@@ -25,22 +25,16 @@ Imports:

     graph,

     graphics,

     utils,

-    base64enc,

-    plyr,

+    jsonlite,

     dplyr,

     grDevices,

     methods,

     ggcyto (>= 1.11.4),

     yaml,

-    lattice,

     stats,

-    corpcor,

-    RUnit,

-    tibble,

-    RcppParallel,

-    xml2

+    tibble

 biocViews: ImmunoOncology, FlowCytometry, DataImport, DataRepresentation

-LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1), flowWorkspace

+LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib, flowWorkspace

 Suggests:

     testthat,

     flowWorkspaceData ,

@@ -55,9 +49,9 @@ Collate:

     'AllClasses.R'

     'GatingSet2cytobank.R'

     'GatingSet2flowJo.R'

-    'RcppExports.R'

     'gate-methods.R'

     'compensation.R'

+    'cpp11.R'

     'cytobank2GatingSet.R'

     'cytobankExperiment.R'

     'cytolibml_bin_path.R'

@@ -72,6 +66,5 @@ Collate:

     'transforms.R'

     'utils.R'

     'writeGatingML.R'

-    'zzz.R'

 SystemRequirements: xml2, GNU make, C++11    

 Encoding: UTF-8

@@ -6,8 +6,6 @@ S3method(extend,ellipsoidGate)

 S3method(extend,polygonGate)

 S3method(extend,rectangleGate)

 S3method(print,cytobank_experiment)

-export(CytoML.par.get)

-export(CytoML.par.set)

 export(GatingSet2cytobank)

 export(GatingSet2flowJo)

 export(ce_get_channels)

@@ -62,7 +60,6 @@ importClassesFrom(methods,missing)

 importClassesFrom(methods,numeric)

 importClassesFrom(methods,oldClass)

 importFrom(RBGL,tsort)

-importFrom(RcppParallel,RcppParallelLibs)

 importFrom(Rgraphviz,layoutGraph)

 importFrom(Rgraphviz,renderGraph)

 importFrom(XML,"xmlAttrs<-")

@@ -85,11 +82,10 @@ importFrom(XML,xmlTreeParse)

 importFrom(XML,xmlValue)

 importFrom(XML,xpathApply)

 importFrom(XML,xpathSApply)

-importFrom(base64enc,base64decode)

-importFrom(base64enc,base64encode)

 importFrom(cytolib,cytolib_LdFlags)

 importFrom(dplyr,"%>%")

 importFrom(dplyr,arrange)

+importFrom(dplyr,bind_rows)

 importFrom(dplyr,count)

 importFrom(dplyr,enquo)

 importFrom(dplyr,filter)

@@ -190,6 +186,8 @@ importFrom(graph,removeNode)

 importFrom(graphics,abline)

 importFrom(graphics,polygon)

 importFrom(graphics,text)

+importFrom(jsonlite,base64_dec)

+importFrom(jsonlite,base64_enc)

 importFrom(jsonlite,fromJSON)

 importFrom(jsonlite,toJSON)

 importFrom(methods,as)

@@ -199,15 +197,9 @@ importFrom(methods,new)

 importFrom(methods,selectMethod)

 importFrom(methods,show)

 importFrom(methods,slot)

-importFrom(plyr,ldply)

-importFrom(plyr,name_rows)

 importFrom(tibble,tibble)

 importFrom(utils,localeToCharset)

 importFrom(utils,menu)

 importFrom(utils,packageVersion)

-importFrom(xml2,read_xml)

-importFrom(xml2,write_xml)

-importFrom(xml2,xml_add_sibling)

-importFrom(xml2,xml_comment)

 importFrom(yaml,read_yaml)

 useDynLib(CytoML,.registration = TRUE)

@@ -174,9 +174,9 @@ export_gates_cytobank <- function(gs, flowEnv, trans.Gm2objs, trans, compId, sho

 }

-#' @importFrom base64enc base64encode base64decode

+#' @importFrom jsonlite base64_enc base64_dec

 base64encode_cytobank <- function(x){

-  x <- base64encode(charToRaw(x))

+  x <- base64_enc(charToRaw(x))

   x <- gsub("=", ".", x)

   x <- gsub("\\+", "_", x)

   x <- gsub("/", "-", x)

@@ -186,7 +186,7 @@ base64decode_cytobank <- function(x){

   x <- gsub("\\.", "=", x)

   x <- gsub("_", "\\+", x)

   x <- gsub("-", "/", x)

-  base64decode(x)

+  base64_dec(x)

 }

@@ -47,7 +47,6 @@ GatingSet2flowJo <- function(...){

 #' @importFrom flowWorkspace gs_clone gs_update_channels pData<- cs_unlock cs_lock gs_copy_tree_only cs_load_meta 

 #' @export

 #' @rdname gatingset_to_flowjo

-#' @importFrom xml2 read_xml write_xml

 gatingset_to_flowjo <- function(gs, outFile, showHidden = FALSE, docker_img = NULL, ...){

   res <- check_binary_status()

   if(res!="binary_ok"){

@@ -93,24 +92,13 @@ gatingset_to_flowjo <- function(gs, outFile, showHidden = FALSE, docker_img = NU

   if(length(res) > 0)

     stop(res)

