Documentation ? about ramp-db HOT 4 OPEN

Hi Emilie,

Please see our textbook chapter for a more detailed vignette on how to set up and run the functions of the package.

The function you are looking for is probably getPathwayFromAnalyte

It's difficult to diagnose your problem without the specific error message you are receiving. Some suggestions that may help:

• Have you been able to access the ramp database through mySQL (outside of R)?
• Is your mySQL version older than 5.7? The RaMP package will not work with newer versions of mySQL due to changes in password encryption
• Is 'mycode' the proper password for your account?

from ramp-db.

The error function is "impossible to find the function xxx".
I have MySQL 5.7, and i imported all ramp db. I tried it in MySQL command line using your example (select * from analytesynonym where synonym = "glucose";) and obtained 2lines of result, while having all tables required. "Mycode" is the good password, here is what happen when i run the command line :
> connectToRaMP(dbname = "ramp", username = "root", conpass = "mycode",host = "localhost") <MySQLConnection:0,0>

from ramp-db.

It's odd that you're able to use connectToRaMP but none of the other package functions. Have you tried restarting R and/or reinstalling the RaMP package? You don't actually need to use connectToRaMP prior to running getPathwayFromAnalyte, although running them in sequence doesn't seem to be a problem on my system.

from ramp-db.

it's not all functions, only some. For example, rampFindSynonymFromSynonym and rampFindSourceFromId are not recognized, but getPathwayFromAnalyte and runCombinedFisherTest work well. I restarted R but it didn't fix anything, and i didn't reinstall RaMP because no warnings appeared when i installed it...

from ramp-db.