Question: AnnotationHub: change download location of database
gravatar for Guido Hooiveld
2.0 years ago by
Guido Hooiveld2.2k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.2k wrote:


I face a problem that drives me nuts, and although likely easy to solve I don't know how...

I would like to make use of the AnnotationHub interface. When loading the library, it starts downloading the SQLite database. So far, so good...The problem is that this SQLite database is (automatically) saved in the folder "M:\My Documents\AppData\.AnnotationHub". As you can deduce, this (M:) is a network drive at which I have limited storage capacity. After downloading the SQLite file I go over the space I have on this network drive, likely resulting in this error: 

> hub = AnnotationHub()
updating AnnotationHub metadata: retrieving 1 resource

  |======================================================================| 100%
Error in sqliteSendQuery(con, statement, :
  rsqlite_query_send: could not execute1: unable to open database file
In addition: There were 50 or more warnings (use warnings() to see the first 50)

I therefore would like to set/change the location where this SQLite file is stored.

Since I am working on a Win7 machine, I changed the "start in" directory of the short cut used to start R (RGui.exe) to a local dir (from "M:\My Documents"), but this did unfortunately not solve the problem. Idem for changing the Win7 "Environment Variables" (System properties) for the TEMP and TMP directories. Any other suggestions?



> sessionInfo()
R version 3.2.2 Patched (2015-11-03 r69595)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] AnnotationHub_2.2.2  BiocGenerics_0.16.1  BiocInstaller_1.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1                  IRanges_2.4.1               
 [3] digest_0.6.8                 mime_0.4                    
 [5] R6_2.1.1                     xtable_1.8-0                
 [7] DBI_0.3.1                    stats4_3.2.2                
 [9] magrittr_1.5                 RSQLite_1.0.0               
[11] httr_1.0.0                   stringi_1.0-1               
[13] curl_0.9.3                   S4Vectors_0.8.1             
[15] tools_3.2.2                  stringr_1.0.0               
[17] Biobase_2.30.0               shiny_0.12.2                
[19] httpuv_1.3.3                 AnnotationDbi_1.32.0        
[21] htmltools_0.2.6              interactiveDisplayBase_1.8.0


ADD COMMENTlink modified 2.0 years ago by Martin Morgan ♦♦ 20k • written 2.0 years ago by Guido Hooiveld2.2k
gravatar for Martin Morgan
2.0 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

See ?hubOption, especially CACHE. Also the cache argument to AnnotationHub(). Probably you should experiment with providing an alternative path to AnnotationHub(), and if that works create a system variable ANNOTATION_HUB_CACHE="c:/My/Cache" as appropriate.

ADD COMMENTlink written 2.0 years ago by Martin Morgan ♦♦ 20k

Thanks Martin; problem solved!

For the archive:

Per your suggestion, to try I first within R set the path to local dir:


setHubOption("CACHE", "D:\\R_TMP\\.myHub")

hub = AnnotationHub()

After concluding this worked, I then permanently stored this directory as Environment Variable (system variable) in Windows:

Open Windows Explorer, right-click "Computer".

Then: properties -> Advanced system settings -> Advanced -> Environment variables -> User variables for... -> New.

Variable name: ANNOTATION_HUB_CACHE , Variable value: D:\R_TMP\.myHub


ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Guido Hooiveld2.2k
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