BIG BIG Problem with R node and KNIME 3.1

KNIME Analytics Platform
#1

Hey,

I have got a huge problem with the R Snippet node and KNIME 3.1. The output of my node is a SVG file, which worked perfectly fine until KNIME 3.0.1. Now the same workflow, same node, same R code outputs a SVG file with just an empty container. True story! Please help!

Here is what the output looks like:

<?xml version="1.0" encoding="UTF-8"?>
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="720pt" height="360pt" viewBox="0 0 720 360" version="1.1">
<g id="surface16">
</g>
</svg>

Best,
Marc

#2

https://tech.knime.org/forum/knime-general/r-nodes-not-working-after-uodate-to-31

#3

I am aware of this RServe issue, but I have RServe installed and the node pretends to work fine. Even the Validate Script option shows no anomalies.

#4

Hi Marc, 

thank you for reporting, I am currently working on this. Could you please mention what operating system including architecture (32/64 bit) you are working on.

R code outputs a SVG file with just an empty container

Do I understand correctly, that you are creating the SVG as a string in R and outputing that string?

Greetings, Jonathan

#5

Hey Jonathan,

I am working on Windows 7 Professional SP-1 (64 Bit). The R version is 3.2.2 and, as mentioned above, I have RServe installed.

The node/snippet writes a SVG plot to disk and returns the correspondend URL on its outport.

Thanks,
Marc

#6

Jonathan,

I just prepared a workflow for you. If you can provide me with an email address, I can send the workflow to you (I don't want to upload the workflow here).

Best,
Marc

#7

Hi Marc, 

I sent you an email to the adress you provided for your forum account. You may attach the workflow in an answer.

Thank you in advance!

Jonathan

#8

Done. ;-)

#9

Hi Marc, 

first of all, thank you for the workflow, I was able to find/solve the problem. I am answering here, since it may be interesting to other users.

You are using ggplot to draw a plot onto the SVG device. These plots need to be printed to actually appear on the device. The reason this worked before is that our previous method of executing R code printed every individual command, just as R does, too, and I believe it should be so for the nodes aswell.

I was able to get your workflow running by calling print on the result of the ggplot() call:

print(ggplot(...))

I hope that is okay for now, solving the problem on the KNIME R Integration side will probably take a while. Maybe some day, you will even be able to create the SVG directly from R as image output.

Hope that helps.

Greetings, Jonathan.

#10

Thank you very much for your help, I have been playing around for some hours and finally found a very simple and convenient solution:

We can use ggsave for saving our ggplot2 plots instead of using the Cairo package/functions.

This works very well and I wouldn't even call it a "workaround". Furthermore it leads me to think that it is not a ggplot2 specific issue, but a Cairo issue?!

Best,
Marc

@Jonathan:

If you are interested, I can provide you with the updated workflow via email.