Hej Jack Zhu and Sean Davis!

I wanted to retrieve data that have recently been submitted (end of august) to the SRA, but I cannot do it using SRAdb, as the database I can fetch using getSRAdbFile() is "outdated", dating from early august: c("schema version", "creation timestamp")c("1.0", "2016-08-06 00:25:18") It corresponds to this file: 'https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz'

I could not find the info, but I suppose updating this db is something you do manually? How often do you do it? And is it something you could share the code to, so that end-user could do it too?

Thanks in advance for your answer,

Cheers,

Nico

My session info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] SRAdb_1.30.0         RCurl_1.95-4.8       bitops_1.0-6        
[4] graph_1.50.0         BiocGenerics_0.18.0  RSQLite_1.0.0       
[7] DBI_0.5-1            BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] httr_1.2.1      R6_2.1.3        tools_3.3.1     GEOquery_2.38.4 Biobase_2.32.0 
[6] stats4_3.3.1    XML_3.98-1.4   

Thanks for the report.  Should be fixed now. Yes, we have code, but it is not packaged up in a user-friendly way.  The data are actually processed into a local mysql database and then the ETL and packaging into SQLite are done from there.  This is for historical reasons and we simply haven't had the resources to unravel it.