-  else

-  {

-    tree <- read_xml(tmpfile)

-    add_version_info(tree) 

-    invisible(write_xml(tree, file = outFile))

-    

+  else {

+     file.rename(tmpfile, outFile)

   }

 }

-#' @importFrom xml2 xml_comment xml_add_sibling

-add_version_info <- function(tree)

-{

-  info <- Sys.info()

-  xml_add_sibling(tree, xml_comment(paste0("CytoML-version: ", packageVersion("CytoML"))), .where = "before")

-  xml_add_sibling(tree, xml_comment(paste0("hostname: ", info[["nodename"]])), .where = "before")

-  xml_add_sibling(tree,  xml_comment(paste0("user: ", info[["user"]])), .where = "before")

-}

+

 check_docker_status <- function(docker_img = NULL){

   if(Sys.info()["sysname"] == "Windows")

     errcode <- system2("WHERE", "docker", stdout = FALSE)

deleted file mode 100644

@@ -1,35 +0,0 @@

-# Generated by using Rcpp::compileAttributes() -> do not edit by hand

-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

-

-setLogLevel <- function(loglevel) {

-    invisible(.Call(`_CytoML_setLogLevel`, loglevel))

-}

-

-open_workspace <- function(filename, sample_name_location, xmlParserOption) {

-    .Call(`_CytoML_open_workspace`, filename, sample_name_location, xmlParserOption)

-}

-

-parse_workspace <- function(ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads = 1L) {

-    .Call(`_CytoML_parse_workspace`, ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads)

-}

-

-get_keywords_by_id <- function(ws, sample_id) {

-    .Call(`_CytoML_get_keywords_by_id`, ws, sample_id)

-}

-

-get_keywords_by_name <- function(ws, sample_name) {

-    .Call(`_CytoML_get_keywords_by_name`, ws, sample_name)

-}

-

-get_sample_groups <- function(ws) {

-    .Call(`_CytoML_get_sample_groups`, ws)

-}

-

-get_samples <- function(ws) {

-    .Call(`_CytoML_get_samples`, ws)

-}

-

-get_xml_file_path <- function(ws) {

-    .Call(`_CytoML_get_xml_file_path`, ws)

-}

-

new file mode 100644

@@ -0,0 +1,33 @@

+# Generated by cpp11: do not edit by hand

+

+setLogLevel <- function(loglevel) {

+  invisible(.Call(`_CytoML_setLogLevel`, loglevel))

+}

+

+open_workspace <- function(filename, sample_name_location, xmlParserOption) {

+  .Call(`_CytoML_open_workspace`, filename, sample_name_location, xmlParserOption)

+}

+

+parse_workspace <- function(ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads) {

+  .Call(`_CytoML_parse_workspace`, ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads)

+}

+

+get_keywords_by_id <- function(ws, sample_id) {

+  .Call(`_CytoML_get_keywords_by_id`, ws, sample_id)

+}

+

+get_keywords_by_name <- function(ws, sample_name) {

+  .Call(`_CytoML_get_keywords_by_name`, ws, sample_name)

+}

+

+get_sample_groups <- function(ws) {

+  .Call(`_CytoML_get_sample_groups`, ws)

+}

+

+get_samples <- function(ws) {

+  .Call(`_CytoML_get_samples`, ws)

+}

+

+get_xml_file_path <- function(ws) {

+  .Call(`_CytoML_get_xml_file_path`, ws)

+}

@@ -293,17 +293,18 @@ setMethod("pData","cytobank_experiment",function(object){

   get_pd(object)

 })

-#' @importFrom plyr name_rows

+#' @importFrom dplyr bind_rows

 get_pd <- function(ce){

-  res <- ldply(ce$experiment$fcsFiles, function(sample){

+  res <- bind_rows(lapply(ce$experiment$fcsFiles, function(sample){

                                 data.frame(as.list(

                                   c(name = sample[["filename"]]

                                       , unlist(sample[["tags"]])

-                                      , .rownames = sample[["filename"]]#sample[["sampleName"]]

+                                      # , .rownames = sample[["filename"]]#sample[["sampleName"]]

                                     )

                                   )

                                   , check.names = FALSE)

                       })

-  res <- name_rows(res)

+  )

+  rownames(res) <- res[["name"]]

   res

 }

@@ -94,7 +94,7 @@ open_diva_xml <- function(file,options = 0,...){

 #' @export

 diva_get_sample_groups <- function(x){

-    ldply(

+  do.call(rbind, 

         xpathApply(x@doc, "/bdfacs/experiment/specimen",function(specimen){

               samples <- xpathApply(specimen, "tube",function(tube){

                                             c(tube = xmlGetAttr(tube,"name")

@@ -102,7 +102,7 @@ diva_get_sample_groups <- function(x){

                                             )

                                   })

-              samples <- ldply(samples)

+              samples <- do.call(rbind, lapply(samples, function(i)data.frame(t(i))))

               samples[["specimen"]] <- xmlGetAttr(specimen, "name")

               samples

             })

@@ -122,7 +122,6 @@ diva_get_sample_groups <- function(x){

 #' @return

 #' A \code{data.frame} with columns \code{tub}, \code{name}, and \code{specimen}

 #' @importFrom methods selectMethod

-#' @importFrom plyr ldply

 #' @export

 diva_get_samples <- diva_get_sample_groups

@@ -66,8 +66,8 @@ open_flowjo_xml <- function(file,options = 0, sample_names_from = "keyword", ...

