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Update checkS3methods to ignore deprecated/defunct functions - R Dev Day issue 76 #7775

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Run time

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Job	Run time
MacOS (macOS-13)	48m 8s
Windows (check)	50m 22s
MacOS (macOS-14)	21m 15s
Windows (installer)	21m 48s
Linux (gcc, debian:stable)	33m 11s
Linux (gcc, debian:testing)	35m 1s
Linux (clang, debian:stable)	34m 43s
Linux (clang, debian:testing)	34m 3s
	4h 38m 31s