Using R 3.4.2, BioC 3.6, SingleCellExperiment_1.0.0. The following example code from ?SingleCellExperiment produces an error
library(SingleCellExperiment) ncells <- 100 u <- matrix(rpois(20000, 5), ncol=ncells) v <- log2(u + 1) pca <- matrix(runif(ncells*5), ncells) tsne <- matrix(rnorm(ncells*2), ncells) sce <- SingleCellExperiment( assays = list(counts=u, logcounts=v), reducedDims = SimpleList(PCA=pca, tSNE=tsne) )
The error message is
Error in checkSlotAssignment(object, name, value) : assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “SingleCellExperiment”; is(value, "GenomicRangesORGRangesList") is not TRUE
This on a fresh Centos7 VM. If I'm not mistaken these examples are also tested as a part of the build process so I'm very puzzled how the code could fail on me.
EDIT: This appears to work perfectly fine on my MacBook Pro. It may be something strange in the setup of the Unix server I'm on.