 }

 set_log_level <- function(level = "none"){

-  if(.Platform$OS.type != "windows")

-    stop("Please call 'flowWorkspace::set_log_level' for non-windows platforms!")

+  # if(.Platform$OS.type != "windows")

+    # stop("Please call 'flowWorkspace::set_log_level' for non-windows platforms!")

   valid_levels <- c("none", "GatingSet", "GatingHierarchy", "Population", "Gate")

   level <- match.arg(level, valid_levels)

   setLogLevel( as.integer(match(level, valid_levels) - 1))

@@ -188,7 +188,6 @@ setMethod("parseWorkspace",signature("flowjo_workspace"),function(obj, ...){

 #' @rdname flowjo_to_gatingset

 #' @export 

 #' @importFrom utils menu

-#' @importFrom RcppParallel RcppParallelLibs

 #' @importFrom dplyr enquo

 #' @importFrom flowWorkspace cytoset get_default_backend

 flowjo_to_gatingset <- function(ws, name = NULL

@@ -292,8 +291,10 @@ backend <- match.arg(backend, c("h5", "tile"))

     {

       compensation <- sapply(compensation, check_comp, simplify = FALSE)

     }else

+    {

       compensation <- check_comp(compensation)

-      

+      compensation <- list(compensation)

+    } 

   }

   args <- list(ws = ws@doc

                  , group_id = groupInd - 1

deleted file mode 100644

@@ -1,106 +0,0 @@

-## Store state info in this internal global environment

-CytoML.state <- new.env(hash = FALSE)

-CytoML.state[["par"]] <- list()

-

-#' workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

-#' and matched with this list to dispatch to the one of the three workspace parsers 

-CytoML.par.init <- function(){

-  

-  fj_ver <- list(win = c("1.61", "1.6")

-                , macII = c("2.0")

-                , macIII = c("3.0")

-                , vX = c("1.8", "20.0")

-                )

-                          

-   mac_II_path <- list(group = "/Workspace/Groups/GroupNode"# abs path

-                    , sampleRef = ".//SampleRefs/SampleRef"#relative GroupNode

-                    , sample = "/Workspace/SampleList/Sample"#abs path

-                    , sampleNode = "./SampleNode"#relative to sample

-                    , popNode = "./Population"#relative to sampleNode

-                    , attrName = "name"

-                    , compMatName = "name"

-                    , compMatChName = "name"

-                    , compMatVal = "value"

-                    )

-  mac_II_path[["sampleID"]] <- mac_II_path[["sample"]]

-                    

-  #mac version 3.0 (flowJo version 9.7.2-9.7.4)

-  mac_III_path <- mac_II_path

-  mac_III_path[["sample"]] <- sub("SampleList", "Samples", mac_III_path[["sample"]]) 

-  mac_III_path[["attrName"]] <- "nodeName"

-  mac_III_path[["compMatName"]] <- "matrixName"

-  mac_III_path[["compMatChName"]] <- "fluorName"

-  mac_III_path[["compMatVal"]] <- "spillValue"

-  mac_III_path[["sampleID"]] <- mac_III_path[["sample"]]

-  ####windows version

-  #inherit most paths from mac                                      

-  win_path <- mac_II_path

-  win_path[["popNode"]] <- "./*/Population"

-  win_path[["gateDim"]] <- "*[local-name()='dimension']"#relative to gateNode

-  win_path[["gateParam"]] <- "*[local-name()='parameter']"#relative to dimNode

-  win_path[["sampleID"]] <- file.path(win_path[["sample"]],"DataSet")

-

-  ####version X

-  #inherit most paths from win

-  vX_path <- win_path

-  vX_path[["gateParam"]] <- "*[local-name()='fcs-dimension']";                                        

-  

-  CytoML.state[["par"]] <- list(flowJo_versions = fj_ver 

-                                      , nodePath = list(win = win_path

-                                                        , macII = mac_II_path

-                                                        , macIII = mac_III_path

-                                                        , vX = vX_path

-                                                        )

-                                                                 )

-  

-}

-

-## call the init function

-CytoML.par.init()                                                           

-

-#' CytoML.par.set sets a set of parameters in the CytoML package namespace.

-#' 

-#' @param value A named list of values to set for category name or a list of such lists if name is missing.

-#' @rdname CytoML.par.get

-#' @export

-CytoML.par.set <- function (name, value) 

-{

-    old <- CytoML.state[["par"]]

-    if(name%in%names(old)){

-      CytoML.state[["par"]][[name]] <- lattice:::updateList(old[[name]], value)  

-    }else

-      stop(name, " is not a valid CytoML parameters!")

-    

-  invisible()

-}

-

-#' Query and set session-wide parameter defaults.

-#' 

-#' CytoML.par.get gets a set of parameters in the CytoML package namespace.

-#' 

-#' It is currently used to add/remove the support for a specific flowJo versions (parsed from xml node '/Workspace/version' in flowJo workspace)

-#' 

-#' @param name The name of a parameter category to get or set.

