Trellis graphics in R don't work with cardoonPlot about flow HOT 9 CLOSED

Same thing happens on newest arbor.arborworkflows.com

from flow.

I'm not familiar with R, but is it possible something is wrong with the script itself?

The error (which seems to be spawned by cardoonPlot) is that a png file under /tmp doesn't exist. I ran the script under strace and it looks like the only time it tries to access that file is to read it - so that analysis isn't creating the image anywhere.

pinging @jeffbaumes in case he has any ideas.

from flow.

thanks for looking into this, Dan. CardoonPlot has malfunctioned before, but I have never looked inside to determine why/when.

Unfortunately, the scatterplot function in arbor seems to not be working for the CSVs I tried yet, either, or I would have suggested this alternative.

On Jul 6, 2016, at 11:30 AM, Dan LaManna [email protected] wrote:

I'm not familiar with R, but is it possible something is wrong with the script itself?

The error (which seems to be spawned by cardoonPlot) is that a png file under /tmp doesn't exist. I ran the script under strace and it looks like the only time it tries to access that file is to read it - so that analysis isn't creating the image anywhere.

pinging @jeffbaumes https://github.com/jeffbaumes if he has any ideas.

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from flow.

Josef,
I will look at this tomorrow morning if it is still broken.

On Jul 6, 2016, at 11:45 AM, [email protected] [email protected] wrote:

thanks for looking into this, Dan. CardoonPlot has malfunctioned before, but I have never looked inside to determine why/when.

Unfortunately, the scatterplot function in arbor seems to not be working for the CSVs I tried yet, either, or I would have suggested this alternative.

On Jul 6, 2016, at 11:30 AM, Dan LaManna <[email protected] mailto:[email protected]> wrote:

I'm not familiar with R, but is it possible something is wrong with the script itself?

The error (which seems to be spawned by cardoonPlot) is that a png file under /tmp doesn't exist. I ran the script under strace and it looks like the only time it tries to access that file is to read it - so that analysis isn't creating the image anywhere.

pinging @jeffbaumes https://github.com/jeffbaumes if he has any ideas.

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from flow.

I vaguely remembered @hafen (original cardoonTools author) mentioning that sometimes expression() is not needed. And indeed if you remove the expression() wrapping from the trellis example it seems to work. Unfortunately I cannot recall the details of when it is needed and when it is not.

from flow.

You're correct @jeffbaumes, in the toy example I gave above, removing expression() does indeed fix it. However, this does not solve the problem in my real example (sorry for not testing the toy example enough...). Rather I don't need to use cardoonTools to recreate the problem at all, and the result is different whether I run the script interactively in R or when I run it through Arbor. In fact, I can run this exact script in R via SSH on arbor1 without any issue, but it fails when run via Arbor (same error message as above):
{ "description": "", "inputs": [], "mode": "r", "name": "TrellisFigure", "outputs": [ { "format": "png.base64", "id": "GLSplot", "name": "GLSplot", "type": "image" } ], "script": "y <- rnorm(100)\nx <- rnorm(100)\n\nglsfit <- nlme::gls(y~x)\n\nfile <- tempfile(fileext = sprintf(\".%s\", \"png\"))\nresult <- list()\npng(file, width=1000, height=1000, res=72)\nplot(glsfit)\ndev.off()\nbytes <- file.info(file)$size\nresult$png <- base64enc:::base64encode(readBin(file, \"raw\", n = bytes))\nfile.remove(file)\n\nGLSplot <- result$png" }

from flow.

The issue is sourcing the script does not tell R to make the plot for Trellis graphics. Not an Arbor problem: http://stackoverflow.com/questions/6783120/r-package-lattice-wont-plot-if-run-using-source
Thanks guys.

from flow.

Wow that is a crazy one. Thanks for digging into it.

from flow.

The cardoonPlot() function is looking for either an expression (when using base R graphics) or a lattice or ggplot2 object. It doesn't know what to do with a function (I suppose it should check for that).

So the first json shown should be changed to something like this:

{ "description": "", "inputs": [], "mode": "r", "name": "TrellisFigure", "outputs": [ { "format": "png.base64", "id": "plot", "name": "plot", "type": "image" } ], "script": "library(cardoonTools)\nlibrary(lattice) \nattach(mtcars)\n\n# create factors with value labels \ngear.f<-factor(gear,levels=c(3,4,5),\n \tlabels=c(\"3gears\",\"4gears\",\"5gears\")) \ncyl.f <-factor(cyl,levels=c(4,6,8),\n labels=c(\"4cyl\",\"6cyl\",\"8cyl\")) \n\n# kernel density plot \nplotObj <- densityplot(~mpg, \n \tmain=\"Density Plot\", \n \txlab=\"Miles per Gallon\")\n \t\n\nplot <- cardoonPlot(expression(plotObj))\nplot <- plot$png" }

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