I currently have the `pleasure` of dealing with students who have problems with installing AnnotationHub and/or downloading resources. Here are some comments including some possible bug reports.
1) I think it is extremely dangerous that `cache(ahub)` starts by asking to download all resources! May I suggest this only happens with a specific setting like `cache(ahub, download=TRUE)` or something similar. 2) `cache(ahub)` deletes all cached information, except the sqlite database. Could we get a way to remove everything? 3) While I can understand the difference between cache and hubCache, I would suggest that hubCache(ahub) = NULL removes all cached material included the sqlite database. 4) It seems that AnnotationHub in the release version of Bioconductor defaults to using https://. Wasn't full support for https:// introduced in R 3.2.2; if so, it seems to be a critical bug that it is using https:// 5) Perhaps it should be considered that the default hubCache path is versioned, perhaps with Bioc version, perhaps with something else. This might cause problems for people running multiple versions of R. 6) I strongly suggest that the output printed when retrieving an AnnotationHub resource includes the download url. 7) If you run AnnotationHub without having GenomicRanges / rtracklayer installed, it downloads the resource and then pangs out with an error. To me it seems more natural to pang out with an error immediately, especially since when it works, it appears from message printing that loading the library happens prior to download. Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel