Getting "error: database is corrupt" when using ExperimentHub()
Entering edit mode
shinx558 • 0
Last seen 7.9 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, 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: ‘’
  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)

[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 • 1.5k views
Entering edit mode
Last seen 2.4 years ago
United States


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

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


Entering edit mode

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.



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