Question: Corrupt AnnotationHub database - previously posted fix not working
gravatar for tullyij1
12 months ago by
tullyij10 wrote:

Hi, I'm new to R/Biocunductor and trying to access AnnotationHub.  I get an error message whenever I try to run the script

> ah=AnnotationHub()
updating metadata: retrieving 1 resource
Error: database is corrupt; remove it and try again
  database: ‘/Users/ian//.AnnotationHub/annotationhub.sqlite3’
  reason: missing tables
In addition: Warning message:
download failed
  hub path: ‘’
  cache path: ‘/Users/ian//.AnnotationHub/annotationhub.sqlite3’
  reason: there is no package called ‘curl’ 

I've searched through the previous topics and found the fixes that have been posted previously (link below), however, when I run them I receive the same error message. AnnotationHub corrupt database

Session info:

R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] AnnotationHub_2.6.5 BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10                  IRanges_2.8.2                 digest_0.6.12                
 [4] mime_0.5                      R6_2.2.0                      xtable_1.8-2                 
 [7] DBI_0.6-1                     stats4_3.3.3                  RSQLite_1.1-2                
[10] BiocInstaller_1.24.0          httr_1.2.1                    S4Vectors_0.12.2             
[13] tools_3.3.3                   Biobase_2.34.0                shiny_1.0.1                  
[16] yaml_2.1.14                   httpuv_1.3.3                  AnnotationDbi_1.36.2         
[19] memoise_1.0.0                 htmltools_0.3.5               interactiveDisplayBase_1.12.0


Thank you in advance

ADD COMMENTlink modified 12 months ago • written 12 months ago by tullyij10
gravatar for tullyij1
12 months ago by
tullyij10 wrote:

Turns out it was fairly straightforward

...reason: there is no package called ‘curl’  can be fixed with: install.packages("curl")

After doing this the AnnotationHub() command worked fine.


ADD COMMENTlink written 12 months ago by tullyij10
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