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Question: AnnotationHub - Problem with SSL CA certificate
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gravatar for dalloliogm
23 months ago by
dalloliogm40
European Union
dalloliogm40 wrote:

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.

ADD COMMENTlink written 23 months ago by dalloliogm40

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.

ADD REPLYlink written 23 months ago by Jim Java30
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