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LabKey Running R and Virtual Frame Buffer Server Config...

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LabKey Running R and Virtual Frame Buffer Server Config... diego  2016-02-25 14:35
Status: Closed
 
Running:
FreeBSD 10.2 (64bit)
LabKey Server 15.3 (Latest Updates)
Tomcat 8.0.28
tomcat user: www
tomcat directory: /usr/local/apache-tomcat-8.0/
R-project: 3.2.2
VFB server: xorg-vfbserver-1.18.0.1 (pkg install)


Have successfully installed R but I am having issues configuring the VFB server to work on LabKey Server. Followed the tutorial below, but it seems as though some steps might be different for FreeBSD... Please advise!


https://www.labkey.org/home/Documentation/wiki-page.view?name=configVirtualFrame

Configuration Test Output
=========================
jpeg png tiff tcltk X11 aqua
       TRUE TRUE TRUE TRUE FALSE FALSE
   http/ftp sockets libxml fifo cledit iconv
       TRUE TRUE TRUE TRUE FALSE TRUE
        NLS profmem cairo ICU long.double libcurl
       TRUE TRUE TRUE TRUE TRUE FALSE
> proc.time()
   user system elapsed
  0.152 0.010 0.182

===== END OUTPUT =====

Thanks in advance!
Diego
 
 
Jon (LabKey DevOps) responded:  2016-02-25 23:14
Hi Diego,

The output looks good to me. The last section is to test that when R is run inside of the LabKey, the X11,JPEG and PNG devices are available,

Your output specifically indicates that those three things are listed as TRUE, so I would have to say it looks like it's working.

What do you feel is different or out of place?

Regards,

Jon
 
diego responded:  2016-02-26 11:05
Jon,

You are correct, R is working in LabKey Server, Histrogram screenshot attached. On the confirmation I am not sure where I find "ReportID"

reportId: 'db:XX'

Getting a "Unable to display the specified report"

Tutorial --> https://www.labkey.org/home/Documentation/wiki-page.view?name=rHistogram

Thanks,
Diego
 
Jon (LabKey DevOps) responded:  2016-03-01 16:02
Hi Diego,

You can get that report ID number by viewing the report.

If you look at the Create an R Histogram instructions, the section that says:

From the grid view, select Views > "Reagent Histogram"
Click the View tab to see the R report.
Notice the reportId in the URL. You will need this number to reference the report in your confirmation page. In this URL example, the reportId is 90:

http://localhost:8080/labkey/list/home/Request%20Reagent%20Tutorial/grid.view?listId=1&query.reportId=db%3A90

unencoded:

http://localhost:8080/labkey/list/home/Reagent Request Tutorial/grid.view?listId=1&query.reportId=db:90


So all you need to do is to view your Reagent Histogram view you created and then get that ID number from your address bar.

Regards,

Jon
 
diego responded:  2016-03-02 11:48
Jon,

I followed your instructions and it turns out the "reportID" is 27, the only issue now, is that the histrogram never loads. Simply states "loading", have attached a screenshot and the code I am using.

Thanks,
Diego
 
Jon (LabKey DevOps) responded:  2016-03-02 12:16
Hi Diego,

I'll try to reproduce this on my end, but can you also run some kind of developer web-debugging console on your browser, like Firebug? I'm curious to see whether you get any kind of javascript error that gets caught in the console when the wiki page loads.

Also, does the same behavior appear in other browsers? I know that Firefox can be more fickle with how it handles JS compared to Chrome.

Regards,

Jon
 
diego responded:  2016-03-02 12:35
Jon,

Have installed firebug and indeed it does throw an error. Will try it on chrome. Screenshot attached.

Diego
 
diego responded:  2016-03-02 12:45
Jon,

Same result running Chrome... "Loading"

Diego
 
diego responded:  2016-03-02 12:55
Jon,

Nevermind, noticed that the block of code was pasted twice, and was throwing the error. It is all fixed now!

Thanks,
Diego
 
Jon (LabKey DevOps) responded:  2016-03-02 13:01
Great! Glad to know it's working now!