-#'

-#' 

-#' @examples

-#'  #get the flowJo versions currently supported 

-#'  old <- CytoML.par.get("flowJo_versions")

-#' 

-#'  #add the new version

-#'  old[["win"]] <- c(old[["win"]], "1.7")    

-#'  CytoML.par.set("flowJo_versions", old)

-#'  

-#'  CytoML.par.get("flowJo_versions")

-#' 

-#' @export 

-#' @rdname CytoML.par.get

-CytoML.par.get <- function (name = NULL) 

-{

-  lPars <- CytoML.state[["par"]]

-  if (is.null(name)) 

-    lPars

-  else if (name %in% names(lPars)) 

-    lPars[[name]]

-  else NULL

-}

@@ -15,7 +15,6 @@

 #include <boost/lexical_cast.hpp>

 #include <boost/tokenizer.hpp>

 #include "search_sample.hpp"

-#define TBB_PREVIEW_SERIAL_SUBSET 1

 //solve windows build issues

 #ifdef Free

@@ -26,19 +25,13 @@

 #endif

-#include <tbb/tbb.h>

-#include "tbb/task_scheduler_init.h"

-#include <tbb/spin_mutex.h>

-using namespace tbb;

 namespace CytoML

 {

-typedef tbb::spin_mutex GsMutexType;

 class flowJoWorkspace:public workspace{

 private:

 	string versionList;//used for legacy mac ws

-	GsMutexType GsMutex, TransMutex, h5Mutex;

 public:

@@ -92,7 +85,6 @@ public:

 	 		trans_local trans, trans_raw;

 	 		{

-				GsMutexType::scoped_lock lock1(TransMutex);//biexp interpolation could be performed on the shared global trans object

 				//prefixed version

 				trans = getTransformation(root,comp,transFlag,_gTrans, true);

@@ -205,17 +197,10 @@ public:

 		 * try to parse each sample

 		 */

 		GatingSet & gs = *gsPtr;

-		tbb::task_scheduler_init init(config.num_threads);

+		for (int i = 0; i < sample_infos.size(); i++)

+			this->parse_sample(sample_infos[i], config, data_dir, cf_dir, gTrans, gs, cytoset);

-		if(config.num_threads <=1)

-			tbb::serial::parallel_for<int>(0, sample_infos.size(), 1, [&, this](int i){

-				this->parse_sample(sample_infos[i], config, data_dir, cf_dir, gTrans, gs, cytoset);

-			});

-		else

-			tbb::parallel_for<int>(0, sample_infos.size(), 1, [&, this](int i){

-							this->parse_sample(sample_infos[i], config, data_dir, cf_dir, gTrans, gs, cytoset);

-						});

 		if(gsPtr->size() == 0)

 			throw(domain_error("No samples in this workspace to parse!"));

 		//keep the cs in sync with backend file

@@ -499,11 +484,7 @@ public:

 				CytoFramePtr ptr;

 				{

-					if(config_const.fmt == FileFormat::H5)

-					{

-

-						GsMutexType::scoped_lock lock(h5Mutex);

-					}

+				

 						frptr->write_to_disk(cf_filename, config_const.fmt);

 						ptr = load_cytoframe(cf_filename, false);

 				}

@@ -514,7 +495,6 @@ public:

 			  gh->set_cytoframe_view(CytoFrameView(frptr));

 			{

-			  GsMutexType::scoped_lock lock(GsMutex);

 			  if(gs.find(uid) != gs.end()){

 			    throw(domain_error("Duplicated GUIDs detected within group: " + uid

                             + "\n Consider adding additional keywords to the GUID with argument \"additional.keys\""

@@ -21,6 +21,8 @@ extern WS_VERSION_TYPE_MAP ws_ver_type_map; //declare global var

 												{"1.8", WS_TYPE::WS_VX},\

 												{"20.0", WS_TYPE::WS_VX}\

 												};\

+		CytoML::CytoStream  cytocout;

+

 namespace CytoML

 {

@@ -13,9 +13,48 @@

 #include "cytolib/nodeProperties.hpp"

 using namespace std;

+#include <cstdio>

+#include <streambuf>

+

+namespace CytoML {

+

+    class Cytostreambuf : public std::streambuf {

+    public:

+        Cytostreambuf(){}

+

+    protected:

+        std::streamsize xsputn(const char *s, std::streamsize n) {

+        Rprintf("%.*s", n, s);

+        return n;

+    }

+

+        int overflow(int c = traits_type::eof()) {

+        if (c != traits_type::eof()) {

+            char_type ch = traits_type::to_char_type(c);

+            return xsputn(&ch, 1) == 1 ? c : traits_type::eof();

+        }

+        return c;

+    }

+

+

+       

+    };

+

+    class CytoStream : public std::ostream {

+        Cytostreambuf  cytobuf;

+    public:

+        CytoStream() : std::ostream(&cytobuf){}

+    };

+    

+

+}

+

+

+    

+extern CytoML::CytoStream  cytocout;

+

 #ifdef ROUT

-#include <RcppArmadillo.h>

-#define COUT Rcpp::Rcout //flowWorkspace is still using Rcpp, so we don't bother replace COUT with PRINT yet

+#define COUT cytocout

 #endif

deleted file mode 100644

@@ -1,33 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/zzz.R

-\name{CytoML.par.set}

-\alias{CytoML.par.set}

-\alias{CytoML.par.get}

-\title{CytoML.par.set sets a set of parameters in the CytoML package namespace.}

-\usage{

-CytoML.par.set(name, value)

-

-CytoML.par.get(name = NULL)

-}

-\arguments{

-\item{name}{The name of a parameter category to get or set.}

-

-\item{value}{A named list of values to set for category name or a list of such lists if name is missing.}

-}

-\description{

-CytoML.par.get gets a set of parameters in the CytoML package namespace.

