annotationhub, download corrrupt,
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acaugu ▴ 10
@acaugu-8986
Last seen 6.1 years ago
United States
> 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 
annotationhub • 1.2k views
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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 and that the problem is on your end -- an outdated certificate bundle.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()? 

 

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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.

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acaugu ▴ 10
@acaugu-8986
Last seen 6.1 years ago
United States

Here is the session info: thanks for your help.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.0 AnnotationHub_2.2.0  GenomicRanges_1.22.0 GenomeInfoDb_1.6.0   IRanges_2.4.0        S4Vectors_0.8.0     
[7] BiocGenerics_0.16.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1                  AnnotationDbi_1.32.0         XVector_0.10.0               magrittr_1.5                
 [5] zlibbioc_1.16.0              xtable_1.7-4                 R6_2.1.1                     stringr_1.0.0               
 [9] httr_1.0.0                   tools_3.2.2                  Biobase_2.30.0               DBI_0.3.1                   
[13] htmltools_0.2.6              digest_0.6.8                 interactiveDisplayBase_1.8.0 shiny_0.12.2                
[17] curl_0.9.3                   RSQLite_1.0.0                mime_0.4                     stringi_0.5-5               
[21] httpuv_1.3.3                
 
 
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