"Warning: Recycling array of length 1 in vector-array arithmetic is deprecated"

[griffinfarrow]

I am using QDNAseq to do some CNA analysis (and loving it - thank you!)
I've got a custom dataset and I'm running into an error that I assume is a deprecation one. When I call QDNAseq::callBins() on my data, I get a warning raised repeatedly that

Warning: Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead.

Is this a known issue of the package? Or is it possibly something weird in my data?
I've been sent copy number data without calls and I'm trying to use the package to process it without the raw .BAM files so I have been quite well-acquainted with strange warnings.

[HenrikBengtsson]

Yes, this is known and its coming from the CGHcall package. From news(package = "QDNAseq");

QDNAseq/NEWS.md

Lines 181 to 186 in c07ae77

	* `callBins()` produces warnings on `Recycling array of length 1 in
	vector- array arithmetic is deprecated. Use c() or as.vector()
	instead.` in R (>= 3.4.0). This is a problem in the package
	**CGHcall** dependency and is something that needs to be fixed
	there. For further details, please see
	https://github.com/tgac-vumc/CGHcall/issues/2.

I created a CGHcall issue (tgac-vumc/CGHcall#2) many moons ago. They're the ones that have to fix this. At the moment I think these warnings are harmless, but the day these warnings are escalated to errors in base R, which is what reports on this, things will break.