fix issues with switch from linux to windows

.github/workflows/run-ss3-with-est.yml

@@ -61,7 +61,7 @@ jobs:
             file.copy(file.path(dir, "ss.par"), file.path(dir, "ss_ref.par"))
             # run the models with estimation and see if model finishes without error
             message("running ss on ", basename(dir))
-            system(paste0("cd ", dir, " && ../ss -nox"))
+            system(paste0("cd ", dir, " && ss"))
             model_ran <- file.exists(file.path(dir, "control.ss_new"))
             return(model_ran)
           }
@@ -147,12 +147,12 @@ jobs:
         shell: Rscript {0}
 
       - name: Determine results of test
-        run: cd test-models-repo && Rscript .github/r_scripts/check_failed.R
+        run: cd test-models-repo && Rscript .github\r_scripts\check_failed.R
 
       - name: Archive results
         uses: actions/upload-artifact@main
         if: always()
         with:
           name: 'result_textfiles'
-          path: test-models-repo/run_R/
+          path: test-models-repo\run_R\