-}

-\details{

-It is currently used to add/remove the support for a specific flowJo versions (parsed from xml node '/Workspace/version' in flowJo workspace)

-}

-\examples{

- #get the flowJo versions currently supported 

- old <- CytoML.par.get("flowJo_versions")

-

- #add the new version

- old[["win"]] <- c(old[["win"]], "1.7")    

- CytoML.par.set("flowJo_versions", old)

- 

- CytoML.par.get("flowJo_versions")

-

-}

deleted file mode 100644

@@ -1,13 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/zzz.R

-\name{CytoML.par.init}

-\alias{CytoML.par.init}

-\title{workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

-and matched with this list to dispatch to the one of the three workspace parsers}

-\usage{

-CytoML.par.init()

-}

-\description{

-workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

-and matched with this list to dispatch to the one of the three workspace parsers

-}

similarity index 90%

rename from inst/include/CytoML.h

rename to src/CytoML_types.h

@@ -11,5 +11,8 @@ using namespace cytolib;

 #ifdef FALSE

   #undef FALSE

 #endif

+#ifdef TRUE

+  #undef TRUE

+#endif

 #endif // __flowWorkspace_h__

@@ -4,13 +4,13 @@ CXX_STD = CXX11

 #so can't use the default libs shipped with Rtools4

 VERSION=2.9.8

 RWINLIB=../windows/libxml2-$(VERSION)

-PKG_CPPFLAGS =-DROUT -I../inst/include/ -I$(RWINLIB)/include/libxml2 -DLIBXML_STATIC -fpermissive -DRCPP_PARALLEL_USE_TBB=1

+PKG_CPPFLAGS =-DROUT -I../inst/include/ -I$(RWINLIB)/include/libxml2 -DLIBXML_STATIC -fpermissive

 #needs to wrap in $(shell) to strip the quotes returned by rhdf5lib::pkgconfig

 RHDF5_LIBS= $(shell "${R_HOME}/bin/Rscript" -e "Rhdf5lib::pkgconfig('PKG_CXX_LIBS')")

 libxmllibs=-L$(RWINLIB)/lib${R_ARCH} -lxml2 -llzma -liconv -lz

-PKG_LIBS += $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(libxmllibs) `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags();cat(' ');RProtoBufLib:::LdFlags();cat(' ');RcppParallel::RcppParallelLibs()"` ${RHDF5_LIBS} -lws2_32

+PKG_LIBS += $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(libxmllibs) `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags();cat(' ');RProtoBufLib:::LdFlags()"` ${RHDF5_LIBS} -lws2_32

 all: clean winlibs

deleted file mode 100644

@@ -1,147 +0,0 @@

-// Generated by using Rcpp::compileAttributes() -> do not edit by hand

-// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

-

-#include "../inst/include/CytoML.h"

-#include <RcppArmadillo.h>

-#include <Rcpp.h>

-

-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) {

-BEGIN_RCPP

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< unsigned short >::type loglevel(loglevelSEXP);

-    setLogLevel(loglevel);

-    return R_NilValue;

-END_RCPP

-}

-// open_workspace

-XPtr<flowJoWorkspace> open_workspace(string filename, int sample_name_location, int xmlParserOption);

-RcppExport SEXP _CytoML_open_workspace(SEXP filenameSEXP, SEXP sample_name_locationSEXP, SEXP xmlParserOptionSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< string >::type filename(filenameSEXP);

-    Rcpp::traits::input_parameter< int >::type sample_name_location(sample_name_locationSEXP);

-    Rcpp::traits::input_parameter< int >::type xmlParserOption(xmlParserOptionSEXP);

-    rcpp_result_gen = Rcpp::wrap(open_workspace(filename, sample_name_location, xmlParserOption));

-    return rcpp_result_gen;

-END_RCPP

-}

-// parse_workspace

-XPtr<GatingSet> parse_workspace(XPtr<flowJoWorkspace> ws, int group_id, List subset, bool execute, string path, XPtr<GatingSet> cytoset, string backend_dir, string backend, bool includeGates, vector<string> additional_keys, bool additional_sampleID, vector<string> keywords, bool is_pheno_data_from_FCS, bool keyword_ignore_case, float extend_val, float extend_to, bool channel_ignore_case, bool leaf_bool, bool include_empty_tree, bool skip_faulty_gate, List comps, bool transform, string fcs_file_extension, bool greedy_match, FCS_READ_PARAM fcs_parse_arg, int num_threads);

