As reported in <https://github.com/yihui/knitr/issues/1383#issuecomment-289256967> with a sample package in <https://github.com/pdbailey0/knitIgnore>, if a vignette in the vignettes directory is listed in .Rbuildignore, R CMD build will not include it in the tarball, but will include it in the vignette database vignettes.rds, leading to a check warning. Thanks to Paul Bailey and Yihui Xie
for pointing this out.
I will fix it for R 3.4.0.
Fixed in R-devel and R-3.4.0 alpha.
That fix (which made it into 3.4.0) wasn't quite right; will try again in R-patched.
Should now be fixed in R-devel and R-patched (as of r72629).