makeDb error when running analysis_code.R

[brianhigh]

I got this makeDb error when running analysis_code.R:

> makeDb(dbfile = dbfile, tablename = tablename, textfile = textfile, cutoff = 5)
Error in if (.allows_extensions(db)) { : 
  missing value where TRUE/FALSE needed
Error in !dbPreExists : invalid argument type

Perhaps an update to a package since your code was developed has created an incompatibility. Any ideas for a solution? Perhaps ...

library(checkpoint)
checkpoint("2014-10-08")

... as suggedted on the sqldf homepage ... though that did not work for me.

See also:

• https://stat.ethz.ch/pipermail/r-sig-db/2014q3/001474.html
• https://github.com/seth/RSQLite.extfuns/blob/master/R/init_extension.R
• https://github.com/alyssafrazee/derfinder/blob/master/R/makeDb.R
• https://github.com/alyssafrazee/derfinder/blob/master/R/read.csv.sql.R

[brianhigh]

Using older versions of RSQLite and others seems to work around this problem for now.

library(devtools)
install_url("http://cran.r-project.org/src/contrib/Archive/locfdr/locfdr_1.1-7.tar.gz")
install_url("http://cran.r-project.org/src/contrib/Archive/RSQLite/RSQLite_0.11.1.tar.gz")
install_url("http://cran.r-project.org/src/contrib/Archive/RSQLite.extfuns/RSQLite.extfuns_0.0.1.tar.gz")
install_url("http://cran.r-project.org/src/contrib/Archive/sqldf/sqldf_0.4-6.tar.gz")
install_github('derfinder', 'alyssafrazee') # beta version
library(derfinder)

[lcolladotor]

Similar to https://github.com/alyssafrazee/derfinder/issues/9 Just use the archived versions. Run this version of derfinder using R 2.15.x

[brianhigh]

I tried today with R 2.15.x and this issue does not come up with R 2.15.3. So, this issue can be closed.