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Raymond S Lindsey

GAPIT output

When using sumitR to run the R package Gapit, do I assume that all necessary packages and libraries for the operation of GAPIT have already been installed as well? Also, I believe that I have some errors in my code that are preventing the run from completing properly, but I can’t locate an output file from submitR that says where the issue is. Any suggestions as to how I can begin troubleshooting this?

Thanks.

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    Rob Campbell

    Hi Ray, I sent detailed info via email. I’ll make sure to post a summary and any conclusions we find here. – Rob Campbell

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    Rob Campbell

    To document what we found for other users, here are some things to keep in mind: – SubmitR has trouble with spaces in R script file names. The job will seem to run but there’s no R output. Future versions of SubmitR will produce a warning if the R script filename(s) include(s) spaces. – GAPIT problems: GAPIT is installed and available for use with SubmitR. R scripts should not attempt to install or remove R libraries. This causes errors when R is run on DiaGrid‘s computing resources (cluster, etc.). R scripts can check to make sure specific libraies are available. – R Libraries: SubmitR now displays the R libraries that are available to users’ script in the “Info” tab.

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    Rob Campbell

    To document what we found for other users, here are some things to keep in mind:BR BRSubmitR has trouble with spaces in R script file names. The job will seem to run but there’s no R output. Future versions of SubmitR will produce a warning if the R script filename(s) include(s) spaces. BR BR – GAPIT problems: GAPIT is installed and available for use with SubmitR. R scripts should not attempt to install or remove R libraries. This causes errors when R is run on DiaGrid‘s computing resources (cluster, etc.). R scripts can check to make sure specific libraies are available. BR BR – R Libraries: SubmitR now displays the R libraries that are available to users’ script in the “Info” tab. BR

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