I am new to DataShield and my first step was to complete the tutorial from your site.
However, I have run into several problems:
When running ds.mean(x=‘D$LAB_HDL’, datasources=opals) the following error occurs:
Error in matrix(unlist(ss.obj), nrow = Nstudies, byrow = TRUE)[, 1:4] : subscript out of bounds
I am new to both R and DataShield, so any hint of what could be going wrong here would be of great help.
Running ds.dim(‘D’) produces the following error:
Error: Command ‘dimDS(D)’ failed on ‘dstesting-100’: Error while evaluating 'dsBase::dimDS( D )'
The same error seems to occur for a few other functions including ds.table1d(x=‘D$GENDER’),ds.histogram(x=‘D$LAB_HDL’, datasourcs=opals) and ds.glm(formula=D$DIS_DIAB~D$PM_BMI_CONTINUOUS+D$LAB_HDL*D$GENDER, family=‘binomial’).
Has anyone came across similar problems? I appreciate your help!
sorry for the delay, has anything changed in the past day and a half?
One more thing could you please check, is what version you are running on the virtual machine/server side?
To do this, you log in via the browser, going to the address 192.168.56.100:8080/ (when you’ve already got the VM/ VMs up and running) and entering the username/password combination: administrator / datashield_test& (this is specified on the wiki tutorial as well in case you need to refer back to it).
Then once you are in you should go through the following route:
Ah right! You’ll be pleased to know, it looks like we have tracked the problem down, fingers crossed!
You can see on this server side version it is running a modified version 4, but on client side, your devtools::sessioninfo told us it was running version 5. This is a mismatch that explains why many of your functions weren’t working- the client and server weren’t able to communicate the commands and requests to each other.
The instructions to fix this are as follows. You need to delete every one of the packages in that table, by clicking on the “remove” link under the “Actions” column. Next, Click on the add package button, and you will see the dialogue come up:
Could you help me out, just by checking that the following graphing functions work for you;
Because a couple of weeks ago when I first followed the instructions the graphs weren’t working for me, if they do for you that would be useful to know.
Secondly, did you end up with v4.1 packages on your server just by following the prescribed instructions? Because if so that is an issue with our documentation that we will try to fix as soon as possible.
Very happy to hear it’s all working for you, good luck using it and please feel free to post any more questions!
I was just extensively testing all the functions; the visualization functions, ds.histogram, ds.contourPlot and ds.heatmap do not work for me either. Interestingly, I remember contour plot and heatmap did work with v4.1 packages on my server.
Furthermore, ds.glm(…) does not work, as well.
Regrading the packages on my server, it just came to my mind that some things were already set-up about six months ago (or more) because I am building upon someone else’s work - explaining possibly why I have ended up with v4.1 on the server.
Can you tell me what arguments are you using in the graphical functions and what kind of error you get? Because the graphical functions have been changed in v5 and probably something was not updated on the wiki’s tutorial.
in my first week when i set up using v5 both ends the graphs never worked. Lately I’ve got pre-release v6 installed, graphs do work on that. Stuart and I have not yet got to the bottom of what is going on with v5.
The new versions of graphical functions use a new feature of Opal that generates a seed random number generator at each server. So they require Opal 2.14 or higher to operate. The VMs in the wiki might based on an older version of Opal.