Entering edit mode
> ah <- AnnotationHub() updating AnnotationHub metadata: retrieving 1 resource Error: 'AnnotationHub' database corrupt; remove it and try again database: ‘C:/Users/acaugu/Documents/AppData/.AnnotationHub/annotationhub.sqlite3’ reason: missing tables In addition: Warning messages: 1: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 2: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 3: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 4: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 5: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 6: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 7: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 8: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 9: download failed hub path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’ cache path: ‘C:/Users/acaugu/Documents/AppData/.AnnotationHub/annotationhub.sqlite3’ reason: Peer certificate cannot be authenticated with given CA certificates
The root problem is the at the end 'Peer certificate cannot be authenticated with given CA certificates'. This seems like a technical problem with the 'certificates' used to verify that the AnnotationHub server is the computer it says it is. It seems that the certificate from the AnnotationHub server is valid (maybe Dan can confirm this?) and that the problem is on your end -- an outdated certificate bundle. I'm not really sure how to address this, other than by googling or speaking with your local system administrator.
Can you update your question by providing the output of sessionInfo()?
My understanding of these things is not terribly sophisticated, but if i go to https://annotationhub.bioconductor.org/ in the Chrome browser and click on the green lock in the URL bar, it does show me that the certificate is valid. I suggest perhaps trying on a different machine (and maybe from another location) and see if you get the same results. If not then it probably is an issue for your local system administrator. I'll echo the request for sessionInfo() (if you could also post a comment when you've updated your post then we'll see it right away); that will help us to look into this further.