@@ -7,6 +7,11 @@

 using namespace Rcpp;

+#ifdef RCPP_USE_GLOBAL_ROSTREAM

+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();

+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();

+#endif

+

 // setLogLevel

 void setLogLevel(unsigned short loglevel);

 RcppExport SEXP _CytoML_setLogLevel(SEXP loglevelSEXP) {

@@ -42,7 +42,7 @@ test_that("no gate",{

   wsFile <- file.path(path, "no-gate.wsp")

-  ws <- open_flowjo_xml(wsFile, sampNloc = 'sampleNode')

+  ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')

   expect_equal(nrow(fj_ws_get_samples(ws)), 1)

   gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path,"Cytotrol/NHLBI/Tcell/"), include_empty_tree = TRUE)

   expect_equal(range(gh_pop_get_data(gs[[1]]))[,5], c(50.70029, 256.91464), tol = 1e-6)

@@ -55,7 +55,7 @@ test_that("flog-- offset and decades that expose the previous logGml2-based flog

   wsFile <- file.path(path, "flog/log.wsp")

-  ws <- open_flowjo_xml(wsFile, sampNloc = 'sampleNode')

+  ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')

   gs <- flowjo_to_gatingset(ws, name = 1, path = file.path(path,"Cytotrol/NHLBI/Tcell/"))

   res <- gh_pop_compare_stats(gs[[1]])

   expect_equal(res[, xml.freq], res[, openCyto.freq], tol = 0.01)

@@ -66,7 +66,7 @@ test_that("which.lines",{

   wsFile <- file.path(path, "flog_PnE/Liver.wsp")

-  ws <- open_flowjo_xml(wsFile, sampNloc = 'sampleNode')

+  ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')

   set.seed(1)

   gs <- flowjo_to_gatingset(ws, name = 2, which.lines = 5e4)

   expect_equal(nrow(gh_pop_get_data(gs[[1]])), 5e4)

@@ -95,7 +95,7 @@ test_that("set T value properly through PnE instead of PnR for flog transform wh

   wsFile <- file.path(path, "flog_PnE/Liver.wsp")

-  ws <- open_flowjo_xml(wsFile, sampNloc = 'sampleNode')

+  ws <- open_flowjo_xml(wsFile, sample_names_from = 'sampleNode')

   gs <- flowjo_to_gatingset(ws, name = 2)

   res <- gh_pop_compare_stats(gs[[1]])

@@ -241,7 +241,7 @@ test_that("curlyQuad gate ",{

 test_that("EllipsoidGate defined on log-transformed channels ",{

       thisPath <- file.path(path, "ellipsoid_log")

       wsFile <- file.path(thisPath, "xml_spillover2.xml")

-      ws <- open_flowjo_xml(wsFile, sampNloc = "sampleNode")

+      ws <- open_flowjo_xml(wsFile, sample_names_from = "sampleNode")

       capture.output(gs <- flowjo_to_gatingset(ws, name=1, execute = T, subset = "spillover_B2.fcs"))

       res <- gh_pop_compare_stats(gs[[1]])

@@ -434,7 +434,7 @@ test_that("v 10.0.7 - vX 20.0 (PROVIDE/CyTOF) ellipseidGate (fasinh)",{

       thisPath <- file.path(path, "PROVIDE")

       wsFile <- file.path(thisPath, "batch1 local and week 53.wsp")

-      ws <- open_flowjo_xml(wsFile, sampNloc = "sampleNode")

+      ws <- open_flowjo_xml(wsFile, sample_names_from = "sampleNode")

       gs <- flowjo_to_gatingset(ws, name = 1, subset = 3, execute = FALSE)

       expect_is(gs, "GatingSet")

@@ -449,7 +449,7 @@ test_that("v 10.0.7 - vX 20.0 (PROVIDE/CyTOF) ellipseidGate (fasinh)",{

       #switch to the corrected wsp

       wsFile <- file.path(thisPath, "count_corrected.wsp")

-      ws <- open_flowjo_xml(wsFile, sampNloc = "sampleNode")

+      ws <- open_flowjo_xml(wsFile, sample_names_from = "sampleNode")

       capture.output(gs <- flowjo_to_gatingset(ws, name = 1, subset = 3))

       gh <- gs[[1]]

       thisCounts <- gh_pop_compare_stats(gh)[, list(xml.count,openCyto.count, node)]

@@ -587,9 +587,9 @@ test_that("v 7.6.5 - win 1.61 (PBMC)",{

       wsFile <- file.path(thisPath, "Exp2_Tcell.wsp")

       ws <- open_flowjo_xml(wsFile)

-      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, sampNloc = "sampleNode", execute = FALSE)

+      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, sample_names_from = "sampleNode", execute = FALSE)

       expect_is(gs, "GatingSet")

-      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, sampNloc = "sampleNode")

+      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, sample_names_from = "sampleNode")

       gh <- gs[[1]]

       thisCounts <- gh_pop_compare_stats(gh)

@@ -597,17 +597,17 @@ test_that("v 7.6.5 - win 1.61 (PBMC)",{

     })

-test_that("v 7.6.5 - win 1.61 (sampNloc = 'sampleNode')",{

+test_that("v 7.6.5 - win 1.61 (sample_names_from = 'sampleNode')",{

       thisPath <- file.path(path, "Cytotrol/Miami")

       wsFile <- file.path(thisPath, "flowJo/Cytotrol_061112_Tcell.wsp")

       ws <- open_flowjo_xml(wsFile)

-      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, path = file.path(thisPath,"Tcell"), sampNloc = "sampleNode", execute = FALSE)

+      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, path = file.path(thisPath,"Tcell"), sample_names_from = "sampleNode", execute = FALSE)

       expect_is(gs, "GatingSet")

-      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, path = file.path(thisPath,"Tcell"), sampNloc = "sampleNode")

+      gs <- flowjo_to_gatingset(ws, name = 1, subset = 1, path = file.path(thisPath,"Tcell"), sample_names_from = "sampleNode")

       gh <- gs[[1]]

       thisCounts <- gh_pop_compare_stats(gh)

       expect_equal(thisCounts[, xml.freq], thisCounts[, openCyto.freq], tol = 2e-4)