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HTML output not created

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Laura Lee, modified 4 Years ago.

HTML output not created

Youngling Posts: 95 Join Date: 3/31/16 Recent Posts

Hi all-

I'm using SS version V3.30.11.00 and I am attempting to create the output with the SS_plots function within r4ss, which I have successfully run with version 3.24. The *.png files are created but not the html output. My code is as follows:

mydir <- "C:/SS3/SS3_v330/example"

output <- SS_output(mydir,printhighcor=100,printlowcor=100,printstats=FALSE,ncols=400)

Model_Output_Report_1 <- output$input$warn

printdir="SS_plots" #Output to "plots" folder in output directory
invisible(do.call(file.remove,list(list.files(printdir,full.names=TRUE)))) 
SS_plots(output, png=TRUE, printfolder=printdir, rows=1, cols=1,verbose=FALSE,datplot=T)

When I run, I receive the following error:

Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(yr) : no non-missing arguments to min; returning Inf
2: In max(yr) : no non-missing arguments to max; returning -Inf

 

I would appreciate any assistance. Thank you in advance for your time.

 

Cheers,

Laura

IT
Ian Taylor, modified 4 Years ago.

RE: HTML output not created

Youngling Posts: 117 Join Date: 12/8/14 Recent Posts

Hi Laura,

The html files only get created if it gets all the way through the png files, so it's likely that the error occurred after most but not all of them had been created and the function could not get past the error.

First, it's probably good to confirm that you have any recent changes to r4ss by reinstalling via

devtools::install_github('r4ss/r4ss')

 

If the error still occurs, could you email me your model input files so I can try to replicate the error and debug the r4ss code?

 

While waiting for a fix to the code, you should be able to bypass the error by specifying a subset of the plots created by the SS_plots command using a command like

SS_plots(model, plot=c(1:11, 13:24))

where the vector of plot numbers passed to the plot input should exclude whichever plot group was last reported. That is, if you see the following messages before the error occurred, but nothing about group 8, then you can assume that the error was in group 7 and specify plot=c(1:6, 8:24).

Starting biology plots (group 1)
Starting selectivity and retention plots (group 2)
Starting timeseries plots (group 3)
Starting recruitment deviation plots (group 4)
Skipping estimation of recruitment bias adjustment (group 5) because uncertainty=FALSE
Starting spawner-recruit curve plot (group 6)
Starting catch plots (group 7)

 

Laura Lee, modified 4 Years ago.

RE: HTML output not created

Youngling Posts: 95 Join Date: 3/31/16 Recent Posts

Thanks so much, Ian. I've attached my input files.

Attachments: