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.
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;
I have received some comments from development. Try this:
Let me know if you are still having problems.
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.
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.
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.