-RcppExport SEXP _CytoML_parse_workspace(SEXP wsSEXP, SEXP group_idSEXP, SEXP subsetSEXP, SEXP executeSEXP, SEXP pathSEXP, SEXP cytosetSEXP, SEXP backend_dirSEXP, SEXP backendSEXP, SEXP includeGatesSEXP, SEXP additional_keysSEXP, SEXP additional_sampleIDSEXP, SEXP keywordsSEXP, SEXP is_pheno_data_from_FCSSEXP, SEXP keyword_ignore_caseSEXP, SEXP extend_valSEXP, SEXP extend_toSEXP, SEXP channel_ignore_caseSEXP, SEXP leaf_boolSEXP, SEXP include_empty_treeSEXP, SEXP skip_faulty_gateSEXP, SEXP compsSEXP, SEXP transformSEXP, SEXP fcs_file_extensionSEXP, SEXP greedy_matchSEXP, SEXP fcs_parse_argSEXP, SEXP num_threadsSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< XPtr<flowJoWorkspace> >::type ws(wsSEXP);

-    Rcpp::traits::input_parameter< int >::type group_id(group_idSEXP);

-    Rcpp::traits::input_parameter< List >::type subset(subsetSEXP);

-    Rcpp::traits::input_parameter< bool >::type execute(executeSEXP);

-    Rcpp::traits::input_parameter< string >::type path(pathSEXP);

-    Rcpp::traits::input_parameter< XPtr<GatingSet> >::type cytoset(cytosetSEXP);

-    Rcpp::traits::input_parameter< string >::type backend_dir(backend_dirSEXP);

-    Rcpp::traits::input_parameter< string >::type backend(backendSEXP);

-    Rcpp::traits::input_parameter< bool >::type includeGates(includeGatesSEXP);

-    Rcpp::traits::input_parameter< vector<string> >::type additional_keys(additional_keysSEXP);

-    Rcpp::traits::input_parameter< bool >::type additional_sampleID(additional_sampleIDSEXP);

-    Rcpp::traits::input_parameter< vector<string> >::type keywords(keywordsSEXP);

-    Rcpp::traits::input_parameter< bool >::type is_pheno_data_from_FCS(is_pheno_data_from_FCSSEXP);

-    Rcpp::traits::input_parameter< bool >::type keyword_ignore_case(keyword_ignore_caseSEXP);

-    Rcpp::traits::input_parameter< float >::type extend_val(extend_valSEXP);

-    Rcpp::traits::input_parameter< float >::type extend_to(extend_toSEXP);

-    Rcpp::traits::input_parameter< bool >::type channel_ignore_case(channel_ignore_caseSEXP);

-    Rcpp::traits::input_parameter< bool >::type leaf_bool(leaf_boolSEXP);

-    Rcpp::traits::input_parameter< bool >::type include_empty_tree(include_empty_treeSEXP);

-    Rcpp::traits::input_parameter< bool >::type skip_faulty_gate(skip_faulty_gateSEXP);

-    Rcpp::traits::input_parameter< List >::type comps(compsSEXP);

-    Rcpp::traits::input_parameter< bool >::type transform(transformSEXP);

-    Rcpp::traits::input_parameter< string >::type fcs_file_extension(fcs_file_extensionSEXP);

-    Rcpp::traits::input_parameter< bool >::type greedy_match(greedy_matchSEXP);

-    Rcpp::traits::input_parameter< FCS_READ_PARAM >::type fcs_parse_arg(fcs_parse_argSEXP);

-    Rcpp::traits::input_parameter< int >::type num_threads(num_threadsSEXP);

-    rcpp_result_gen = Rcpp::wrap(parse_workspace(ws, group_id, subset, execute, path, cytoset, backend_dir, backend, includeGates, additional_keys, additional_sampleID, keywords, is_pheno_data_from_FCS, keyword_ignore_case, extend_val, extend_to, channel_ignore_case, leaf_bool, include_empty_tree, skip_faulty_gate, comps, transform, fcs_file_extension, greedy_match, fcs_parse_arg, num_threads));

-    return rcpp_result_gen;

-END_RCPP

-}

-// get_keywords_by_id

-KW_PAIR get_keywords_by_id(XPtr<flowJoWorkspace> ws, int sample_id);

-RcppExport SEXP _CytoML_get_keywords_by_id(SEXP wsSEXP, SEXP sample_idSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< XPtr<flowJoWorkspace> >::type ws(wsSEXP);

-    Rcpp::traits::input_parameter< int >::type sample_id(sample_idSEXP);

-    rcpp_result_gen = Rcpp::wrap(get_keywords_by_id(ws, sample_id));

-    return rcpp_result_gen;

-END_RCPP

-}

-// get_keywords_by_name

-KW_PAIR get_keywords_by_name(XPtr<flowJoWorkspace> ws, string sample_name);

-RcppExport SEXP _CytoML_get_keywords_by_name(SEXP wsSEXP, SEXP sample_nameSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< XPtr<flowJoWorkspace> >::type ws(wsSEXP);

-    Rcpp::traits::input_parameter< string >::type sample_name(sample_nameSEXP);

-    rcpp_result_gen = Rcpp::wrap(get_keywords_by_name(ws, sample_name));

-    return rcpp_result_gen;

