ExperimentHub - Error: database is corrupt
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@francoiscollin-11775
Last seen 5.0 years ago

Good morning.

I'm having an error trying to use ExperimentHub. Helpful advise would be greatly appreciated.

>>>>>>>>>

library(ExperimentHub)
eh <- ExperimentHub()

metadata: retrieving 1 resource
Error: database is corrupt; remove it and try again
  database: ‘/Users/francois/.ExperimentHub/experimenthub.sqlite3’
  reason: missing tables
In addition: Warning message:
download failed
  hub path: ‘http://experimenthub.bioconductor.org:3000/metadata/experimenthub.sqlite3’
  cache path: ‘/Users/francois/.ExperimentHub/experimenthub.sqlite3’
  reason: Couldn't connect to server 

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: 

other attached packages:
 [1] alpineData_0.99.0        ExperimentHubData_0.99.9
 [3] AnnotationHubData_1.2.2  futile.logger_1.4.3     
 [5] GenomicRanges_1.24.3     GenomeInfoDb_1.8.7      
 [7] IRanges_2.6.1            S4Vectors_0.10.3        
 [9] ExperimentHub_0.99.6     AnnotationHub_2.4.2     
[11] BiocGenerics_0.18.0      knitr_1.14              
[13] rmarkdown_1.1            BiocInstaller_1.22.3    

 

ExperimentHub • 633 views
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@valerie-obenchain-4275
Last seen 23 months ago
United States

Hi,

The point of including sessionInfo() is to show the version of R and Bioconductor packages. You're having a problem with ExperimentHub but have omitted the portion of the output that shows the version of that package.

From the error message I'm guessing you have an old version of ExperimentHub. Neither the current release version (1.0.0) or devel (1.1.0) use port 3000 anymore (e.g., 'http://experimenthub.bioconductor.org:3000/metadata/experimenthub.sqlite3’) . Please update the package and try again. If you still have problems show the full output of sessionInfo().

Valerie

 

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