m_png() does not produce output in RStudio Server

[sup27606]

Hi,
Thank you for this very useful package.
I am trying to display the image generated by r3dmol using the m_png() function, but can't get it to work.

I tried the example given in the manual, but it produced a blank image with a question mark (see screenshot below).

The issue is specific to Rstudio server running on Linux, because native RStudio can display the image.

Also, I would like to programmatically generate the png objects and embed in a pdf document. However, I cannot seem to use any PNG processing function in R on the image object. For example, writePNG() throws an error saying, "image must be a matrix or array of raw or real numbers".

I saw a message from 2 years back saying, saving PNG to file can't be done. I was wondering if its possible now and if not, is there a workaround?

[swsoyee]

Thank you for using this package.

Actually, the PNG output is achieved using the webshot method, which is essentially a browser screenshot.

Therefore, in a server environment, it may not be possible to call a browser to take a screenshot, and thus the image cannot be generated.

You might consider whether it’s possible to display the generated widget in a browser within the server environment, and then find a way to capture and return the screenshot.

[sup27606]

Hi,
Thank you for pointing to the webshots package. According to the resources on the webshots2 package website, it may be possible to install the headless version of Chromium and Google Chrome in a server environment and use that to create png screenshots. I am working with our admin to install Chromium on our server to test this approach.

I am closing this as resolved for now. I will report back once I am successful with the webshots approach.

[sup27606]

Hi there,
Our admin was able to install Chrome within a Singularity image with R in it. When I run r3dmol, I can create and display the png image in the Viewer, but having trouble saving it to disk using webshot2.

In the documentation of m_png(), it states that the output is a base64 PNG image wrapped by tag. Is it possible to extract the base64 image data as a character string? I can then render the string as a PNG image using a package such as base64enc.

Thank you!