-END_RCPP

-}

-// get_sample_groups

-List get_sample_groups(XPtr<flowJoWorkspace> ws);

-RcppExport SEXP _CytoML_get_sample_groups(SEXP wsSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< XPtr<flowJoWorkspace> >::type ws(wsSEXP);

-    rcpp_result_gen = Rcpp::wrap(get_sample_groups(ws));

-    return rcpp_result_gen;

-END_RCPP

-}

-// get_samples

-List get_samples(XPtr<flowJoWorkspace> ws);

-RcppExport SEXP _CytoML_get_samples(SEXP wsSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< XPtr<flowJoWorkspace> >::type ws(wsSEXP);

-    rcpp_result_gen = Rcpp::wrap(get_samples(ws));

-    return rcpp_result_gen;

-END_RCPP

-}

-// get_xml_file_path

-string get_xml_file_path(XPtr<flowJoWorkspace> ws);

-RcppExport SEXP _CytoML_get_xml_file_path(SEXP wsSEXP) {

-BEGIN_RCPP

-    Rcpp::RObject rcpp_result_gen;

-    Rcpp::RNGScope rcpp_rngScope_gen;

-    Rcpp::traits::input_parameter< XPtr<flowJoWorkspace> >::type ws(wsSEXP);

-    rcpp_result_gen = Rcpp::wrap(get_xml_file_path(ws));

-    return rcpp_result_gen;

-END_RCPP

-}

-

-static const R_CallMethodDef CallEntries[] = {

-    {"_CytoML_setLogLevel", (DL_FUNC) &_CytoML_setLogLevel, 1},

-    {"_CytoML_open_workspace", (DL_FUNC) &_CytoML_open_workspace, 3},

-    {"_CytoML_parse_workspace", (DL_FUNC) &_CytoML_parse_workspace, 26},

-    {"_CytoML_get_keywords_by_id", (DL_FUNC) &_CytoML_get_keywords_by_id, 2},

-    {"_CytoML_get_keywords_by_name", (DL_FUNC) &_CytoML_get_keywords_by_name, 2},

-    {"_CytoML_get_sample_groups", (DL_FUNC) &_CytoML_get_sample_groups, 1},

-    {"_CytoML_get_samples", (DL_FUNC) &_CytoML_get_samples, 1},

-    {"_CytoML_get_xml_file_path", (DL_FUNC) &_CytoML_get_xml_file_path, 1},

-    {NULL, NULL, 0}

-};

-

-RcppExport void R_init_CytoML(DllInfo *dll) {

-    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);

-    R_useDynamicSymbols(dll, FALSE);

-}

new file mode 100644

@@ -0,0 +1,93 @@

+// Generated by cpp11: do not edit by hand

+// clang-format off

+

+#include "CytoML_types.h"

+#include "cpp11/declarations.hpp"

+

+// parseFlowJoWorkspace.cpp

+void setLogLevel(int short loglevel);

+extern "C" SEXP _CytoML_setLogLevel(SEXP loglevel) {

+  BEGIN_CPP11

+    setLogLevel(cpp11::as_cpp<cpp11::decay_t<int short>>(loglevel));

+    return R_NilValue;

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+cpp11::external_pointer<flowJoWorkspace> open_workspace(std::string filename, int sample_name_location, int xmlParserOption);

+extern "C" SEXP _CytoML_open_workspace(SEXP filename, SEXP sample_name_location, SEXP xmlParserOption) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(open_workspace(cpp11::as_cpp<cpp11::decay_t<std::string>>(filename), cpp11::as_cpp<cpp11::decay_t<int>>(sample_name_location), cpp11::as_cpp<cpp11::decay_t<int>>(xmlParserOption)));

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+cpp11::external_pointer<GatingSet> parse_workspace(cpp11::external_pointer<flowJoWorkspace> ws, int group_id, cpp11::list subset, bool execute, std::string path, cpp11::external_pointer<GatingSet> cytoset, std::string backend_dir, std::string backend, bool includeGates, vector<std::string> additional_keys, bool additional_sampleID, vector<std::string> keywords, bool is_pheno_data_from_FCS, bool keyword_ignore_case, float extend_val, float extend_to, bool channel_ignore_case, bool leaf_bool, bool include_empty_tree, bool skip_faulty_gate, cpp11::list comps, bool transform, std::string fcs_file_extension, bool greedy_match, SEXP fcs_parse_arg, int num_threads);

