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Misc fixes found when running package checks on newer releases of R #5074

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Run time

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Job	Run time
sipnet (4.2)	1m 27s
test (4.2)	1m 26s
sipnet (4.1)	1m 30s
check (check_base, 4.2)	1m 2s
test (4.1)	1m 39s
check (check_base, 4.1)	1m 4s
check (check_modules, 4.2)	1m 39s
check (check_modules, 4.1)	1m 6s
check (check_models, 4.2)	1m 9s
check (check_models, 4.1)	1m 2s
	13m 4s