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...alled. However, if I do R CMD build --no-vignettes PKGNAME R CMD check PKGNAME_VERSION.tar.gz the package passes R CMD check! Presumably because R CMD check installs the package first. This took me a long time to track down (inspired by a recent addition of dataset to the Bioconductor package Genominator and a subsequent failed build - specifically the dataset yeastAnno.sources and the vignette withShortRead.Rnw). I am using lazy loading (in case it matters, which I don't think it does). It seems like the relevant fix is to include pdf versions of the vignette(s) in inst/doc. On one hand...

This is about the Bioconductor package Genominator. As part of the vignette building process, we create two sizable sqlite3 databases, in the vignette directory (inst/doc). When we build the source tarball, these databases are deleted, but when a Windows binary is being made on the Bioconductor build servers the file(s) are not removed (as fa...