I asked about slow indexing in RSQLite for a genetic database. Seth Falcon's suggestion of making sure that the identifiers were stored as integer rather than string made a big difference. SNPs come from the factory as "rs100092" and stripping the "rs" off the front is easy.
Other advice about larger or smaller SQLite cache size didn't seem to have much impact in my setting, and I didn't try the advice about getting a different database.
Despite it's many other virtues, SQLite is still slow at indexing.
Thanks to all.
-thomas=
Thomas Lumley Assoc. Professor, Biostatistics
tlumley at u.washington.edu University of Washington, Seattle