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, bind.data) : 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 locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  AnnotationHub_2.2.2 BiocGenerics_0.16.1 BiocInstaller_1.20.0 loaded via a namespace (and not attached):  Rcpp_0.12.1 IRanges_2.4.1  digest_0.6.8 mime_0.4  R6_2.1.1 xtable_1.8-0  DBI_0.3.1 stats4_3.2.2  magrittr_1.5 RSQLite_1.0.0  httr_1.0.0 stringi_1.0-1  curl_0.9.3 S4Vectors_0.8.1  tools_3.2.2 stringr_1.0.0  Biobase_2.30.0 shiny_0.12.2  httpuv_1.3.3 AnnotationDbi_1.32.0  htmltools_0.2.6 interactiveDisplayBase_1.8.0 >