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salihkafkas
Community Trekker

Add-Ins outcross mapping

I installed outcross linkage map analysis in Add-Ins in JMP Genomics software. I wrote also -RLANG in the first lane of sasv9.cfg file under C:\Program Files\SASHome\SASFoundation\9.4\nls\en\sasv9.cfg. However, I still get below error message when I run linkage analysis. 

I need your experience on it.

Best wishes

Salih

 

ERROR: The RLANG system option must be specified in the SAS configuration file or on the SAS invocation command line to enable the
submission of R language statements.
16632 if ^isOK then do;

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5 REPLIES 5

Re: Add-Ins outcross mapping

Hi Salih,

 

I have received some comments from development. Try this:

  1. Completely shut down JMP Genomics and make sure JMP and SAS are not running in the background (Use Task Manager to find out)
  2. Restart the computer to make sure any registry or system variables are now being recognized that might have been added by R installation
  3. Open a SAS session (Start>SAS>SAS 9.4) and type the following in the Editor Window:
    1. proc options option=RLANG;

      run;

    2. Click on the button that looks like a running man at the top in the toolbar
  4. Check in the Log and it should return a message in the log window
  5. If it returns:
    1. "NORLANG   Do not support access to R language interfaces", you do not have permission to call R from the SAS system.
    2. "RLANG   Support access to R language interfaces", you can call R from the SAS system. Check your R_Home Environtment. See this link:

https://stackoverflow.com/questions/19525903/editing-sas-config-files-to-execute-r-making-sas-play-w...

 

Let me know if you are still having problems.

 

Chris

 

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
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salihkafkas
Community Trekker

Re: Add-Ins outcross mapping

Dear Chris,

THANKS.

It worked and I did not get RLANG error message.

However, I got below error message when I attempted to run recombination
and linkage group analysis under add-ins: outcross linkage map analysis. I
used default sample file (simuf1) to run recombination and linkage group
analysis.

The following error occured in process LinkageGroupOutcross

ERROR: R: Error in rf.2pts(outcross.obj, LOD = NULL, max.rf = NULL, verbose
= FALSE) :
ERROR: R: could not find function "rf.2pts"
ERROR: R: Error in get.2pts.analysis(twopts.obj) : object 'twopts.obj' not
found
ERROR: R: Error in eval(expr, p) : object 'rfmat.obj' not found
ERROR: R: Calls: .SASExportDataExchangeFile -> eval.parent -> eval -> eval

Please may you write what is the reason to get an error message.

I also run linkage map order using default files

The following error occured in process LinkageMapOrderOutcross
ERROR: R: Error in make.seq(twopts.obj, "all") : could not find function
"make.seq"
ERROR: R: Error in eval(expr, p) : object 'mappedm.final' not found
ERROR: R: Calls: .SASExportDataExchangeFile -> eval.parent -> eval -> eval

Please may you write what is the reason to get an error message.

*I also run QTL analysis and did not get any Error message.*
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Re: Add-Ins outcross mapping

Hi Salih,

I believe one of the developers for JMP Genomics may have answered your question by directly emailing you. Here is the comment so others who might find themselves with the same situation can also have the answer.

 

Plesae make sure that the OneMap R package is installed and re-start JMP Genomics.

If you are still getting an error message, let us know.

 

Chris

Chris Kirchberg
Principal Systems Engineer, Life Sciences - JMP Global Technical Enablement
SAS Institute, Inc. - Denver, CO
Tel: +1-919-531-9927 ▪ Mobile: +1-303-378-7419 ▪ E-mail: chris.kirchberg@jmp.com
JMP – A Division of SAS Institute | www.jmp.com
sbrlsi
Staff

Re: Add-Ins outcross mapping

ERROR: R: Error in rf.2pts(outcross.obj, LOD = NULL, max.rf = NULL, verbose= FALSE)

ERROR: R: could not find function "rf.2pts"

 

The error messages displayed above are due to updates in the OneMap package (beginning on version 2.1.0). These updates have effects in some R functions (functions names, and some internal routines), and they will cause errors in the Outcross Add-In of JMP Genomics up to version 9.0. The necessary fixes in JMP Genomics have already taken place to make the Outcross Add-In compatible with versions OneMap 2.1.0 and 2.1.1 (the latest OneMap version available in CRAN on April 9th, 2018). These fixes will be available in the next release of JMP Genomics. Meanwhile, please contact the Technical Support team to inquire assistance with this issue.

 

Highlighted
sbrlsi
Staff

Re: Add-Ins outcross mapping

Alternatively, you can install OneMap version 2.0.4 or earlier from the the archive https://cran.r-project.org/src/contrib/Archive/onemap/. This version is compatible with the Outcross Add-In in JMP Genomics 9.0 and earlier. For your conveniecy, I'm attaching OneMap_2.0.4.zip for Windows system.

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