Getting "error: database is corrupt" when using ExperimentHub()
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shinx558 • 0
@shinx558-11013
Last seen 5.3 years ago

Hello! I am doing undergraduate bioinformatics research this summer, and as I am new to R, I have had trouble trying to access some data.

I am trying to download from GSE62944 (according to here https://www.bioconductor.org/packages/devel/data/experiment/vignettes/GSE62944/inst/doc/GSE62944.html), but I am running into errors when I try to use ExperimentHub. I do not have a problem when I run library (ExperimentHub), but when I try to run eh = ExperimentHub(), I get the following problem:

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

My output for sessionInfo() is

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 10586)

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

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

other attached packages:
[1] devtools_1.12.0      ExperimentHub_0.99.9 AnnotationHub_2.4.2  BiocGenerics_0.18.0  BiocInstaller_1.22.3

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'S4Vectors' is missing or broken

 

I would appreciate any help. Thank you.

experimenthub gse62944 • 859 views
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@valerie-obenchain-4275
Last seen 23 months ago
United States

Hi,

The current version of ExperimentHub is 0.101.10 - I also see a strange error for S4Vectors. I would recommend first updating all packages with biocLite().

As an fyi, you can always check the most current package versions on the build report

http://www.bioconductor.org/checkResults/devel/bioc-LATEST/

If you still see the 'corrupt' error after updating remove the .ExperimentHub/ directory then try ExperimentHub() again.

Valerie

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I've updated all the packages as well as removed the ExperimentHub/ directory, but they did not fix the problem. I have tried reinstalling R and my computer also.

Thank you for the advice.

-Chris

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