(values, is.numeric)
	if (length(is_num) > 0)
	values[is_num] = format(values[is_num], scientific=FALSE, trim=TRUE)

which boils down to:

format(list(a=3, b=1000), scientific=FALSE, trim=TRUE)
#     a      b
#   "3" "1000"

library(BiocGenerics)
format(list(a=3, b=1000), scientific=FALSE, trim=TRUE)
# [1] "   3" "1000"

because BiocGenerics provides a format.list, whereas base::format.default handles the list case with an if (is.list(x)). So the dispatch moves from base::format.default to BiocGenerics::format.list, which itself uses base::format.AsIs:

# https://github.com/Bioconductor/BiocGenerics/blob/devel/R/format.R#L29
format.list <- base::format.AsIs

# https://github.com/wch/r-source/blob/tags/R-4-4-2/src/library/base/R/format.R#L277-L292
format.AsIs <- function(x, width = 12, ...)
{
    ...
    format.default(rvec, justify = "right") # note the lack of passing '...', dropping trim=TRUE
}

A workaround is calling format.default explicitly in fill_template:

clustermq/R/util.r

Lines 35 to 37 in c7a0800

	is_num = sapply(values, is.numeric)
	if (length(is_num) > 0)
	values[is_num] = format.default(values[is_num], scientific=FALSE, trim=TRUE)