Entering edit mode
I am trying to install AnnotationHub in a freshly installed Ubuntu system. I am getting some errors that seem to be related to missing libraries installed in the system.
The first time I tried to install AnnotationHub I got some errors related to libcurl, but these were solved by installing libcurl. However now I am receiving another error related to a missing SSL CA certificate, and I am not sure about what should I install. In any case the error message doesn't seem to be clear enough so I though better to report it here.
The AnnotationHub installation itself works correctly, but then the library doesn't work:
biocLite("AnnotationHub")
> ahub = AnnotationHub()
updating AnnotationHub metadata: retrieving 1 resource
Error: 'AnnotationHub' database corrupt; remove it and try again
database: ‘/home/gioby/.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: download failed
hub path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
cache path: ‘/home/gioby/.AnnotationHub/annotationhub.sqlite3’
reason: Problem with the SSL CA cert (path? access rights?)
>
The ~/.AnnotationHub folder is writable to all users, and the same error occurs when I install it with root privilegies.
One possibility (but unlikely) is that you might need to wipe out the AnnotationHub metadata DB and start again:
removeCache()If that fails, what happens when you try downloading any URL to disk, say
curl::curl_fetch_disk("www.google.com", tempfile())or
curl::curl_fetch_disk("https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3", tempfile())? If you still get the same "SSL CA cert" error, then you might want to try reinstalling packages "httr" and "curl".
This doesn't look like an AnnotationHub-specific problem, but rather something related to Internet file handling.