+extern "C" SEXP _CytoML_parse_workspace(SEXP ws, SEXP group_id, SEXP subset, SEXP execute, SEXP path, SEXP cytoset, SEXP backend_dir, SEXP backend, SEXP includeGates, SEXP additional_keys, SEXP additional_sampleID, SEXP keywords, SEXP is_pheno_data_from_FCS, SEXP keyword_ignore_case, SEXP extend_val, SEXP extend_to, SEXP channel_ignore_case, SEXP leaf_bool, SEXP include_empty_tree, SEXP skip_faulty_gate, SEXP comps, SEXP transform, SEXP fcs_file_extension, SEXP greedy_match, SEXP fcs_parse_arg, SEXP num_threads) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(parse_workspace(cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<flowJoWorkspace>>>(ws), cpp11::as_cpp<cpp11::decay_t<int>>(group_id), cpp11::as_cpp<cpp11::decay_t<cpp11::list>>(subset), cpp11::as_cpp<cpp11::decay_t<bool>>(execute), cpp11::as_cpp<cpp11::decay_t<std::string>>(path), cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<GatingSet>>>(cytoset), cpp11::as_cpp<cpp11::decay_t<std::string>>(backend_dir), cpp11::as_cpp<cpp11::decay_t<std::string>>(backend), cpp11::as_cpp<cpp11::decay_t<bool>>(includeGates), cpp11::as_cpp<cpp11::decay_t<vector<std::string>>>(additional_keys), cpp11::as_cpp<cpp11::decay_t<bool>>(additional_sampleID), cpp11::as_cpp<cpp11::decay_t<vector<std::string>>>(keywords), cpp11::as_cpp<cpp11::decay_t<bool>>(is_pheno_data_from_FCS), cpp11::as_cpp<cpp11::decay_t<bool>>(keyword_ignore_case), cpp11::as_cpp<cpp11::decay_t<float>>(extend_val), cpp11::as_cpp<cpp11::decay_t<float>>(extend_to), cpp11::as_cpp<cpp11::decay_t<bool>>(channel_ignore_case), cpp11::as_cpp<cpp11::decay_t<bool>>(leaf_bool), cpp11::as_cpp<cpp11::decay_t<bool>>(include_empty_tree), cpp11::as_cpp<cpp11::decay_t<bool>>(skip_faulty_gate), cpp11::as_cpp<cpp11::decay_t<cpp11::list>>(comps), cpp11::as_cpp<cpp11::decay_t<bool>>(transform), cpp11::as_cpp<cpp11::decay_t<std::string>>(fcs_file_extension), cpp11::as_cpp<cpp11::decay_t<bool>>(greedy_match), cpp11::as_cpp<cpp11::decay_t<SEXP>>(fcs_parse_arg), cpp11::as_cpp<cpp11::decay_t<int>>(num_threads)));

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+SEXP get_keywords_by_id(cpp11::external_pointer<flowJoWorkspace> ws, int sample_id);

+extern "C" SEXP _CytoML_get_keywords_by_id(SEXP ws, SEXP sample_id) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(get_keywords_by_id(cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<flowJoWorkspace>>>(ws), cpp11::as_cpp<cpp11::decay_t<int>>(sample_id)));

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+SEXP get_keywords_by_name(cpp11::external_pointer<flowJoWorkspace> ws, std::string sample_name);

+extern "C" SEXP _CytoML_get_keywords_by_name(SEXP ws, SEXP sample_name) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(get_keywords_by_name(cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<flowJoWorkspace>>>(ws), cpp11::as_cpp<cpp11::decay_t<std::string>>(sample_name)));

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+cpp11::list get_sample_groups(cpp11::external_pointer<flowJoWorkspace> ws);

+extern "C" SEXP _CytoML_get_sample_groups(SEXP ws) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(get_sample_groups(cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<flowJoWorkspace>>>(ws)));

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+cpp11::list get_samples(cpp11::external_pointer<flowJoWorkspace> ws);

+extern "C" SEXP _CytoML_get_samples(SEXP ws) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(get_samples(cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<flowJoWorkspace>>>(ws)));

+  END_CPP11

+}

+// parseFlowJoWorkspace.cpp

+std::string get_xml_file_path(cpp11::external_pointer<flowJoWorkspace> ws);

+extern "C" SEXP _CytoML_get_xml_file_path(SEXP ws) {

+  BEGIN_CPP11

+    return cpp11::as_sexp(get_xml_file_path(cpp11::as_cpp<cpp11::decay_t<cpp11::external_pointer<flowJoWorkspace>>>(ws)));

+  END_CPP11

+}

+

+extern "C" {

+/* .Call calls */

+extern SEXP _CytoML_get_keywords_by_id(SEXP, SEXP);

+extern SEXP _CytoML_get_keywords_by_name(SEXP, SEXP);

+extern SEXP _CytoML_get_sample_groups(SEXP);

+extern SEXP _CytoML_get_samples(SEXP);

+extern SEXP _CytoML_get_xml_file_path(SEXP);

+extern SEXP _CytoML_open_workspace(SEXP, SEXP, SEXP);

+extern SEXP _CytoML_parse_workspace(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);

+extern SEXP _CytoML_setLogLevel(SEXP);

+

+static const R_CallMethodDef CallEntries[] = {

+    {"_CytoML_get_keywords_by_id",   (DL_FUNC) &_CytoML_get_keywords_by_id,    2},

+    {"_CytoML_get_keywords_by_name", (DL_FUNC) &_CytoML_get_keywords_by_name,  2},

+    {"_CytoML_get_sample_groups",    (DL_FUNC) &_CytoML_get_sample_groups,     1},

+    {"_CytoML_get_samples",          (DL_FUNC) &_CytoML_get_samples,           1},

+    {"_CytoML_get_xml_file_path",    (DL_FUNC) &_CytoML_get_xml_file_path,     1},

+    {"_CytoML_open_workspace",       (DL_FUNC) &_CytoML_open_workspace,        3},

+    {"_CytoML_parse_workspace",      (DL_FUNC) &_CytoML_parse_workspace,      26},