Possible empty tables in the current SQLite file

[chappers2]

I posted a question to Bioconductor support asking for help because getSRA() was returning empty tables from the full SQLite file, but not the demo. There was a response that suggested that the current SQLite file contains empty tables, as suggested by the following code:

con <- dbConnect(SQLite(), "SRAmetadb.sqlite")
sapply(dbListTables(con), function(x) nrow(dbGetQuery(con, paste("select * from", x, "limit 10;"))))
col_desc experiment fastq metaInfo run
10 10 10 2 10
sample sra sra_ft sra_ft_content sra_ft_segdir
10 10 0 0 0
sra_ft_segments study submission
0 10 10

as compared to the file that comes with SRAdb

con2 <- dbConnect(SQLite(), file.path(system.file('extdata', package='SRAdb'),'SRAmetadb_demo.sqlite'))
sapply(dbListTables(con), function(x) nrow(dbGetQuery(con2, paste("select * from", x, "limit 10;"))))
col_desc experiment fastq metaInfo run
10 10 10 2 10
sample sra sra_ft sra_ft_content sra_ft_segdir
10 10 10 10 1
sra_ft_segments study submission
10 10 10

I was able to reproduce this on my system using the SQLite file from https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz and from https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz.

Does this diagnosis appear correct? If so, can it be easily fixed?

With many thanks

Mike.